{ "metadata": { "created_at": "2025-06-30T11:53:11.365131", "version": "1.0", "description": "Euro-BioImaging combined search index", "dataset_type": "full", "statistics": { "technologies": 122, "nodes": 41, "website_pages": 50, "total_entries": 213 }, "bm25_file": "eurobioimaging_bm25_index.pkl" }, "technologies": [ { "id": "73094724", "name": "3D Correlative Light and Electron Microscopy (3D-CLEM)*", "original_id": "f0acc857-fc72-4094-bf14-c36ac40801c5", "description": "In 3D CLEM, 3D or volume EM methods are combined with 3D light microscopy techniques. Registration between the modalities has to be done in all 3 dimensions, making 3D CLEM a challenging method.", "documentation": "## 3D Correlative Light and Electron Microscopy (3D-CLEM)\\*\n---\n**In 3D CLEM, 3D or volume EM methods are combined with 3D light microscopy techniques. Registration between the modalities has to be done in all 3 dimensions, making 3D CLEM a challenging method.**\n\n", "provider_node_ids": [ "90c8b0d6", "0c8677f6", "fc1893d4", "64543c53", "09122290" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "f68070c5", "name": "4Pi microscopy", "original_id": "68a3b6c4-9c19-4446-9617-22e7d37e0f2c", "description": "Dual-objective microscopy achieving 100nm resolution for live-cell imaging.", "documentation": "## 4 PI MICROSCOPY\n---\n**4Pi microscope is a laser scanning fluorescence microscope with an improved axial resolution. The typical value of 500–700nm can be improved to 100–150nm which corresponds to an almost spherical focal spot with 5–7 times less volume than that of standard confocal microscopy. To achieve a full spherical wavefront with a solid angle of 4π two opposing objective lenses are matched coherently, so the two individual wavefronts add up and join forces.**\n\n## AI Generated Documentation\n\n### Overview\n4Pi microscopy is a sophisticated laser scanning fluorescence microscopy technique that enhances axial resolution to approximately 100-150 nanometers, a significant improvement over conventional confocal microscopy, which typically achieves 500-700 nanometers. This technology utilizes two opposing objective lenses to achieve coherent illumination and detection, allowing for high-resolution imaging of biological samples.\n\n### Key Capabilities\nThe unique configuration of 4Pi microscopy involves juxtaposed dual objectives that focus light at a common focal point, facilitating constructive and destructive interference of emitted light. This results in a point-spread function that is about 1.5 times sharper laterally and seven times sharper axially compared to standard confocal systems. The solid angle for illumination and detection approaches 4π steradians, enabling simultaneous excitation and collection of emitted light from all directions. This capability allows for nearly isotropic resolution, crucial for three-dimensional imaging applications.\n\n### Applications\n4Pi microscopy is particularly valuable in biological research, enabling detailed imaging of live cells and dynamic processes within them. Applications include studying the structural plasticity of organelles such as mitochondria and the Golgi apparatus, as well as observing cellular processes like photobleaching recovery. The technique is also beneficial for visualizing microtubule dynamics and other cytoskeletal structures, providing insights into cellular architecture and function at the nanoscale.\n\n### Advantages\nThe primary advantages of 4Pi microscopy include its ability to produce high-resolution, three-dimensional images with minimal photodamage to live specimens. This makes it an essential tool for researchers investigating complex biological systems, as it allows for real-time observation of molecular interactions and cellular dynamics. The integration of multiphoton excitation with high-performance detection systems further enhances its capabilities, making it a powerful method for advanced microscopy in both biological and materials sciences. Overall, 4Pi microscopy represents a significant advancement in the field of super-resolution imaging, offering unique features that differentiate it from other microscopy techniques.\n\n## References\n\n1. https://en.wikipedia.org/wiki/4Pi_Microscope\n2. https://zeiss-campus.magnet.fsu.edu/referencelibrary/superresolution/fourpi.html\n3. https://www.microscopyu.com/references/4pi-superresolution-microscopy\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "4f1ca4db", "64543c53" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "b015d920", "name": "Anisotropy/Polarization Microscopy (AM)", "original_id": "508bc4d4-b392-430b-8b08-a0b1a5503eee", "description": "Biomolecular interactions and conformational changes, both in vivo and in vitro, can be followed by fluorescence polarization/anisotropy imaging, which uses polarized excitation and polarization sensitive detection to follow the orientation and dynamic rearrangement of dipole moments of fluorescence tags. In addition to steady-state anisotropy quantification time-resolved anisotropy measurements are possible, giving a detailed insight into local changes of molecular dynamics on a nanosecond time scale.\r\nFluorescence Anisotropy Imaging (FAIM) is based on the quantification of fluorescence depolarization through the separation of the parallel and perpendicularly polarized components of the fluorescence signal upon polarized excitation. The measured quantity (fluorescence anisotropy) is dependent on molecular dynamics of the fluorophore and can probe local viscosity changes. Additionally, it is the only method able to evaluate homo-FRET and hence, is a powerful tool to evaluate interactions.\r\n", "documentation": "## Anisotropy/Polarization Microscopy (AM)\n---\n**Biomolecular interactions and conformational changes, both in vivo and in vitro, can be followed by fluorescence polarization/anisotropy imaging, which uses polarized excitation and polarization sensitive detection to follow the orientation and dynamic rearrangement of dipole moments of fluorescence tags. In addition to steady-state anisotropy quantification time-resolved anisotropy measurements are possible, giving a detailed insight into local changes of molecular dynamics on a nanosecond time scale.\nFluorescence Anisotropy Imaging (FAIM) is based on the quantification of fluorescence depolarization through the separation of the parallel and perpendicularly polarized components of the fluorescence signal upon polarized excitation. The measured quantity (fluorescence anisotropy) is dependent on molecular dynamics of the fluorophore and can probe local viscosity changes. Additionally, it is the only method able to evaluate homo-FRET and hence, is a powerful tool to evaluate interactions.**\n\n", "provider_node_ids": [ "90c8b0d6", "ca2e3748", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "151b4761", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "63775639", "name": "Array tomography (AT)", "original_id": "8874ab3f-bf24-4673-9375-93f9f82bf8b5", "description": "Many biological functions depend critically upon fine details of tissue’s molecular architecture that have resisted exploration by existing imaging techniques. Array tomography (AT) encompasses electron microscopy modalities that offer unparalleled opportunities to explore 3D cellular architectures of large samples in extremely fine structural and molecular detail. AT can capture 3D ultrastructure easily and rapidly compared to traditional serial-section electron microscopy methods. \r\n\r\nTo perform AT, samples are first fixed and embedded in resin blocks. These blocks are then sectioned by an ultramicrotome into ribbons of sections. Different techniques and hardware are available, with various degrees of automation leading to the collection of sections from very large samples (full organisms, large pieces of tissues in the mm range). Ribbons are collected on conductive substrates and transferred to the SEM for imaging. Due to the ribbon in which the sections are collected, the spatial relation of individual imaged sections is maintained and the acquired images can be computationally combined to allow the visualisation of the 3D structure of the sample at high resolution.\r\n\r\nArray Tomography is also available in a correlative mode (CAT) which offers the unique capacity of merging the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy.\r\n", "documentation": "## Array Tomography (AT)\n---\n**Many biological functions depend critically upon fine details of tissue’s molecular architecture that have resisted exploration by existing imaging techniques. Array tomography (AT) encompasses electron microscopy modalities that offer unparalleled opportunities to explore 3D cellular architectures of large samples in extremely fine structural and molecular detail. AT can capture 3D ultrastructure easily and rapidly compared to traditional serial-section electron microscopy methods.**\nTo perform AT, samples are first fixed and embedded in resin blocks. These blocks are then sectioned by an ultramicrotome into ribbons of sections. Different techniques and hardware are available, with various degrees of automation leading to the collection of sections from very large samples (full organisms, large pieces of tissues in the mm range). Ribbons are collected on conductive substrates and transferred to the SEM for imaging. Due to the ribbon in which the sections are collected, the spatial relation of individual imaged sections is maintained and the acquired images can be computationally combined to allow the visualisation of the 3D structure of the sample at high resolution.\nArray Tomography is also available in a correlative mode (CAT) which offers the unique capacity of merging the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy.\n\n", "provider_node_ids": [ "90c8b0d6", "ca2e3748", "d039b533", "46ccfb38", "fc1893d4", "9beefd47", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } }, { "id": "a9f0fcad", "name": "Atomic Force Microscopy (AFM)*", "original_id": "fffa14c2-451f-4421-97dd-808d5dcd7e47", "description": "Atomic Force Microscopy (AFM) is a technique allowing the characterization of sample morphology at nanoscale. Images are acquired by raster scanning a nanometric tip in gentle contact or intermittent contact with the sample. The tip is positioned at the end of a micrometric force transducer, the AFM cantilever: it records the variation of sample topography due to changes of tip-sample interaction during scanning operation. In addition, by measuring the tip-sample interaction force as a function of the tip-sample distance, AFMs can evaluate sample elastic and viscous properties.", "documentation": "## Atomic Force microscopy (AFM) \\*\n---\n**Atomic Force Microscopy (AFM) is a technique allowing the characterization of sample morphology at nanoscale. Images are acquired by raster scanning a nanometric tip in gentle contact or intermittent contact with the sample. The tip is positioned at the end of a micrometric force transducer, the AFM cantilever: it records the variation of sample topography due to changes of tip-sample interaction during scanning operation. In addition, by measuring the tip-sample interaction force as a function of the tip-sample distance, AFMs can evaluate sample elastic and viscous properties.**\nAFM is nowadays recognized as an outstanding technique in the membrane field. Vertical and lateral resolution in the nanometer range can be achieved in buffer, a great advantage as compared to other structural biology techniques. In addition, due to a high signal to noise ratio, AFM often does not require image averaging, limiting the number of acquisitions. AFM has been widely used to probe at the nanoscale both topography and physical properties of biological membranes, purified or in intact cells. Besides this application, it is an instrument suitable to get high resolution pictures of filamentous structures (amyloid fibres, DNA, intrinsically disordered proteins…) as well as viral particles or bacteria.\nInitially limited by the time to acquire an image, tremendous progress in AFM during the last 10 years laid on the development of high-speed (HS)-AFM that enables dynamic imaging of biological samples.\nIn addition, AFM topography can also be combined with fluorescence microscopy (conventional and super resolution microscopy as well as spectroscopy) to correlate topography and mapping of a component of interest.\n![](upload/AFM.jpg)\nTopography of a supported lipid bilayer after direct incorporation of photosynthetic complexes imaged by atomic force microscopy” from Berquand et al, 2007, Ultramicroscopy 107, 928-933\n\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "2b34e271", "ca2e3748", "46ccfb38", "fc1893d4", "64543c53", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "eeee8c89", "name": "Brillouin Scattering Microscopy (BSM) *", "original_id": "34cd0603-169d-4b3e-a449-edb6ce4aa921", "description": "Non-invasive, label-free imaging of mechanical properties at sub-cellular resolution.", "documentation": "## AI Generated Documentation\n\n### Overview\nBrillouin Scattering Microscopy (BSM) is an advanced optical imaging technique that utilizes the principles of Brillouin light scattering to non-invasively probe the mechanical properties of biological samples at the microscale. This method has emerged as a pivotal tool in mechanobiology, allowing researchers to investigate the viscoelastic properties of cells and tissues with high spatial resolution, typically down to the diffraction limit of light.\n\n### Key Capabilities\nBSM operates by analyzing the frequency shifts of laser light scattered by acoustic waves (phonons) within a sample, enabling the measurement of mechanical properties such as elasticity and viscosity. The technique is characterized by its ability to generate three-dimensional maps of mechanical properties, providing insights into the heterogeneity of biological tissues. Recent advancements in optical spectrometers have significantly improved the speed, spectral resolution, and sensitivity of BSM, making it suitable for real-time imaging of living cells.\n\n### Applications\nBSM is particularly valuable in biomedical research for studying the mechanical properties of cells and tissues, which are crucial for understanding various biological processes, including cell differentiation, tissue development, and disease progression. For example, BSM can be utilized to assess mechanical alterations in cancerous tissues, offering insights into tumor mechanics and potential therapeutic targets. Additionally, it plays a vital role in evaluating the biomechanical properties of soft tissues, which is essential for the development of biomaterials and tissue engineering strategies.\n\n### Advantages\nThe non-contact nature of BSM eliminates the risk of damaging delicate biological samples, allowing for the characterization of living cells in their natural state. This capability provides a more accurate representation of their mechanical properties compared to traditional methods. Furthermore, BSM's ability to produce detailed mechanical property maps enhances our understanding of the complex interactions within biological systems. Overall, Brillouin Scattering Microscopy stands out as a transformative technology in the field of biomedical sciences, bridging the gap between mechanical properties and biological function without the need for labels or invasive procedures.\n\n## References\n\n1. https://www.nature.com/articles/s43586-023-00286-z\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC6624783/\n3. https://www.nature.com/articles/s41592-019-0543-3\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "89bab6f3", "name": "Challenges Framework", "original_id": "d1bb5b08-1df7-40f6-b181-a7e3abdf3e42", "description": "Multimodal imaging integration, advanced algorithms, 3D fusion, cancer diagnostics.", "documentation": "## Challenges framework\n---\n**T****he Challenges Framework flagship Node organizes a series of Grand Challenges in Medical Image Analysis focused at standardized evaluation of different image analysis algorithms in the field. The goal of this Node is to go much further and create a generic open-source platform that allows MIC researchers to make their data and evaluated software available for on-line collaboration and cloud computing. The Node physically consists of storage, computational resources, and web access. It includes a repository with relevant data for challenges, software for download of training data, upload of results and display of results.**\n|\n| |\n\n## AI Generated Documentation\n\n### Overview\nThe Challenges Framework in bioimaging represents a structured approach to overcoming the multifaceted obstacles faced in the integration and application of various imaging modalities. This framework is designed to enhance the understanding of complex biological systems by facilitating the use of multiple imaging techniques, such as optical bioimaging, magnetic resonance imaging (MRI), and computed tomography (CT). By addressing the challenges associated with data analysis and image interpretation, the framework aims to improve the efficacy and applicability of bioimaging technologies in both research and clinical settings.\n\n### Key Capabilities\nThe Challenges Framework supports the integration of diverse imaging modalities, allowing researchers to obtain a comprehensive view of biological structures and processes. Key capabilities include:\n- **Multimodal Imaging**: Combines different imaging techniques to leverage their strengths, providing enhanced spatial and temporal resolution.\n- **Advanced Algorithms**: Incorporates machine learning and computer vision techniques to improve image analysis, enabling tasks such as automated segmentation and classification of cellular structures.\n- **3D Image Fusion**: Facilitates the creation of high-quality 3D representations from multiple 2D images, addressing issues of signal degradation and enhancing image clarity.\n\n### Applications\nThe framework is applied across various domains, including:\n- **Cancer Diagnostics**: Enhances the detection and characterization of tumors through improved imaging techniques and analysis methods.\n- **Neuroscience**: Supports the study of neural networks and brain function by integrating imaging modalities that capture both structural and functional data.\n- **Developmental Biology**: Allows for the observation of dynamic biological processes in real-time, providing insights into cellular interactions and developmental pathways.\n\n### Advantages\nThe Challenges Framework offers several distinct advantages:\n- **Holistic Insights**: By integrating multiple imaging modalities, researchers gain a more complete understanding of biological phenomena, which is crucial for complex systems.\n- **Innovation in Methodology**: Encourages the development of new analytical techniques and algorithms, fostering collaboration and advancing the field of bioimaging.\n- **Benchmarking and Recognition**: Provides a platform for researchers to benchmark their methods against established challenges, promoting scientific advancements and recognition within the community.\n\nIn conclusion, the Challenges Framework serves as a vital tool for researchers in bioimaging, enabling the integration of advanced imaging technologies and methodologies to enhance our understanding of biological systems and improve diagnostic capabilities in healthcare.\n\n## References\n\n1. https://www.nature.com/articles/s44303-024-00010-w\n2. https://biomedicalimaging.org/2025/challenges/\n3. https://pubmed.ncbi.nlm.nih.gov/34976590/\n4. https://www.nature.com/articles/s41592-023-01900-4\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "f68673b1", "64543c53" ], "abbr": "", "category": { "id": "b73300b1-0934-4e73-86be-a829aa06ee16", "name": "Medical Image Data services" } }, { "id": "53fc2771", "name": "Coherent Anti-Stokes Raman Scattering microscopy (CARS)*", "original_id": "65a6530c-bc26-4e36-bab3-a72a09e9e3a0", "description": "Label-free, high-resolution vibrational imaging for live cells and tissues.", "documentation": "## Coherent Anti-Stokes Raman Scattering microscopy (CARS) \\*\n---\n**CARS microscopy is one of the label-free multiphoton imaging techniques. It allows for chemically specific imaging of biological materials without use of fluorescent labels. CARS is a three-photon nonlinear optical process where two synchronous and spatially overlapped optical beams are used to probe molecular vibrations in the sample material. The method is based on stimulated Raman scattering which makes CARS imaging much faster than confocal Raman mapping based on spontaneous Raman scattering (at least 100 times faster). Different experimental realizations of CARS microscopy exist. Typical is the visualization of a selected single vibrational frequency, for example the CH2 symmetric stretching mode around 2800 cm-1. Spectral scanning is realized by tuning the excitation wavelength step-by-step. The alternative approach is hyperspectral CARS which is based on broadband excitation and detection of vibrational frequencies in a wider spectral range simultaneously.**\nModalities offered within Euro-BioImaging include single-frequency CARS imaging, combined into multi-mode simultaneous imaging of CARS, SHG and 2P-fluorescence signals.\nCARS has been proven useful in some very specific application fields. The CARS technique is particularly well suited for high-resolution label-free imaging of lipids due to the high concentration of carbon-hydrogen bonds in the lipid material. Lipid imaging has been applied to a great variety of samples including lipid droplets in fixed and live cell cultures, various tissue sections, and even small animals in vivo (e.g. zebrafish). In pharmaceutical applications, CARS microscopy is gaining more and more interest. Applications include visualization of chemical component distribution in dosage forms and drug carriers, dissolution and release, solid-state transformations during dissolution, and drug delivery into cells and tissues.\n![](upload/CARS.PNG)\nSimultaneous imaging of GFP-labelled protein ATGL-1, taking part in lipid metabolism of C.elegans, and unstained lipid droplets by CARS in a living embryo of C. elegans. Data acquired in collaboration with Zdenek Kostrouch (1st Medical Faculty, Charles University, Czech Republic)\n\n## AI Generated Documentation\n\n### Overview\nCoherent Anti-Stokes Raman Scattering (CARS) microscopy is a powerful nonlinear optical imaging technique that enables high-resolution vibrational imaging of biological and chemical systems. First introduced in 1982, CARS microscopy has undergone significant advancements, particularly in laser technology, allowing for enhanced imaging capabilities without the need for fluorescent labels, which can introduce artifacts and photobleaching.\n\n### Key Capabilities\nCARS microscopy utilizes two laser beams—pump and Stokes—that are tightly focused and co-propagated through the sample. This interaction generates a coherent anti-Stokes signal that is significantly stronger than spontaneous Raman scattering, resulting in high signal-to-noise ratios. Key capabilities include:\n- **High Spatial Resolution**: Achieves sub-micrometer resolution, allowing for detailed structural analysis of samples.\n- **Three-Dimensional Imaging**: Capable of providing 3D images, enabling the visualization of complex structures in biological tissues.\n- **High Sensitivity**: Effective for detecting low concentrations of chemical species, making it suitable for various applications in life sciences and materials research.\n- **Multiplexing**: Recent advancements have led to multiplex CARS, allowing simultaneous imaging of multiple vibrational modes, thus providing richer chemical information.\n\n### Applications\nCARS microscopy is extensively used in several fields, including:\n- **Biology**: Non-invasive imaging of live cells and tissues, enabling real-time observation of cellular processes, lipid distributions, and metabolic activities without the need for chemical labeling.\n- **Medicine**: Characterization of cancerous tissues and monitoring of disease progression, providing insights into cellular environments and interactions.\n- **Materials Science**: Analysis of polymers and complex materials, facilitating the study of phase separation and molecular dynamics.\n\n### Advantages\nCARS microscopy offers several distinct advantages over traditional imaging techniques:\n- **Label-Free Imaging**: Eliminates the need for fluorescent dyes, reducing potential artifacts and photobleaching, thus preserving the natural state of the sample.\n- **Non-Invasive**: Allows deep tissue imaging without damaging the sample, making it ideal for in vivo studies.\n- **High Temporal Resolution**: Capable of capturing dynamic processes in real-time, providing insights into fast biological events.\n\nIn summary, CARS microscopy is a unique and versatile imaging modality that combines high sensitivity, specificity, and non-invasive capabilities, making it an invaluable tool in modern biological and chemical research.\n\n## References\n\n1. https://www.sciencedirect.com/science/article/pii/S0168900206018547\n2. https://www.annualreviews.org/content/journals/10.1146/annurev.anchem.1.031207.112754\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "23f7a2fd", "46ccfb38" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "6709f67e", "name": "Correlated Optical Coherence Tomography/PhotoAcoustic Tomography (OCT/PAT)", "original_id": "7d45b891-c707-4e63-b145-a2dfabea68e2", "description": "Multimodal imaging: OCT/PAT combines high-res structural and functional insights.", "documentation": "## Bimodal Photoacoustic / Optical Coherence Tomography (PAT/OCT) \\*\n---\n**Photoacoustic Imaging (PAI)****is a hybrid optical imaging modality which detects laser pulse induced ultrasonic waves. It can resolve the absorbers located in turbid media. Since the contrast is purely based on optical absorption, the imaging depth of PAI goes beyond the optical mean free path. Depending on specific configurations, PAI can be divided into photoacoustic microscopy (PAM) and photoacoustic tomography (PAT).**\n**Optical Coherence Tomography (OCT), on the other hand, uses scattering contrast. When light impinges upon layered structures, backscattered light from interfaces in the sample interferes with a reference light beam, forming modulated interferogram, which can in turn lead to the reconstruction of inner structures of biological samples in vivo. By using wideband low coherence light sources, OCT can achieve subcellular spatial resolution as well as high temporal resolution. In addition to structural imaging, an extension of OCT, namely OCT angiography (OCTA), can produce contrast based on speckle or phase variance, which has seen increasing applications in ophthalmology and dermatology.**\n**OCT can be combined with PAM to form the so-called optical coherence photoacoustic microscopy (OC-PAM) system whereas when PAT is combined with OCT, the system is named optical coherence photoacoustic tomography (OC-PAT).**\nOC-PAT is normally used for large field of view imaging. The lateral imaging range can reach up to 15 mm × 15 mm and the imaging depth can reach 5 mm and deeper in soft tissue. One unique application for such a system is in dermatology as demonstrated below.\n![](upload/Pictureoctpat.png)\n*(a) OCT B-scan of skin over the dashed line in (b). (b) Photo of a surgical scar. (c) Depth color coded image of skin vasculature between 0.5 mm and 1 mm in z direction using acquired with bimodal OCTA/PAT imaging. (d) Depth color coded image of skin vasculature between 1 mm and 4 mm in z direction acquired with bimodal OCTA/PAT imaging. (e) Skin vasculature in gray scale between 0 mm and 0.5 mm in z direction imaged by OCTA. (f) Transition zone en face view showing the same vessels resolved by both OCTA (green) and PAT (red). (g) and (h) OCT/OCTA/PAT merged volume 3D rendering at two perspectives. Scale bar= 1 mm except in (a). [source: Z. Chen et al, **]*\nThe OC-PAT system can also be easily adapted for mouse imaging, zebrafish imaging, and other types of small animal imaging.\nThe OC-PAM system features a smaller field of view and a shallower penetration depth, but provides improved spatial resolution compared with the OC-PAT system. As a microscopic system, it is superb to image small organisms such as zebrafish embryos and organoids. The figure below shows the OC-PAM results of zebrafish embryo imaging.\n![](upload/octpat.png)\n*Tail segment of zebrafish: (a) The brightfield microscopy image. (b) The OCM image. (c) The PAM image (logarithmic scale, inset: the focus stacked image of the green dash box region). (d) The overlay of (b) and (c) (gray: OCM; red: PAM). DLAV: dorsal longitudinal anastomotic vessel; Se: intersegmental vessel; CA: caudal artery; CV: caudal vein. Scale bar: 100 μm. Source: S. Deng et al, [https://doi.org/10.1063/5.0059...](https://doi.org/10.1063/5.0059351)*\nOCT/PAT is available at the [Austrian Bioimaging Node.](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n**REFERENCES**\n● K.M. Meiburger, et al. “Automatic segmentation and classification methods using optical coherence tomography angiography (OCTA): a review and handbook,”  \n●M. Liu and W. Drexler, “Optical coherence tomography angiography and photoacoustic imaging in dermatology,” \n#### OCT/PAT USE CASES\n| **Use case** | **Node** | **DOI** |\n| --- | --- | --- |\n| In vivo Zebrafish larva imaging | [Austrian BioImaging Node CMI](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi) | |\n| Human skin imaging | [Austrian BioImaging Node CMI](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi) | [https://doi.org/10.1364/boe.7.00339](https://doi.org/10.1364/boe.7.003390) |\n\n## AI Generated Documentation\n\n**Overview** \nCorrelated Optical Coherence Tomography/PhotoAcoustic Tomography (OCT/PAT) is a cutting-edge imaging technology that integrates the high-resolution structural imaging capabilities of Optical Coherence Tomography (OCT) with the functional imaging strengths of PhotoAcoustic Tomography (PAT). This multimodal approach allows for comprehensive analysis of biological tissues, providing both morphological and functional information in a non-invasive manner.\n\n**Key Capabilities** \nOCT operates using near-infrared light, typically in the 800-1300 nm range, achieving axial resolutions of 1-15 micrometers and a penetration depth of several hundred microns. It utilizes interferometric techniques to capture backscattered light, enabling the reconstruction of detailed cross-sectional images of tissue. In contrast, PAT employs pulsed laser light to generate ultrasound waves from tissue absorption, achieving spatial resolutions of 50-100 micrometers and depths of several centimeters. The integration of these two modalities allows OCT/PAT to provide simultaneous imaging of tissue structure and blood flow dynamics, enhancing the diagnostic capabilities significantly.\n\n**Applications** \nOCT/PAT is particularly valuable in clinical settings such as ophthalmology, where it is used for imaging retinal structures and assessing vascular conditions. Its applications extend to oncology for tumor characterization, allowing differentiation between malignant and benign tissues based on optical and acoustic properties. Additionally, it is utilized in dermatology for skin imaging and in cardiovascular research to study vascular health and pathology.\n\n**Advantages** \nThe primary advantage of OCT/PAT lies in its ability to deliver complementary information that enhances diagnostic accuracy. While OCT excels in providing detailed structural images, PAT offers insights into tissue composition and function, such as blood oxygenation and flow. This multimodal approach not only improves the understanding of complex biological systems but also facilitates more effective monitoring of disease progression and treatment responses. Furthermore, the non-invasive nature of both techniques reduces patient discomfort and risk, making them suitable for repeated assessments. Overall, OCT/PAT represents a significant advancement in imaging technology, providing a powerful tool for both clinical diagnostics and biomedical research.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC7370601/\n2. https://link.springer.com/referencework/10.1007/978-3-319-06419-2\n3. https://link.springer.com/rwe/10.1007/978-3-319-06419-2_53\n4. https://www.ncbi.nlm.nih.gov/books/NBK554044/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "64543c53" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "8597af30", "name": "Correlative Array Tomography (CAT)", "original_id": "bf1c0e97-73b5-49b9-aadd-628fb5a74b82", "description": "Many biological functions depend critically upon fine details of tissue’s molecular architecture that have resisted exploration by existing imaging techniques. Array tomography (AT) encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore 3D cellular architectures of large samples in extremely fine tructural and molecular detail. Fluorescence-AT achieves much higher resolution and molecular multiplexing than most other fluorescence microscopy methods, while electron-AT can capture 3D ultrastructure easily and rapidly compared to traditional serial-section electron microscopy methods. The Correlative mode of Array Tomography (CAT) furthermore offers the unique capacity of merging the molecular discrimination strengths of multichannel fluorescence microscopy with the ultrastructural imaging strengths of electron microscopy and validating single-modality conclusions since each technique provides unique information based on fundamentally different contrast methods. This new technology covers the current state-of-the-art in volume electron microscopy imaging applied to very large and complex biological samples, including neural circuits, organs (e.g., pancreas, kidney, heart), small model organisms and subcellular organelle networks. ", "documentation": "", "provider_node_ids": [ "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "59bcd971", "name": "Correlative X-ray and EM (CXEM)*", "original_id": "5defb921-d677-4e30-b22e-3fcf4e13fb1f", "description": "In correlative X-ray and EM, X-ray imaging can be used to gain insights into the structure and position of the sample inside the resin block, as prepared for EM. This allows for more precise targeting of the sites of interest when preparing thin sections or in volume EM approaches. This method can also be combined with light microscopy imaging of the sample prior to fixation.\r\n\r\nAdditionally, X-ray fluorescence imaging can be performed and correlated with TEM imaging of the sample to analyse the distribution of different elements with subcellular resolution.\r\n", "documentation": "## Correlative X-ray and EM (CXEM)\\*\n---\n**In correlative X-ray and EM, X-ray imaging can be used to gain insights into the structure and position of the sample inside the resin block, as prepared for EM. This allows for more precise targeting of the sites of interest when preparing thin sections or in volume EM approaches. This method can also be combined with light microscopy imaging of the sample prior to fixation.\nAdditionally, X-ray fluorescence imaging can be performed and correlated with TEM imaging of the sample to analyse the distribution of different elements with subcellular resolution.**\n\n", "provider_node_ids": [ "0c8677f6", "fc1893d4", "64543c53" ], "abbr": "", "category": { "id": "3e5e6cdb-f76e-47a8-85d7-7fc1e45d31d1", "name": "X-ray and EM" } }, { "id": "593e3440", "name": "Cryo Correlative Light and Electron Microscopy (Cryo-CLEM)*", "original_id": "b93ab925-06a5-4538-b645-bb53fea3be5a", "description": "Cryo-CLEM combines cryo-fixation and cryo-fluorescence microscopy with subsequent cryo-FIB, cryo-TEM, cryo-SEM, or cryo-ET. Alternatively after cryo-fluorescence microscopy samples can be cryo-substituted and embedded in resins, followed by room temperature FIB-SEM, TEM, or ET. The main advantage of cryo-CLEM is better preservation of spatial correlation between fluorescence and EM images, compared to standard CLEM using chemical fixation, and the possibility to use the full palette of fluorophores compared to in-resin fluorescence CLEM experiments.", "documentation": "## Cryo Correlative Light and Electron Microscopy (Cryo-CLEM) \\*\n---\n**Longer description for technology info page:\nCryo-CLEM combines cryo-fixation and cryo-fluorescence microscopy with subsequent cryo-FIB, cryo-TEM, cryo-SEM, or cryo-ET. Alternatively after cryo-fluorescence microscopy samples can be cryo-substituted and embedded in resins, followed by room temperature FIB-SEM, TEM, or ET. The main advantage of cryo-CLEM is better preservation of spatial correlation between fluorescence and EM images, compared to standard CLEM using chemical fixation, and the possibility to use the full palette of fluorophores compared to in-resin fluorescence CLEM experiments.**\n\n", "provider_node_ids": [ "90c8b0d6", "d039b533", "64543c53", "09122290" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "a7128dd1", "name": "Cryo Electron Tomography (Cryo-ET)*", "original_id": "12381c41-aaa0-4c3f-ad16-3432e4a2d278", "description": "Cryo-electron tomography (cryoET) is a specialized transmission electron microscopy technique in which samples are tilted and imaged under cryogenic conditions, resulting in a series of 2D images that can be computationally combined to produce a 3D reconstruction. And if a sample contains identical or repeating structures, subtomogram averaging could be a possibility to enhance the resolution of the structure of interest.\r\nThis is the method of choice for visualization of hydrated proteins, viruses, cells and small organisms. No chemical fixation and staining is used. It is a powerful tool that serves to fill the gap between protein structures and cellular structure.", "documentation": "## Cryo Electron Tomography (Cryo-ET)\\*\n---\n**Cryo-electron tomography (cryoET) is a specialized transmission electron microscopy technique in which samples are tilted and imaged under cryogenic conditions, resulting in a series of 2D images that can be computationally combined to produce a 3D reconstruction. And if a sample contains identical or repeating structures, subtomogram averaging could be a possibility to enhance the resolution of the structure of interest.\nThis is the method of choice for visualization of hydrated proteins, viruses, cells and small organisms. No chemical fixation and staining is used. It is a powerful tool that serves to fill the gap between protein structures and cellular structure.**\n\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "d039b533", "b19711d3", "0c8677f6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "3a9c25c4-6003-4889-a4ca-d33c6266dd89", "name": "Cryo-EM" } }, { "id": "4b452472", "name": "Cryo Focussed Ion beam (Cryo-FIB)*", "original_id": "f2ff62e2-91f2-4b66-afe3-550535eee8b5", "description": "Cryo-electron tomography of structures inside thick cells requires the preparation of thin lamella, which are thin enough to be used in cryoET. Cryo-FIB milling is the method of choice to prepare these lamella. To prepare the lamella, cryo-EM samples are exposed to a focussed ion beam to remove the parts of the sample outside the area of interest until only the thin lamella remains. The resulting lamella can then be used in further high-resolution imaging. \r\nMost systems use a beam of focused Gallium ions to achieve the FIB milling.\r\n", "documentation": "## Cryo Focussed Ion beam (Cryo-FIB)\\*\n---\n**Cryo-electron tomography of structures inside thick cells requires the preparation of thin lamella, which are thin enough to be used in cryoET. Cryo-FIB milling is the method of choice to prepare these lamella. To prepare the lamella, cryo-EM samples are exposed to a focussed ion beam to remove the parts of the sample outside the area of interest until only the thin lamella remains. The resulting lamella can then be used in further high-resolution imaging.\nMost systems use a beam of focused Gallium ions to achieve the FIB milling.**\n\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "b19711d3", "0c8677f6", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "3a9c25c4-6003-4889-a4ca-d33c6266dd89", "name": "Cryo-EM" } }, { "id": "904149e2", "name": "Cryo Scanning Electron Microscopy (Cryo-SEM)*", "original_id": "a6f51330-a473-4d6a-878d-ab4b7db5217f", "description": "Cryo-SEM is an excellent technique for imaging of liquid and semi-liquid materials surfaces, hydrated biological specimens (e.g. biofilms, extracellular matrix, hyphae, etc.) in close-to native state. In this method, a beam of focussed ions is scanned across the sample surface (SEM) under cryogenic conditions. ", "documentation": "## Cryo Scanning Electron Microscopy (Cryo-SEM)\\*\n---\n**Cryo-SEM is an excellent technique for imaging of liquid and semi-liquid materials surfaces, hydrated biological specimens (e.g. biofilms, extracellular matrix, hyphae, etc.) in close-to native state. In this method, a beam of focussed ions is scanned across the sample surface (SEM) under cryogenic conditions.\nIn combination with the high-pressure freezing and freeze fracturing/etching techniques, inner structures of samples can also be observed**\n\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "b19711d3", "9beefd47", "64543c53", "09122290" ], "abbr": "", "category": { "id": "3a9c25c4-6003-4889-a4ca-d33c6266dd89", "name": "Cryo-EM" } }, { "id": "cb003121", "name": "Cryo Transmission Electron Microscopy* (Cryo-TEM)", "original_id": "9765d5cd-99d0-41ce-887b-8d3340917380", "description": "This is transmission electron microscopy performed under cryogenic conditions on cryo-preserved samples. It can be used to determine the structure of protein and viruses to atomic resolution.\r\n", "documentation": "## Cryo Transmission Electron Microscopy (Cryo-TEM)\\*\n---\n**This is transmission electron microscopy performed under cryogenic conditions on cryo-preserved samples. It can be used to determine the structure of protein and viruses to atomic resolution.**\n\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "3a9c25c4-6003-4889-a4ca-d33c6266dd89", "name": "Cryo-EM" } }, { "id": "60f50c0f", "name": "Cryo fluorescence microscopy (CryoFM)", "original_id": "b7fe8a03-c4d9-45e6-bb76-2e0f01cbcee9", "description": "CryoFM enables high-resolution imaging of vitrified samples at sub-200nm.", "documentation": "### Cryo fluorescence microscopy\n---\n**Cryo fluorescence microscopy describes a fluorescence microscopy modality where imaging is performed under cryogenic conditions on samples that underwent cryo-fixation, such as plunge-freezing. This method can be especially useful as a correlative modality in combination with cryo electron microscopy.**\n\n## AI Generated Documentation\n\n**Overview** \nCryo Fluorescence Microscopy (CryoFM) is a cutting-edge imaging technique that merges fluorescence microscopy with cryogenic sample preparation, allowing for the visualization of biological samples in a near-native state at cryogenic temperatures. This method is particularly advantageous for studying the structural and functional dynamics of biomolecules and cellular components without the artifacts introduced by traditional imaging techniques.\n\n**Key Capabilities** \nCryoFM employs rapid vitrification to preserve biological samples, preventing ice crystal formation that can distort cellular architecture. It utilizes specialized fluorophores that maintain their fluorescence properties at low temperatures, enabling high-resolution imaging. The technique can achieve spatial resolutions below 200 nm through the application of super-resolution methods, significantly enhancing the detail visible in biological structures. Additionally, CryoFM can be integrated with other imaging modalities, such as electron microscopy, to provide complementary data about the same sample.\n\n**Applications** \nCryoFM is widely used in structural biology for the visualization of protein complexes, cellular organelles, and other biomolecular assemblies in their functional states. It is instrumental in various research fields, including cell biology, biochemistry, and materials science. Researchers utilize CryoFM to investigate dynamic processes within cells, such as protein interactions, cellular signaling pathways, and the organization of cellular structures. This technique is also valuable in drug discovery, where understanding molecular interactions at the cellular level is crucial for developing effective therapeutics.\n\n**Advantages** \nThe primary advantages of CryoFM include: \n- **Near-native imaging**: Samples are preserved in a state that closely resembles their natural environment, leading to more accurate structural information. \n- **High resolution**: The combination of fluorescence labeling and cryogenic techniques allows for detailed visualization of biological structures, surpassing the capabilities of conventional fluorescence microscopy. \n- **Fluorophore stability**: The behavior of fluorophores at low temperatures can enhance signal-to-noise ratios, improving image quality. \n- **Integration with other techniques**: CryoFM can be combined with electron microscopy for correlative studies, providing a comprehensive view of sample morphology and molecular interactions. \nIn summary, Cryo Fluorescence Microscopy represents a significant advancement in imaging technology, enabling researchers to explore the complexities of biological systems with unprecedented detail and accuracy.\n\n## References\n\n1. https://www.sciencedirect.com/science/article/pii/S1367593114000623\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC4094034/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "23f7a2fd", "b19711d3", "64543c53" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "7cb8eeaf", "name": "Deconvolution widefield microscopy (DWM)", "original_id": "20a9b47c-c7c0-49f8-91c5-f8eba990be63", "description": "Deconvolution is a computational technique for improving the contrast and resolution of digital images. It includes a suite of methods that seek to remove or reverse the blurring present in microscopes images caused by the limited aperture of the microscope objective lens. Nearly any image digitally acquired on a fluorescence microscope can be deconvolved. Three-dimensional datasetsmade up of a series of different widefield planes are particularly well suited for improvement by deconvolution, thereby producing “optical sections”, although with limited results when compared to “confocal” techniques. DWM typically causes less photoxicicity on the samples, so it is well suited for observation of cells in culture for long periods, and it easily allows the observation of unstained live-cells using DIC/Nomarski or Phase-contrast.", "documentation": "## DECONVOLUTION WIDEFIELD MICROSCOPY\n---\n**Deconvolution is a computational technique for improving the contrast and resolution of digital images. It includes a suite of methods that seek to remove or reverse the blurring present in microscopes images caused by the limited aperture of the microscope objective lens. Nearly any image acquired on a digital fluorescence microscope can be deconvolved. In addition, new applications to transmitted light images are now available. Three-dimensional images made up of a series of optical sections are particularly well suited for improvement by deconvolution.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "e532f9cb", "161021f6", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "f1099f78", "c4b25263" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "df1896a3", "name": "EM tomography (ET)", "original_id": "bf273ea1-7987-4a76-815e-9dacb0de489a", "description": "EM tomography allows the gathering of 3D information from individual thick sections of samples, previously fixed for sectioning. \r\nIn TEM tomography thick plastic sections (typically 200-300 nm) are placed on an EM grid and are tilted in the electron beam to +/- 70 degrees. At each tilt angle, a 2D image is acquired and the series of images are later computed to reconstruct the 3D volume: the tomogram.\r\n\r\nSerial thick sections can be imaged the same way, which then results in ssTEM-tomography, which allows the coverage of a larger 3D volume. Complementary modalities, such as STEM tomography can deal with thicker sections (in the μm range).\r\n", "documentation": "## EM Tomography (ET)\n---\n**EM tomography allows the gathering of 3D information from individual thick sections of samples, previously fixed for sectioning.\nIn TEM tomography thick plastic sections (typically 200-300 nm) are placed on an EM grid and are tilted in the electron beam to +/- 70 degrees. At each tilt angle, a 2D image is acquired and the series of images are later computed to reconstruct the 3D volume: the tomogram.\nSerial thick sections can be imaged the same way, which then results in ssTEM-tomography, which allows the coverage of a larger 3D volume. Complementary modalities, such as STEM tomography can deal with thicker sections (in the μm range).**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } }, { "id": "3965a906", "name": "Elemental analysis (EDX)*", "original_id": "697cd405-b01d-45e4-8a65-675e49c12522", "description": "Energy-dispersive X-ray spectroscopy (EDX) is a form of elemental analysis which is performed in combination with electron microscopy. EDX has so far not been routinely used in the life sciences, but thanks to new generation detectors (larger area, more sensitive), EDX is becoming a routine tool in tissue imaging. \r\nEDX provides information about 2D and 3D spatial distribution of elements in the sample, with spatial resolution ranging between units of nm to 1 µm. Imaging is suitable especially for heavier elements, however, modern EDX detectors have become sensitive enough to routinely detect light elements in biological samples. Multiple elements can be mapped simultaneously, or integral spectra can be collected from selected areas. Imaging can be combined with FIB milling for unraveling inner composition of samples.\r\n", "documentation": "## Elemental Analysis\\* (EDX)\n---\n**Energy-dispersive X-ray spectroscopy (EDX) is a form of elemental analysis which is performed in combination with electron microscopy. EDX has so far not been routinely used in the life sciences, but thanks to new generation detectors (larger area, more sensitive), EDX is becoming a routine tool in tissue imaging.\nEDX provides information about 2D and 3D spatial distribution of elements in the sample, with spatial resolution ranging between units of nm to 1 µm. Imaging is suitable especially for heavier elements, however, modern EDX detectors have become sensitive enough to routinely detect light elements in biological samples. Multiple elements can be mapped simultaneously, or integral spectra can be collected from selected areas. Imaging can be combined with FIB milling for unraveling inner composition of samples.**\n\n", "provider_node_ids": [ "90c8b0d6", "d039b533", "9beefd47", "64543c53", "e5f30cac", "f1099f78" ], "abbr": "", "category": { "id": "71c66bf5-90db-427e-8ddc-5bc0e722c489", "name": "Scanning Electron Microscopy (SEM)" } }, { "id": "60335007", "name": "Elemental analysis Correlative Light and Electron Microscopy (EDX-CLEM)*", "original_id": "28b1c72c-e5ab-4292-9ea4-938cd1c77926", "description": "Light microscopy helps to identify features in ultrastructural maps, but does not have EM resolution, therefore light and electron microscopy are correlated and in EDX-CLEM, also combined with Energy-dispersive X-ray spectroscopy (EDX) to allow for simultaneous and correlated elemental detection.", "documentation": "## Elemental analysis Correlative Light and Electron Microscopy (EDX-CLEM)\\*\n---\n**Light microscopy helps to identify features in ultrastructural maps, but does not have EM resolution, therefore light and electron microscopy are correlated and in EDX-CLEM, also combined with Energy-dispersive X-ray spectroscopy (EDX) to allow for simultaneous and correlated elemental detection.**\n\n", "provider_node_ids": [ "d039b533", "64543c53" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "3a4d793f", "name": "Expansion Microscopy (ExM)*", "original_id": "9ee91661-a179-4e37-b036-7ed67bf1140c", "description": "Expansion microscopy (ExM) is a super-resolution approach that achieves sub-diffraction information by physically expanding the specimen. This allows it to seamlessly obtain resolutions of ~50 nm (up to 10 nm) in four colors in any widefield or confocal microscope. \r\nThe Nodes offering this technique can support the user in this sample preparation process, if required, and have imaging systems with the capacity to image the often large expanded samples.", "documentation": "## Expansion Microscopy\\* (ExM)\n---\n**Expansion microscopy (ExM) is a super-resolution approach that achieves sub-diffraction information by physically expanding the specimen. This allows it to seamlessly obtain resolutions of ~50 nm (up to 10 nm) in four colors in any widefield or confocal microscope.\nThe Nodes offering this technique can support the user in this sample preparation process, if required, and have imaging systems with the capacity to image the often large expanded samples.**\n\n", "provider_node_ids": [ "522e8aaa", "638ca876", "90c8b0d6", "1fa342de", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "1f3001ca", "name": "Feedback microscopy (FDBKM)*", "original_id": "c687cadf-a846-4677-a3b4-cf63dbfdacf3", "description": "Biological systems are inherently complex, and the response of even the more stable model can be highly heterogeneous. Therefore, many samples must be imaged to achieve statistically meaningful results. In microscopy, obtaining sufficiently large quantitative datasets during manual operation can become very time-consuming because the operator must first identify the targets of interest and then acquire each with experiment-specific settings. This workflow imposes limits on the number of events that can be recorded and the reproducibility of the results, especially when the phenotypes of interest are rare or occur only during specific biological stages. Feedback microscopy or smart microscopy allows automation of the image acquisition process, often in combination with responsive image analysis to find the sites of interest. This method can also play a key role in driving unbiased imaging of specimens. \r\nIn many cases, AI or deep learning are used in the image analysis and object recognition parts of the feedback microscopy process.\r\n", "documentation": "## Feedback Microscopy (FDBKM)\n---\n**Biological systems are inherently complex, and the response of even the more stable model can be highly heterogeneous. Therefore, many samples must be imaged to achieve statistically meaningful results. In microscopy, obtaining sufficiently large quantitative datasets during manual operation can become very time-consuming because the operator must first identify the targets of interest and then acquire each with experiment-specific settings. This workflow imposes limits on the number of events that can be recorded and the reproducibility of the results, especially when the phenotypes of interest are rare or occur only during specific biological stages. Feedback microscopy or smart microscopy allows automation of the image acquisition process, often in combination with responsive image analysis to find the sites of interest. This method can also play a key role in driving unbiased imaging of specimens.\nIn many cases, AI or deep learning are used in the image analysis and object recognition parts of the feedback microscopy process.**\n\n", "provider_node_ids": [ "1fa342de", "fc1893d4", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "5a688552", "name": "Fluorescence (cross)-correlation spectroscopy (FCS/FCCS)", "original_id": "228e6d27-259f-4785-ab63-b0e1bb0ac5b8", "description": "Fluorescence correlation spectroscopy (FCS) is a correlation analysis of fluctuations in the fluorescence intensity. The analysis provides information on physical parameters of the fluorescent particles (molecules) in solution, such as concentration, average fluorescence intensity and diffusion speed. By following changes on these parameters it is possible to study binding events of the molecules or even conformational changes on them.\r\nFluorescence cross-correlation spectroscopy (FCCS) extends the FCS procedure in that it looks at the correlation between different colors (cross-correlation) rather than just the same color (auto-correlation). In other words, coincident green and red intensity fluctuations correlate if green and red labeled particles are moving together. As a result, FCCS provides a highly sensitive measurement of molecular interactions independent of diffusion rate. \r\n", "documentation": "## Fluorescence (cross)-Correlation Spectroscopy (FCS/FCCS)\n---\n**Fluorescence correlation spectroscopy (FCS) is a correlation analysis of fluctuations in the fluorescence intensity. The analysis provides information on physical parameters of the fluorescent particles (molecules) in solution, such as concentration, average fluorescence intensity and diffusion speed. By following changes on these parameters it is possible to study binding events of the molecules or even conformational changes on them.\nFluorescence cross-correlation spectroscopy (FCCS) extends the FCS procedure in that it looks at the correlation between different colors (cross-correlation) rather than just the same color (auto-correlation). In other words, coincident green and red intensity fluctuations correlate if green and red labeled particles are moving together. As a result, FCCS provides a highly sensitive measurement of molecular interactions independent of diffusion rate.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "e532f9cb", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "e5f30cac", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "0de0802c", "name": "Fluorescence Lifetime Imaging (FLIM)", "original_id": "f98cb04b-dd7f-4c98-a1dd-882f8d706f01", "description": "Fluorescence-lifetime imaging microscopy (FLIM) is an imaging technique for producing an image based on differences in the fluorescence-lifetime rather than its intensity. By quantifying variations in the exponential decay rate of the fluorescence from a fluorescent sample (fluorescence-lifetime) it is possible to report on molecule proximity, pH changes and even polarity. It can be used as an imaging technique in confocal microscopy, two-photon excitation microscopy and multiphoton tomography. Since the fluorescence-lifetime is insensitive to changes in fluorophore intensity or concentration, it is the most quantitatively precise technique to report on fluoresce resonance energy transfer (FRET).", "documentation": "## Fluorescence Lifetime Imaging (FLIM)\n---\n**Fluorescence-lifetime imaging microscopy (FLIM) is an imaging technique for producing an image based on differences in the fluorescence-lifetime rather than its intensity. By quantifying variations in the exponential decay rate of the fluorescence from a fluorescent sample (fluorescence-lifetime) it is possible to report on molecule proximity, pH changes and even polarity. It can be used as an imaging technique in confocal microscopy, two-photon excitation microscopy and multiphoton tomography. Since the fluorescence-lifetime is insensitive to changes in fluorophore intensity or concentration, it is the most quantitatively precise technique to report on fluoresce resonance energy transfer (FRET).**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "e532f9cb", "1fa342de", "161021f6", "ca2e3748", "23f7a2fd", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "e5f30cac", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "018d2770", "name": "Fluorescence Recovery after Photobleaching (FRAP)", "original_id": "898ea266-ec2e-4bdd-b201-e649dfa6e4ba", "description": " Fluorescence recovery after photobleaching (FRAP) denotes an optical technique capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently labeled probes. This technique is very useful in biological studies of cell membrane diffusion and protein binding as it not only reports on the diffusion rates of mobile fractions of molecules but also provides information about the proportion of immobile molecules. In addition, surface deposition of a fluorescent phospholipid bilayer (or monolayer) allows the characterization of hydrophilic (or hydrophobic) surfaces in terms of surface structure and free energy.", "documentation": "## Fluorescence Recovery After Photobleaching (FRAP)\n---\n**Fluorescence recovery after photobleaching (FRAP) denotes an optical technique capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently labeled probes. This technique is very useful in biological studies of cell membrane diffusion and protein binding as it not only reports on the diffusion rates of mobile fractions of molecules but also provides information about the proportion of immobile molecules. In addition, surface deposition of a fluorescent phospholipid bilayer (or monolayer) allows the characterization of hydrophilic (or hydrophobic) surfaces in terms of surface structure and free energy.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "2103118f", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "e9910d1c", "name": "Fluorescence Resonance Energy Transfer (FRET)", "original_id": "6513214e-8838-49a6-bf72-ceed0d7ab5d7", "description": "Fluorescence resonance energy transfer (FRET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through non-radiative dipole-dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance and therefore an excellent reporter on molecule proximity and interaction.", "documentation": "##\n## Fluorescence Resonance Energy Transfer (FRET)\n---\n**Fluorescence resonance energy transfer (FRET) is a mechanism describing energy transfer between two light-sensitive molecules (chromophores). A donor chromophore, initially in its electronic excited state, may transfer energy to an acceptor chromophore through non-radiative dipole-dipole coupling. The efficiency of this energy transfer is inversely proportional to the sixth power of the distance between donor and acceptor, making FRET extremely sensitive to small changes in distance and therefore an excellent reporter on molecule proximity and interaction.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "eebba7a7", "name": "Focussed Ion beam SEM (FIB-SEM) ", "original_id": "6620ed1f-b778-459b-98d1-6fdb898d7927", "description": "A full understanding of the fine organization of cells and tissues requires their high-resolution visualization in three dimensions (3D). Plastic embedded cells can be imaged with automated focused ion beam (FIB) - scanning electron microscopy (SEM). In this technique, the FIB removes a thin slice from the block, after which the exposed face is imaged with the SEM. This process is repeated until the desired volume is imaged, allowing for 3D imaging at high resolution (sub 5 nm) in x, y, and z directions. This technique is especially suited to obtain ultrastructural information of subcellular regions or even an entire cell.", "documentation": "## Focused ion beam scanning EM (FIB-SEM)\n---\n**A full understanding of the fine organization of cells and tissues requires their high-resolution visualization in three dimensions (3D). Plastic embedded cells can be imaged with automated focused ion beam (FIB) - scanning electron microscopy (SEM). In this technique, the FIB removes a thin slice from the block, after which the exposed face is imaged with the SEM. This process is repeated until the desired volume is imaged, allowing for 3D imaging at high resolution (sub 5 nm) in x, y, and z directions. This technique is especially suited to obtain ultrastructural information of subcellular regions or even an entire cell.**\n\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } }, { "id": "745fa0d0", "name": "Fourier transform infrared imaging (FTIR)", "original_id": "2ad67c6b-60d9-4cb6-9c43-b26905c289d7", "description": "Rapid, non-destructive molecular analysis; high sensitivity, versatile applications.", "documentation": "## Fourier Transform Infrared Imaging (FTIR)\n---\n**Fourier transform infrared imaging (FTIR) is a technique which is used to obtain an infrared spectrum of absorption, emission, photoconductivity or Raman scattering of a solid, liquid or gas. An FTIR spectrometer simultaneously collects spectral data in a wide spectral range**.\n\n## AI Generated Documentation\n\n### Overview\nFourier Transform Infrared Imaging (FTIR) is a sophisticated spectroscopic technique that enables the analysis of molecular compositions in various states—solids, liquids, and gases—by measuring the absorption of infrared radiation. FTIR provides a unique spectral fingerprint for each material, allowing for precise identification and characterization based on molecular vibrations.\n\n### Key Capabilities\nFTIR operates primarily in the mid-infrared range (4000 to 400 cm⁻¹), where most organic compounds exhibit characteristic absorption peaks. The technology employs an interferometer to collect data across all infrared frequencies simultaneously, which is a significant advancement over traditional dispersive methods that scan wavelengths sequentially. This capability allows for rapid acquisition of spectra, often within seconds. The resolution of FTIR can reach down to 1 cm⁻¹, enabling detailed analysis of complex mixtures. Additionally, FTIR can be coupled with microscopy techniques (FTIR microscopy) to analyze small sample areas, providing spatially resolved chemical information.\n\n### Applications\nFTIR is widely used across multiple fields:\n- **Material Science**: Identification and characterization of polymers, rubbers, and composites, including deformulation studies through TGA-IR and GC-IR techniques.\n- **Pharmaceuticals**: Quality control and assurance, confirming the identity of raw materials and finished products.\n- **Environmental Monitoring**: Analysis of emissions from vehicles and industrial processes, aiding in compliance with environmental regulations.\n- **Cultural Heritage**: Non-destructive analysis of artworks and historical artifacts, facilitating preservation efforts and material composition studies.\n\n### Advantages\nThe advantages of FTIR imaging include:\n- **Speed**: The ability to acquire spectra rapidly makes FTIR ideal for high-throughput screening applications.\n- **Sensitivity**: High sensitivity allows for the detection of trace amounts of substances, which is crucial for advanced research applications.\n- **Non-destructive Testing**: The non-invasive nature of FTIR is particularly beneficial in contexts where sample integrity must be preserved, such as in art conservation.\n- **Quantitative Analysis**: With the integration of modern software algorithms, FTIR can provide quantitative data regarding the concentration of materials, enhancing its utility in analytical chemistry.\n\nIn summary, FTIR imaging stands out for its rapid, sensitive, and versatile capabilities, making it an essential tool for researchers and professionals in various scientific and industrial domains.\n\n## References\n\n1. https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fourier-transform-infrared-spectroscopy/applications.html\n2. https://scienceinfo.com/ftir-principle-instrumentation-applications/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "64543c53", "09122290" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "04562797", "name": "Genetic encoded EM probes (GE probes)", "original_id": "95ecbb75-ab79-444d-b176-4e7313e32679", "description": "Localising specific proteins of interest represents a challenge in electron microscopy, compared to fluorescence microscopy where the target of interest is normally visualised via fluorescent tags or probes, such as fluorescently-labelled antibodies. \r\nMultiple solutions exist to allow specific targets of interest, particularly proteins, to be localised within EM samples. One such solution are genetically encoded EM probes. These probes, such as APEX and miniSOG, are small tags that can be fused to the gene sequence of proteins of interest and then expressed in the cells/organism of study. These probes then allow their visualisation in samples prepared for EM.\r\nNodes offering this technique can help users in selecting the appropriate tag, preparing the required construct, and in the sample preparation techniques needed to use the probes successfully.", "documentation": "## Genetic encoded EM probes\n---\n**Localising specific proteins of interest represents a challenge in electron microscopy, compared to fluorescence microscopy where the target of interest is normally visualised via fluorescent tags or probes, such as fluorescently-labelled antibodies.\nMultiple solutions exist to allow specific targets of interest, particularly proteins, to be localised within EM samples. One such solution are genetically encoded EM probes. These probes, such as APEX and miniSOG, are small tags that can be fused to the gene sequence of proteins of interest and then expressed in the cells/organism of study. These probes then allow their visualisation in samples prepared for EM.\nNodes offering this technique can help users in selecting the appropriate tag, preparing the required construct, and in the sample preparation techniques needed to use the probes successfully.**\n\n", "provider_node_ids": [ "90c8b0d6", "d039b533", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "722bb380", "name": "High throughput microscopy/high content screening (HTM/HCS)", "original_id": "1c7be92a-16e3-4019-addd-415d2a0fca39", "description": "High-throughput microscopy has created new opportunities for studying biological phenomena in an unbiased manner. Using automated cell manipulations and microscopy platforms, it is possible to easily screen entire genomes for genes that affect any cellular process that can be visualized. HTM techniques rely on fully automated widefield or confocal microscopy systems which facilitate the capture of thousands of images, often in multi-well plates. Labs supporting HCS also have the expertise to automatically deliver drugs to multiwell plates, and to handle, process and analyse thousands of images using high-content screening analysis methodologies. HTM may also refer to “slide scanner technology” or microscopes capable of tile & stitching large areas of tissue at high-resolution, thus producing multi-megapixel 2D datasets. ", "documentation": "## High Throughput Microscopy/High Content Screening (HTM/HCS)\n---\n**High-throughput microscopy has created new opportunities for studying biological phenomena in an unbiased manner. Using automated cell manipulations and microscopy platforms, it is possible to easily screen entire genomes for genes that affect any cellular process that can be visualized. HTM techniques rely on fully automated widefield or confocal microscopy systems which facilitate the capture of thousands of images, often in multi-well plates. Labs supporting HCS also have the expertise to automatically deliver drugs to multiwell plates, and to handle, process and analyse thousands of images using high-content screening analysis methodologies. HTM may also refer to “slide scanner technology” or microscopes capable of tile & stitching large areas of tissue at high-resolution, thus producing multi-megapixel 2D datasets.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "e532f9cb", "1fa342de", "161021f6", "ca2e3748", "23f7a2fd", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "6f0ef2b7", "9beefd47", "64543c53", "e5f30cac", "f1099f78", "09122290", "c4b25263" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "d6cec7b4", "name": "High-speed Imaging (HSI)*", "original_id": "b37476af-5a89-466f-8d24-bf41d9e3ab85", "description": "High-speed imaging includes all imaging techniques capable of gathering data at very high frame rates. The commonly considered cut-off is an exposure time of 1/1000 sec or >250 frames per second. High-speed imaging allows the observation of very fast biological processes, after the data is slowed down following acquisition.", "documentation": "## High-speed Imaging (HSI)\n---\n**High-speed imaging includes all imaging techniques capable of gathering data at very high frame rates. The commonly considered cut-off is an exposure time of 1/1000 sec or >250 frames per second. High-speed imaging allows the observation of very fast biological processes, after the data is slowed down following acquisition.**\n\n", "provider_node_ids": [ "90c8b0d6", "1fa342de", "0c8677f6", "fc1893d4", "64543c53", "a44edc42", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "4e5bcb9e", "name": "I don't know which technology", "original_id": "60471c07-6176-44e0-9694-259b37eb83a2", "description": "Real-time multi-modal imaging: MRI, CT, fluorescence, high-resolution cell dynamics.", "documentation": "## I don't know which Technology\n---\nPlease select this if you are unsure of the service or technology needed for your application and Euro-BioImaging will help you in making the appropriate choice of technology and node for your proposal.\n|\n| |\n\n## AI Generated Documentation\n\n**Overview** \nBioimaging is a cutting-edge technology that integrates various imaging modalities to visualize biological processes in real-time. This technology combines structural imaging techniques such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) with functional imaging methods, including fluorescence and hyperspectral imaging. The result is a comprehensive view of both the anatomy and physiology of biological systems, enabling researchers and clinicians to gain deeper insights into health and disease. \n\n**Key Capabilities** \nBioimaging technologies can achieve high spatial resolutions, often in the range of sub-micrometers to millimeters, depending on the specific technique employed. MRI excels in soft tissue contrast, while CT provides detailed cross-sectional images of dense structures. Fluorescence imaging allows for the visualization of specific cellular components through targeted labeling, and advanced techniques like super-resolution microscopy can resolve structures at the nanometer scale. The integration of these modalities facilitates multi-dimensional imaging, enabling the observation of dynamic biological processes over time. \n\n**Applications** \nBioimaging is widely used in various fields, including medical diagnostics, drug development, and biological research. In clinical settings, it aids in the diagnosis of conditions such as tumors, cardiovascular diseases, and neurological disorders. In research, bioimaging techniques are employed to study cellular dynamics, protein interactions, and metabolic processes in live cells. Additionally, emerging applications in environmental science include monitoring microbial activity and assessing ecosystem health through advanced imaging techniques. \n\n**Advantages** \nThe primary advantages of bioimaging include its non-invasive nature, high-resolution capabilities, and the ability to provide real-time insights into biological processes. This technology enhances diagnostic accuracy and facilitates the monitoring of disease progression and treatment efficacy. Furthermore, the integration of big data analytics and machine learning in bioimaging allows for the extraction of quantitative information from complex datasets, improving the understanding of biological systems and aiding in the development of targeted therapies. Overall, bioimaging stands out as a transformative tool in both research and clinical applications, bridging the gap between technology and biology.\n\n## References\n\n1. https://www.bioimagingtech.com/bioimaging-techniques.html\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC9541884/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "1fa342de", "6e382796", "ca2e3748", "e0395c6a", "f68673b1", "d039b533", "23f7a2fd", "6319df36", "4278635d", "4f1ca4db", "b19711d3", "9c8d648e", "46ccfb38", "3850f7eb", "fc1893d4", "6f0ef2b7", "9beefd47", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53", "a44edc42", "d14abc55", "84334573", "6d068cfb", "e5f30cac", "706cb740", "2103118f", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "214b36cf-184f-4b47-81a9-e8f76c86d53b", "name": "I don't know which technology" } }, { "id": "22875d0d", "name": "Image Analysis -bio (IA bio)*", "original_id": "b33d852f-bbd3-4e24-a4e3-4eb9577bb853", "description": "AI-driven, scalable image analysis for complex biological data interpretation.", "documentation": "## Image Data Analysis\n---\n**Imaging technologies record a specimen and produce a digital output. This digital data could then require multiple rounds of analysis steps to infer knowledge from the images. For large, complex, and multimodal datasets, the analysis process highly benefits from standardised and/or automated procedures, often supported by computational methods. Image analysts are experts who can support users with handling, processing, quantification, statistics as well as interpretation of image data. In a collaborative setting, Image analysts can also support projects with experimental design based on analysis of pilot datasets.**\nEuro-BioImaging offers its users Image Data Analysis (IDA) as a Service through expert Image Analysts at the Nodes. These services are available in conjunction with access to imaging technologies at a Node. Additionally, IDA services include standalone analysis services requested on image data irrespective of where it was acquired. Based on the nature of the data, these services are currently being offered under two different categories:\n* Biological Image Data Analysis (IDA-bio)\n* Medical Image Data Analysis (IDA-med)\nWithin this technology offer, users can access a wide variety of image analysis services including, but not limited to:\n* Implementation of specific image analysis processes like image registration, denoising, deconvolution, colocalization, segmentation, tracking, etc.\n* Machine Learning / Deep Learning solutions for image analysis\n* Image analysis workflows or bespoke analysis software development\n* Access to high performance computing resources for image analysis\n* Access to specialised proprietary and open source image analysis softwares\n* Image reconstruction and visualisation\nEuro-BioImaging encourages and facilitates adoption of practices that lead to Findable, Accessible, Interoperable and Reusable (FAIR) data and analysis workflows. Our Nodes strongly support and implement such practices.\nTo find out more about the specific Image Data Analysis service available, interested users are encouraged to contact the Nodes offering this service.\n\n## AI Generated Documentation\n\n**Overview** \nImage Analysis -bio (IA bio) is a cutting-edge technology designed to automate the analysis of complex biological images, leveraging advanced computational methods and artificial intelligence. This technology is instrumental in handling the vast datasets generated by modern imaging techniques, such as microscopy, enabling researchers to extract meaningful insights from intricate biological phenomena. \n\n**Key Capabilities** \nIA bio systems are characterized by their ability to process multidimensional data with high efficiency and accuracy. They typically employ high-performance computing resources, allowing for parallel processing of large datasets. For instance, systems like the ZEISS arivis Hub utilize multiple processors, each with 16 cores, to facilitate rapid data analysis. The integration of machine learning algorithms enhances the capability to detect subtle patterns and anomalies in imaging data, improving the sensitivity and specificity of analyses. Additionally, these systems support scalable workflows, enabling researchers to adapt their analysis pipelines according to the scale of their experiments. \n\n**Applications** \nThe applications of IA bio span various fields, including cell biology, neuroscience, and drug discovery. It is used for tasks such as quantifying cellular structures, tracking dynamic processes in live cells, and analyzing molecular interactions. The technology is particularly valuable in high-throughput screening environments, where rapid and reliable data analysis is essential for advancing research and development. Furthermore, the emergence of multimodal foundation models in IA bio is set to revolutionize the field, allowing for more sophisticated interpretations of complex biological images. \n\n**Advantages** \nIA bio offers several distinct advantages over traditional image analysis methods. Firstly, it significantly reduces the time required for data processing, allowing researchers to focus on interpretation rather than manual analysis. Secondly, the use of automated systems enhances the reproducibility and objectivity of results, minimizing human error. Thirdly, the scalability of IA bio systems accommodates varying data loads, making them suitable for both small-scale studies and extensive research projects. Lastly, many modern IA bio platforms provide remote accessibility, facilitating collaboration among researchers across different locations. \n\nIn summary, Image Analysis -bio (IA bio) stands out as a transformative technology in biological research, combining advanced imaging capabilities with powerful computational tools to unlock new insights into cellular and molecular mechanisms.\n\n## References\n\n1. https://www.zeiss.com/microscopy/en/resources/insights-hub/life-sciences/scalable-image-analysis-for-biotech-and-pharma.html\n2. https://www.nature.com/articles/s41592-023-01930-y\n3. https://www.nature.com/articles/nbt.3722\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "1fa342de", "161021f6", "23f7a2fd", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "2d0180c4-60ae-450c-bfd0-da2c41c3c8ea", "name": "Biological Image Data Services" } }, { "id": "31d30c68", "name": "Image Scanning microscopy (ISM)", "original_id": "d600c23b-8dbe-44c7-87b4-3c56dee69b34", "description": "Super-resolution imaging with 2x confocal resolution, SPAD detection, live-cell compatible.", "documentation": "## Image Scanning Microscopy (ISM)\n---\n**Image Scanning microscopy is a method for increasing resolution of a confocal microscope. This is achieved by replacing the point detector of a classical confocal with an array detector. Each pixel of the array detector records its own scan image when the sample is scanned with the laser spot and the individual images are then combined into a single image. The final ISM image corresponds theoretically to an image with a confocal taken with an entirely closed pinhole, which results in the increased resolution observed. ISM has the potential to nearly double the resolution of a confocal imaging system. Multiple commercial implementations of Image Scanning Microscopy exist both on laser scanning confocals as well as spinning disk systems, such as AiryScan, rescan confocal microscope and SoRa. Non-commercial ISM solutions are also available and in general ISM can be applied to 2-photon imaging and many other light microscopy modalities. Please contact the Node offering the technology to find out more about the specific implementation offered.**\n\n## AI Generated Documentation\n\n**Overview** \nImage Scanning Microscopy (ISM) is a cutting-edge optical imaging technique that significantly enhances the spatial resolution of conventional confocal microscopy, achieving nearly double the resolution. This method addresses the inherent limitations of traditional confocal systems, particularly the trade-off between resolution and signal-to-noise ratio. By utilizing a fast detector array instead of a single-element detector and confocal pinhole, ISM captures a complete image for each position of the scanned laser beam, resulting in high-resolution imaging of biological samples. \n\n**Key Capabilities** \nISM employs a focused laser beam that scans across the sample while detecting emitted fluorescence using a Single Photon Avalanche Diode (SPAD) array. This configuration allows for rapid and sensitive detection of fluorescence signals, which is essential for imaging samples with low light emission. The effective spatial resolution of ISM is theoretically limited by the excitation wavelength and the numerical aperture of the microscope's objective, following Abbe's formula. Additionally, ISM can be integrated with time-resolved techniques such as Fluorescence Lifetime Imaging (FLIM), enabling researchers to obtain dynamic information about molecular interactions within the sample. \n\n**Applications** \nThis technique is particularly useful in live-cell imaging, where it minimizes photodamage and photobleaching, allowing for prolonged observation of cellular processes. ISM is also applicable in various fields, including developmental biology, neuroscience, and materials science, where high-resolution imaging of complex structures is required. Its ability to provide detailed insights into molecular dynamics makes it a valuable tool for studying cellular mechanisms and interactions. \n\n**Advantages** \nOne of the standout features of ISM is its gentleness on samples, which reduces the risk of photodamage compared to other super-resolution techniques like STED and SIM. This characteristic is crucial for long-term imaging studies. Furthermore, ISM's design allows for straightforward upgrades to existing confocal microscopy systems, enhancing their capabilities without extensive modifications. The access to raw scanned images also facilitates advanced image processing and adaptive reconstruction methods, further improving the quality of the analysis. Overall, ISM represents a significant advancement in microscopy technology, offering enhanced resolution, versatility, and minimal sample disruption, making it an essential tool for modern scientific research.\n\n## References\n\n1. https://www.genoainstruments.com/technology.html\n2. https://www.nature.com/articles/s41592-018-0291-9\n3. https://vicidominilab.github.io/teaching/teaching-2\n4. https://www.sciencedirect.com/science/article/pii/S1367593119300456\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "638ca876", "90c8b0d6", "e532f9cb", "161021f6", "ca2e3748", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "a44edc42", "151b4761", "09122290" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "639a72d3", "name": "Image analysis - med (IA med)*", "original_id": "43eda4d0-9dbf-4749-a020-171692e45495", "description": "AI-driven medical imaging: automated detection, segmentation, real-time analysis.", "documentation": "## Image Data Analysis\n---\n**Imaging technologies record a specimen and produce a digital output. This digital data could then require multiple rounds of analysis steps to infer knowledge from the images. For large, complex, and multimodal datasets, the analysis process highly benefits from standardised and/or automated procedures, often supported by computational methods. Image analysts are experts who can support users with handling, processing, quantification, statistics as well as interpretation of image data. In a collaborative setting, Image analysts can also support projects with experimental design based on analysis of pilot datasets.**\nEuro-BioImaging offers its users Image Data Analysis (IDA) as a Service through expert Image Analysts at the Nodes. These services are available in conjunction with access to imaging technologies at a Node. Additionally, IDA services include standalone analysis services requested on image data irrespective of where it was acquired. Based on the nature of the data, these services are currently being offered under two different categories:\n* Biological Image Data Analysis (IDA-bio)\n* Medical Image Data Analysis (IDA-med)\nWithin this technology offer, users can access a wide variety of image analysis services including, but not limited to:\n* Implementation of specific image analysis processes like image registration, denoising, deconvolution, colocalization, segmentation, tracking, etc.\n* Machine Learning / Deep Learning solutions for image analysis\n* Image analysis workflows or bespoke analysis software development\n* Access to high performance computing resources for image analysis\n* Access to specialised proprietary and open source image analysis softwares\n* Image reconstruction and visualisation\nEuro-BioImaging encourages and facilitates adoption of practices that lead to Findable, Accessible, Interoperable and Reusable (FAIR) data and analysis workflows. Our Nodes strongly support and implement such practices.\nTo find out more about the specific Image Data Analysis service available, interested users are encouraged to contact the Nodes offering this service.\n\n## AI Generated Documentation\n\n### Overview\nImage Analysis - Med (IA Med) is a cutting-edge technology that integrates artificial intelligence (AI) with medical imaging to enhance diagnostic accuracy and streamline clinical workflows. This technology leverages advanced algorithms to process and analyze various types of medical images, including X-rays, CT scans, MRIs, and ultrasound, enabling healthcare professionals to make informed decisions quickly and effectively.\n\n### Key Capabilities\nIA Med is distinguished by its sophisticated capabilities, which include:\n- **Automated Disease Detection**: Utilizing deep learning models, IA Med can identify abnormalities in imaging data, facilitating early diagnosis of conditions such as tumors and fractures.\n- **Precision Image Segmentation**: The technology excels in delineating anatomical structures within images, which is critical for accurate analysis and treatment planning.\n- **3D Image Reconstruction**: IA Med can reconstruct 3D models from 2D imaging data, providing a comprehensive view of complex anatomical structures.\n- **Quantitative Analysis Tools**: These tools allow for the extraction of metrics that assess disease severity and monitor changes over time, enhancing clinical decision-making.\n\n### Applications\nThe applications of IA Med are extensive and include:\n- **Radiographic Imaging**: Enhancing the interpretation of X-rays and CT scans for improved diagnostic outcomes.\n- **Pathology Imaging**: Analyzing microscopic images for tissue sample processing and cell structure assessment, crucial in cancer diagnostics.\n- **Real-Time Image Processing**: Enabling dynamic assessments, such as fetal development tracking and organ function evaluation, which are vital in obstetrics and cardiology.\n- **Research and Development**: Supporting clinical research by enabling longitudinal studies that analyze temporal changes in imaging data, essential for understanding disease progression and treatment efficacy.\n\n### Advantages\nIA Med offers several advantages that set it apart from traditional imaging technologies:\n- **Improved Diagnostic Accuracy**: AI systems reduce human error and enhance pattern recognition, leading to more reliable diagnoses.\n- **Faster Image Processing**: Technologies like NVIDIA's AI platforms accelerate image reconstruction, significantly reducing the time required for analysis and diagnosis.\n- **Enhanced Patient Outcomes**: By providing real-time decision support, IA Med empowers healthcare providers to make informed choices quickly, ultimately improving patient care.\n\nIn conclusion, Image Analysis - Med (IA Med) represents a transformative approach in healthcare, leveraging AI to enhance the efficiency and accuracy of medical imaging processes, thereby driving innovation in diagnostics and patient management.\n\n## References\n\n1. https://www.sciencedirect.com/journal/medical-image-analysis\n2. https://www.nvidia.com/en-us/use-cases/ai-powered-medical-imaging/\n3. https://whoimage.com/articles/medical-image-analysis-comprehensive-guide.html\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "638ca876", "2b34e271", "23f7a2fd", "6319df36", "0c8677f6", "d2be2f9c", "64543c53", "84334573", "6d068cfb" ], "abbr": "", "category": { "id": "b73300b1-0934-4e73-86be-a829aa06ee16", "name": "Medical Image Data services" } }, { "id": "a2a0f4a8", "name": "Imaging Flow Cytometry (IFC)*", "original_id": "c7b4386c-3e1e-43fe-a417-7d649a884405", "description": "Imaging Flow Cytometry combines the speed, sensitivity and strong statistical power of conventional flow cytometry with the detailed imagery, spatial information and functional insight of microscopy all in a single platform. Up to one thousand cells per second can be simultaneously investigated thus allowing quantitative image-based cellular assays in large and highly heterogeneous cell populations, as well as in rare sub populations.", "documentation": "## Imaging Flow Cytometry\\* (IFC)\n---\n**Imaging Flow Cytometry combines the speed, sensitivity and strong statistical power of conventional flow cytometry with the detailed imagery, spatial information and functional insight of microscopy all in a single platform. Up to one thousand cells per second can be simultaneously investigated thus allowing quantitative image-based cellular assays in large and highly heterogeneous cell populations, as well as in rare sub populations.**\n\n", "provider_node_ids": [ "522e8aaa", "fc1893d4", "e5f30cac" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "f65a70b8", "name": "Imaging at Biosafety Level >1 (BSL>1)", "original_id": "2a404490-29a4-4050-beb9-46242d76cb92", "description": "Imaging at Biosafety Levels >1 is offered at several Euro-BioImaging Nodes. Several Nodes offer imaging at BSL2 and select facilities at BSL3 are also available. In these cases the imaging systems are placed in specific environments that fulfill the required safety level standards and allow the imaging of, e.g. pathogenic or infectious organisms, such as viruses. \r\nPlease contact the Nodes offering this access type to get details on the facility, the safety level and and specific considerations required for access.\r\n", "documentation": "## Imaging at Biosafety Levels >1\n---\n**Imaging at Biosafety Levels >1 is offered at several Euro-BioImaging Nodes. Several Nodes offer imaging at BSL2 and select facilities at BSL3 are also available. In these cases the imaging systems are placed in specific environments that fulfill the required safety level standards and allow the imaging of, e.g. pathogenic or infectious organisms, such as viruses.\nPlease contact the Nodes offering this access type to get details on the facility, the safety level and and specific considerations required for access.**\n\n", "provider_node_ids": [ "90c8b0d6", "b19711d3", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "a97f4fa4", "name": "Imaging for Plant Phenotyping (PHENO)*", "original_id": "bbe6c284-d8d3-48ee-976d-635194082df8", "description": "Multi-sensor imaging: RGB, hyperspectral, thermal; high-throughput phenotyping.", "documentation": "## Plant Phenotyping\n---\n**Plant Phenotyping is designed for non-invasive, morphometric and physiological high-throughput phenotyping of small plants (e.g. Arabidopsis) and mid-size crop plants (e.g. wheat, barley).**\nThe system available at PHENOPlant at the Austria BioImaging Node can process samples on agar-plates and different type of pots ranging from 250mL up to 5L and is fully integrated into a state-of-the-art walk-in phytotron providing highly controlled plant growth conditions. Furthermore, the platform facilitates precise environmental (live) simulations across different climate zones as well as controlled plant stress experiments (cold- or heat stress).\nPlants are transported on conveyor belts from the growth area to the imaging cabinets equipped with a wide range of sensors, including multi-excitation PAM kinetic chlorophyll fluorescence imaging, RGB, hyperspectral imaging (VNIR & SWIR), thermal imaging and 3D scanning.\nFollowing the imaging process, the soil water content is adjusted by an automated, gravimetric watering system, facilitating highly controlled drought stress experiments.\nPotential applications are basic and applied plant research questions where objective, reproducible and high-throughput phenotype assessment (morphology and physiology) is requested.  This includes abiotic- and biotic stress response (e.g. drought, cold, heat light, salt, pathogens), plant breeding, but also testing of e.g. fertiliser, biostimulants, herbicides.\nFor a  360 degree plant point of view of Plant Phenotyping, check out this video \n![](upload/mpi.png)\nView from inside the PHENOPlant facility at the Vienna BioCenter Core Facilities\n\n## AI Generated Documentation\n\n**Overview** Imaging for Plant Phenotyping (PHENO) is a cutting-edge technology that integrates multiple imaging modalities to facilitate the non-invasive analysis of plant traits. This system is designed to capture detailed phenotypic data, enabling researchers to monitor plant growth, health, and responses to environmental conditions effectively. The PHENO platform utilizes advanced sensors that operate across various spectral ranges, providing a comprehensive toolset for agricultural research and crop improvement. **Key Capabilities** PHENO systems are characterized by their multi-sensor integration, which includes: - **RGB Cameras**: Capture high-resolution images for structural and color analysis, allowing for the assessment of plant morphology and color indices. - **Hyperspectral Cameras**: Operate across visible, near-infrared, and short-wavelength infrared spectra, enabling reflectance-based analysis to monitor plant health and stress responses. - **Thermal Imaging Cameras**: Measure leaf temperature and stomatal conductance, providing insights into plant water status and thermal regulation. - **Kinetic Chlorophyll Fluorescence Imaging Sensors**: Evaluate photosynthetic performance by measuring chlorophyll fluorescence dynamics, crucial for understanding plant productivity. The system supports both 2D and 3D imaging modes, allowing for detailed morphometric analysis of plants up to 150 cm in height. **Applications** The applications of PHENO technology are diverse and include: - **High-Throughput Phenotyping**: Automated data collection from large numbers of plants, facilitating rapid analysis of traits such as height, leaf area, and biomass. - **Stress Response Monitoring**: Detecting physiological responses to environmental stresses, such as drought or nutrient deficiencies, through spectral data analysis. - **Genetic Research**: Linking phenotypic data with genotypic information to identify genetic markers associated with desirable traits, aiding in plant breeding efforts. **Advantages** PHENO technology offers several advantages over traditional phenotyping methods: - **Non-Invasive Analysis**: Allows for continuous monitoring of plants without damaging them, preserving their integrity for further study. - **High-Throughput Capability**: Enables the processing of large datasets quickly, which is essential for modern agricultural research. - **Comprehensive Data Collection**: The integration of multiple imaging modalities provides a holistic view of plant health and development, facilitating more informed decision-making in crop management and breeding. In summary, Imaging for Plant Phenotyping (PHENO) stands out as a powerful tool in agricultural research, combining advanced imaging technologies to enhance our understanding of plant traits and responses, ultimately contributing to improved crop management and food security.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC4279472/\n2. https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2020.623705/full\n3. https://plantphenotyping.com/products/plantscreen-imaging-sensors/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "3f84bc36", "name": "Immuno-gold EM on resin sections (resin-EM)", "original_id": "fd89b868-7f56-482f-a47c-9978e4bffc1a", "description": "Immuno-gold is a variant of immunohistochemistry where antibodies tagged with gold particles (of different sizes) are used to visualise the localisation of proteins of interest in EM samples. Due to its electron-dense nature the gold particles are easily detected in the final EM images. \r\n\r\nThis method can also be applied on EM samples prepared in different ways (see Immuno-gold EM on thawed cryo-sections). If you are interested in using either of these methods, the Euro-BioImaging Nodes that offer the techniques will support you in selecting the best-suited technique for your sample and scientific question.\r\n\r\nIn this variation of immuno-gold EM, specimens are chemically fixed, embedded in resin and then sectioned. The sections are then stained with probes or antibodies as in immunohistochemistry\r\n", "documentation": "## Immuno-gold EM on resin sections (resin-EM)\n---\n**Immuno-gold is a variant of immunohistochemistry where antibodies tagged with gold particles (of different sizes) are used to visualise the localisation of proteins of interest in EM samples. Due to its electron-dense nature the gold particles are easily detected in the final EM images.\nThis method can also be applied on EM samples prepared in different ways (see Immuno-gold EM on thawed cryo-sections). If you are interested in using either of these methods, the Euro-BioImaging Nodes that offer the techniques will support you in selecting the best-suited technique for your sample and scientific question.\nIn this variation of immuno-gold EM, specimens are chemically fixed, embedded in resin and then sectioned. The sections are then stained with probes or antibodies as in immunohistochemistry.**\n\n", "provider_node_ids": [ "fcf6bac6", "90c8b0d6", "2b34e271", "ca2e3748", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "a44edc42", "e5f30cac", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "e32e05f1", "name": "Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM)", "original_id": "21cc8c37-7778-4025-a6ca-b69fbf5f1951", "description": "Immuno-gold is a variant of immunohistochemistry where antibodies tagged with gold particles (of different sizes) are used to visualise the localisation of proteins of interest in EM samples. Due to its electron-dense nature the gold particles are easily detected in the final EM images. \r\n\r\nThis method can also be applied on EM samples prepared in different ways (see Immuno-gold EM on thawed cryo-sections). If you are interested in using either of these methods, the Euro-BioImaging Nodes that offer the techniques will support you in selecting the best-suited technique for your sample and scientific question.\r\n\r\nIn this variation of immuno-gold EM, specimens are chemically fixed, cryo-protected and frozen. After this treatment, the sample is hard enough to be thin-sectioned by cryo-ultramicrotomy. The cryo-sections are then thawed and exposed to probes or antibodies. This technique is very sensitive and adapted to identifying membrane compartments in cells.\r\n", "documentation": "## Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM)\n---\n**Immuno-gold is a variant of immunohistochemistry where antibodies tagged with gold particles (of different sizes) are used to visualise the localisation of proteins of interest in EM samples. Due to its electron-dense nature the gold particles are easily detected in the final EM images.\nThis method can also be applied on EM samples prepared in different ways (see Immuno-gold EM on thawed cryo-sections). If you are interested in using either of these methods, the Euro-BioImaging Nodes that offer the techniques will support you in selecting the best-suited technique for your sample and scientific question.\nIn this variation of immuno-gold EM, specimens are chemically fixed, cryo-protected and frozen. After this treatment, the sample is hard enough to be thin-sectioned by cryo-ultramicrotomy. The cryo-sections are then thawed and exposed to probes or antibodies. This technique is very sensitive and adapted to identifying membrane compartments in cells.**\n\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "a673b6b7", "name": "Intravital Microscopy (IVM)", "original_id": "f77fcfdb-9148-46b8-9199-d4a176affbc6", "description": "Intravital imaging covers a range of microscopy modalities used for the long term imaging of living animal models (e.g. zebrafish larvae, mice, rats), in various organs or tissues, or as a whole for smaller models. Intravital Imaging can be performed using 2-photon microscopy, light-sheet microscopy or others. The choice is usually made based on the required penetration depth and resolution. These techniques can be combined with optical manipulation systems, such as laser ablation or optogenetic manipulation systems, and also with a range of e.g. neurological or behavioral stimuli especially when awake, immobilized animals are imaged.\r\nIntravital imaging allows the real-time visualization of cellular processes in their native environment in the living organism. It can be performed as repetitive imaging on the same animal, allowing biological processes to be tracked over long periods of time, or as acute experiments.\r\nSome Euro-BioImaging Nodes offer Intravital Imaging in direct association with animal houses, which is required especially for chronic or repeated imaging.\r\nIntravital microscopy is used for a wide variety of applications where dynamic processes in intact tissue environments need to be understood (see the review articles below for a range of examples). These include various analyses of vascular function, following the migration and cell-cell or cell-matrix interactions of e.g. immune cells or invasive/metastatic tumor cells in different tissues, and changes in e.g. neuronal or astrocyte morphology in response to stimulus or injury. Intravital brain imaging is increasingly done in awake rodents, which allows the integration of e.g. sensory cues for analysis of behavioral responses. A constantly increasing variety of functional probes can also be used for intravital microscopy, including calcium indicators, environmental sensors, FRET probes and enzyme-activated probes.\r\n", "documentation": "## Intravital Microscopy (IVM)\n---\n**Intravital imaging covers a range of microscopy modalities used for the long term imaging of living animal models (e.g. zebrafish larvae, mice, rats), in various organs or tissues, or as a whole for smaller models. Intravital Imaging can be performed using 2-photon microscopy, light-sheet microscopy or others. The choice is usually made based on the required penetration depth and resolution. These techniques can be combined with optical manipulation systems, such as laser ablation or optogenetic manipulation systems, and also with a range of e.g. neurological or behavioral stimuli especially when awake, immobilized animals are imaged.\nIntravital imaging allows the real-time visualization of cellular processes in their native environment in the living organism. It can be performed as repetitive imaging on the same animal, allowing biological processes to be tracked over long periods of time, or as acute experiments.**\nSome Euro-BioImaging Nodes offer Intravital Imaging in direct association with animal houses, which is required especially for chronic or repeated imaging.\nIntravital microscopy is used for a wide variety of applications where dynamic processes in intact tissue environments need to be understood (see the review articles below for a range of examples). These include various analyses of vascular function, following the migration and cell-cell or cell-matrix interactions of e.g. immune cells or invasive/metastatic tumor cells in different tissues, and changes in e.g. neuronal or astrocyte morphology in response to stimulus or injury. Intravital brain imaging is increasingly done in awake rodents, which allows the integration of e.g. sensory cues for analysis of behavioral responses. A constantly increasing variety of functional probes can also be used for intravital microscopy, including calcium indicators, environmental sensors, FRET probes and enzyme-activated probes.\n* Pittet MJ, Weissleder R. Intravital imaging. *Cell*. 2011;147(5):983-991. doi:10.1016/j.cell.2011.11.004\n* Secklehner J, Lo Celso C, Carlin LM. Intravital microscopy in historic and contemporary immunology. *Immunol Cell Biol*. 2017;95(6):506-513. doi:10.1038/icb.2017.25\n* Coste A, Oktay MH, Condeelis JS, Entenberg D. Intravital Imaging Techniques for Biomedical and Clinical Research. *Cytometry A*. 2020;97(5):448-457. doi:10.1002/cyto.a.23963\n* Murphy KJ, Reed DA, Trpceski M, Herrmann D, Timpson P. Quantifying and visualising the nuances of cellular dynamics in vivo using intravital imaging. *Curr Opin Cell Biol*. 2021;72:41-53. doi:10.1016/j.ceb.2021.04.007\n*Below: 2-photon intravital microscopy images of living mouse ear skin, captured at the Biomedicum Imaging Unit In Vivo Imaging (BIU-IVI), part of Helsinki In Vivo Animal Imaging Platform (HAIP) in the Finnish Biomedical Imaging (FiBI) EuBI Node.*\n![](upload/ivm1.png)\n![](upload/ivm2.png)\n\n", "provider_node_ids": [ "90c8b0d6", "e532f9cb", "b19711d3", "9c8d648e", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "de231b3c", "name": "Large scale EM (lsTEM)", "original_id": "45e29e42-242f-4c16-b713-83aa34ff73a5", "description": "In large scale EM, either scanning electron microscopy or transmission electron microscopy are performed on samples that have been sectioned. In particular the focus here is to acquire large datasets spanning big fields of view to provide spatial overviews of the sample.", "documentation": "## Large Scale EM (lsTEM)\n---\n**In large scale EM, either scanning electron microscopy or transmission electron microscopy are performed on samples that have been sectioned. In particular the focus here is to acquire large datasets spanning big fields of view to provide spatial overviews of the sample.**\n\n", "provider_node_ids": [ "90c8b0d6", "d039b533", "b19711d3", "46ccfb38", "fc1893d4", "64543c53", "09122290" ], "abbr": "", "category": { "id": "10c95db7-304f-4c1c-9428-fe5662aa4437", "name": "Ultrastructural analysis in 2D " } }, { "id": "019f553c", "name": "Laser scanning confocal microscopy (LSCM/CLSM)", "original_id": "563f1108-ac23-4225-971d-7573c4a5a8d0", "description": "Confocal laser scanning microscopy (CLSM) or laser scanning confocal [LSCM]), often colloquially referred to simply as “confocal”, is a technique for obtaining high resolution optical images with depth selectivity. The key feature of confocal microscopy is its ability to acquire in-focus images from selected depths, a process known as optical sectioning. Images are acquired point-by-point and reconstructed with a computer. This allows three-dimensional reconstructions of topologically complex objects. However, CLSM is significantly slower than widefield or spinning-disk confocal microscopy, because images are acquired pixel-by-pixel and the laser power is concentrated on small diffraction limited spots which increases the phototoxicity load on the samples. CLSM typically requires high-laser power excitation, which can lead to phototoxicity and limited observation of live cells. This technology can be improved with image scanning mic/pixel reassignment to allow non-diffraction limited images which provide resolutions 100-200nm (check with the lab where these improvements are available).", "documentation": "## Laser Scanning Confocal Microscopy (LSCM/CLSM)\n---\n**Confocal laser scanning microscopy (CLSM) or laser scanning confocal [LSCM]), often colloquially referred to simply as “confocal”, is a technique for obtaining high resolution optical images with depth selectivity. The key feature of confocal microscopy is its ability to acquire in-focus images from selected depths, a process known as optical sectioning. Images are acquired point-by-point and reconstructed with a computer. This allows three-dimensional reconstructions of topologically complex objects. However, CLSM is significantly slower than widefield or spinning-disk confocal microscopy, because images are acquired pixel-by-pixel and the laser power is concentrated on small diffraction limited spots which increases the phototoxicity load on the samples. CLSM typically requires high-laser power excitation, which can lead to phototoxicity and limited observation of live cells. This technology can be improved with image scanning mic/pixel reassignment to allow non-diffraction limited images which provide resolutions 100-200nm (check with the lab where these improvements are available).**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "1fa342de", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "2103118f", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "d2871017", "name": "Lattice light-sheet (LLS)", "original_id": "2eacb25e-08da-43da-acdd-4dfd9e7396c1", "description": "Ultra-thin light sheet, isotropic 3D resolution, minimal phototoxicity, 4D imaging.", "documentation": "## Lattice Light-sheet (LLS)\n---\n**Lattice Light Sheet Microscopy (LLS) is a special lightsheet microscope where the excitation plane is very thin (<1 µm) and uniformly flat over typical cellular dimensions (10–100 µm2). TThese illumination planes are created by special light beams called non-diffractive beams or Bessel beams, Airy, or 2D optical lattices. The main advantages of LLSM are its intrinsic optical sectioning, fast imaging (up to 300 frames per second), low photobleaching and phototoxicity, and sub-micrometer spatial resolution over long light sheets (10–100 µm). The typical spatial resolution of LLSM is 270 nm laterally and 550 nm axially (measured at 488 nm excitation, mask: NAin–NAout = 0.44–0.55). The temporal resolution is currently limited by the rate of data transfer to the computer hard disc.**\n\n## AI Generated Documentation\n\n### Overview\nLattice light-sheet microscopy (LLS) is a cutting-edge imaging technique that enables high-resolution, three-dimensional visualization of live biological samples with minimal phototoxicity. Developed by Eric Betzig and his team in the early 2010s, LLS integrates principles from light sheet fluorescence microscopy and Bessel beam technology to provide unprecedented insights into dynamic cellular processes.\n\n### Key Capabilities\nLLS utilizes a structured light sheet generated by a linear array of coherent Bessel-Gauss beams, producing an ultra-thin light sheet that is tightly confined in the axial (Z) direction. This configuration allows for isotropic 3D resolution, which is crucial for accurately capturing cellular structures and processes. The system supports high-speed imaging, capable of capturing images at sub-second intervals over extended periods, facilitating 4D live-cell imaging. LLS operates in two modes: a dithered mode for standard diffraction-limited resolution and a structured illumination mode for enhanced imaging capabilities.\n\n### Applications\nThe versatility of LLS makes it suitable for a wide range of applications in biological research, including:\n- **Developmental Biology**: Observing gene expression patterns in developing embryos, such as mouse models.\n- **Neuroscience**: Investigating neuronal development by analyzing axonal growth cones and synaptic dynamics.\n- **Cardiovascular Research**: Studying living stem cell-derived cardiomyocytes to understand heart function and disease.\n- **Cancer Research**: Characterizing tumor cell behavior and metastatic potential through detailed imaging of cancer cell motility.\n- **Stem Cell Research**: Examining pluripotent stem cell colonies and their differentiation processes.\n\n### Advantages\nThe primary advantages of LLS include:\n- **Reduced Phototoxicity**: By confining excitation to the focal plane, LLS minimizes damage to live specimens, allowing for longer observation times without compromising cell viability.\n- **High Spatiotemporal Resolution**: The use of Bessel beams enables the capture of fine details in cellular processes, providing insights that are unattainable with conventional microscopy techniques.\n- **Versatility**: LLS can be adapted for various biological samples and experimental conditions, making it a valuable tool for a wide range of scientific inquiries.\n\nIn summary, lattice light-sheet microscopy stands out as a revolutionary imaging modality that offers researchers the ability to visualize complex biological phenomena in real-time with exceptional clarity and minimal disruption to living systems.\n\n## References\n\n1. https://www.zeiss.com/microscopy/us/applications/life-sciences/lattice-lightsheet-microscopy-in-life-science-research.html\n2. https://en.wikipedia.org/wiki/Lattice_light-sheet_microscopy\n3. https://www.janelia.org/open-science/lattice-light-microscopy\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "0c8677f6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "e7adfd19", "name": "Light-sheet mesoscopic imaging (SPIM/dSLSM)", "original_id": "a143db52-9cb7-439b-b089-d2bdcfa8d747", "description": "Light sheet microscopy is a mesoscopic imaging technology that combines optical sectioning with multiple-view imaging to observe tissues and living organisms with impressive resolution. This method is often also referred to as single plane illumination microscopy (SPIM) and many different implementations are available. \r\n\r\nThree-dimensional imaging in light-sheet-based microscopy is performed by moving the specimen through the light sheet in small steps and recording a two-dimensional image at each step. Alternatively the light sheet can be moved through the specimen. In multiple-view imaging, the same volume inside the specimen or even the entire specimen is recorded along several angles. The resulting multiple-view information can be combined into a single image stack by data post-processing using a fusion algorithm.\r\n\r\nDifferent implementations are available at Euro-BioImaging Nodes regarding the way in which the lightsheet is generated, the geometry of the illumination path, sample mounting etc. Please consult the Node offering the technique regarding the specific implementation.\r\n", "documentation": "## Light-sheet Mesoscopic Imaging (SPIM/dSLSM)\n---\n**Light sheet microscopy is a mesoscopic imaging technology that combines optical sectioning with multiple-view imaging to observe tissues and living organisms with impressive resolution. This method is often also referred to as single plane illumination microscopy (SPIM) and many different implementations are available.**\nThree-dimensional imaging in light-sheet-based microscopy is performed by moving the specimen through the light sheet in small steps and recording a two-dimensional image at each step. Alternatively the light sheet can be moved through the specimen. In multiple-view imaging, the same volume inside the specimen or even the entire specimen is recorded along several angles. The resulting multiple-view information can be combined into a single image stack by data post-processing using a fusion algorithm.\nDifferent implementations are available at Euro-BioImaging Nodes regarding the way in which the lightsheet is generated, the geometry of the illumination path, sample mounting etc. Please consult the Node offering the technique regarding the specific implementation.\n\n", "provider_node_ids": [ "522e8aaa", "638ca876", "90c8b0d6", "1fa342de", "ca2e3748", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "e5f30cac", "f1099f78", "09122290", "c4b25263" ], "abbr": "", "category": { "id": "88f6b6cb-b1e0-4b33-b15d-b32c118bac24", "name": "Mesoscopic Imaging" } }, { "id": "b773e740", "name": "Long-term vertical-stage confocal/Airyscan microscopy", "original_id": "4e047283-b1c2-416d-ada5-b5a20d95adbd", "description": "90 nm resolution, long-term live-cell imaging, enhanced signal detection.", "documentation": "## AI Generated Documentation\n\n**Overview** \nLong-term vertical-stage confocal/Airyscan microscopy is a cutting-edge imaging technology that combines the principles of confocal microscopy with the super-resolution capabilities of the Airyscan module. This system is designed for high-resolution imaging of live cells and tissues over extended periods, making it particularly valuable for studying dynamic biological processes. The integration of environmental controls ensures stable conditions for long-term imaging, while the vertical-stage configuration allows for precise z-stack acquisitions.\n\n**Key Capabilities** \n- **Super-Resolution Imaging:** Achieves lateral resolution down to 90 nm, significantly enhancing the detail captured compared to traditional confocal microscopy.\n- **High-Speed Acquisition:** Offers an 8x increase in imaging speed relative to standard confocal systems at Nyquist sampling, facilitating rapid data collection.\n- **Advanced Detection Systems:** Utilizes a GaAsP detector for improved light sensitivity and signal-to-noise ratio, along with standard PMTs and an AiryScan FAST option for quick imaging.\n- **Environmental Control:** Features temperature, humidity, and CO2 regulation, allowing for optimal conditions for live-cell imaging.\n- **Definite Focus Module:** This technology eliminates thermal drift and focal offsets, ensuring consistent imaging quality over time.\n\n**Applications** \nLong-term vertical-stage confocal/Airyscan microscopy is widely utilized in various fields of biological research, including:\n- **Cell Biology:** Enables the observation of cellular dynamics, such as migration, division, and interaction with other cells.\n- **Neuroscience:** Facilitates the study of neuronal activity and synaptic interactions in live tissues.\n- **Developmental Biology:** Allows for the monitoring of developmental processes in embryos and organoids over time.\n- **Molecular Interactions:** Supports experiments involving fluorescence resonance energy transfer (FRET) and other co-localization studies to investigate molecular dynamics.\n\n**Advantages** \n1. **Enhanced Sensitivity and Resolution:** The combination of Airyscan technology and advanced detection methods provides superior imaging capabilities, allowing researchers to visualize finer details in biological samples.\n2. **Long-Term Imaging Capability:** The system's environmental controls and stability features enable extended observation periods, crucial for studying dynamic processes without compromising sample integrity.\n3. **User-Friendly Integration:** Airyscan can be seamlessly integrated into existing confocal workflows, allowing researchers to adopt super-resolution techniques without extensive retraining.\n4. **Versatile Imaging Modes:** Supports various imaging techniques, including time-series, tile scans, and co-localization studies, expanding the experimental possibilities for researchers. \n\nIn summary, long-term vertical-stage confocal/Airyscan microscopy offers a powerful and versatile platform for researchers aiming to explore the complexities of biological systems with unprecedented detail and accuracy.\n\n## References\n\n1. https://neuroscience.stanford.edu/shared-resources/nms/our-technology/airyscan2-lsm980-inverted-confocal-imaging-system-neuroscience-microscopy-service\n2. https://medschool.vanderbilt.edu/cisr/lsm-880/\n3. https://www.zeiss.com/microscopy/en/products/light-microscopes/confocal-microscopes/airyscan.html\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "4707da44", "name": "MRI/MRS (< 7T)", "original_id": "60e2adf0-24c7-4004-86ed-0d0bc16af488", "description": "", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)", "provider_node_ids": [ "638ca876", "6e382796", "3850f7eb", "0c8677f6", "9beefd47", "d2be2f9c", "64543c53", "6d068cfb", "f1099f78" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "6324bef6", "name": "MRI/MRS (>= 7T)", "original_id": "253365a2-5192-4a58-b748-aaed6edcff2e", "description": "7T MRI/MRS: ultra-high resolution, dual-mode, advanced neuroscience applications.", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n\n## AI Generated Documentation\n\n**Overview** \nMRI (Magnetic Resonance Imaging) and MRS (Magnetic Resonance Spectroscopy) at 7 Tesla (7T) represent a leap in imaging technology, offering more than twice the magnetic field strength of conventional 3T systems. This ultra-high-field (UHF) technology enables unprecedented image resolution and sensitivity, making it particularly valuable in both clinical and research settings. The MAGNETOM Terra by Siemens is a notable example of a 7T MRI scanner designed for dual functionality, allowing seamless transitions between clinical diagnostics and advanced research applications.\n\n**Key Capabilities** \nThe 7T MRI/MRS systems are characterized by: \n- **Double Signal-to-Noise Ratio (SNR)**: This feature allows for higher resolution imaging, crucial for detecting subtle anatomical details and functional changes. \n- **Dual Mode Functionality**: The ability to switch between clinical and research operations enhances workflow efficiency and data management, facilitating diverse imaging protocols. \n- **Advanced Imaging Techniques**: Techniques such as functional MRI (fMRI) and diffusion tensor imaging (DTI) benefit from the enhanced capabilities of 7T, enabling detailed visualization of brain activity and microstructural integrity.\n\n**Applications** \nThe applications of 7T MRI/MRS are extensive and include: \n- **Neuroscience**: Enhanced imaging of brain structures allows for the identification of subtle lesions, aiding in the diagnosis of neurological disorders like multiple sclerosis and Alzheimer's disease. \n- **Musculoskeletal Imaging**: Improved visualization of joints and soft tissues assists in diagnosing complex musculoskeletal conditions. \n- **Cardiovascular Imaging**: The high-resolution capabilities enable detailed assessment of cardiac anatomy and function, crucial for diagnosing heart diseases. \n- **Oncology**: The sensitivity of 7T MRI allows for earlier detection of tumors and better characterization of their properties, improving treatment planning.\n\n**Advantages** \nThe distinct advantages of 7T MRI/MRS technology include: \n- **Enhanced Diagnostic Accuracy**: The high-resolution images facilitate more precise diagnoses, leading to better-targeted treatment plans. \n- **Research Potential**: The advanced capabilities attract researchers, fostering innovation and the potential for groundbreaking studies in various medical fields. \n- **Non-invasive Insights**: The technology provides detailed insights into physiological processes without the need for invasive procedures, improving patient comfort and safety. \n\nIn summary, 7T MRI/MRS technology represents a transformative advancement in medical imaging, enhancing diagnostic capabilities and research opportunities, and setting a new standard in patient care and clinical research.\n\n## References\n\n1. https://mayomagazine.mayoclinic.org/2024/06/7-tesla-mri-scanner/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC8170917/\n3. https://www.siemens-healthineers.com/en-us/magnetic-resonance-imaging/7t-mri-scanner/magnetom-terra\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "4278635d", "9beefd47", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "83b4baea", "name": "Macro Serial Blockface Fluorescence imaging* (S-BFI)", "original_id": "c5164f47-9c44-4b80-9eb5-81378c45c6ea", "description": "Serial block face imaging (SFBI) is a method used to generate 3-dimensional (3D) reconstruction of a sample via serial image acquisition, here on a microtome. The system can detect the endogenous autofluorescence signal of paraffin-embedded samples. Optimization of quality section recovery offers the possibility to develop correlative approaches and multimodal analysis between the 3D dataset with the 2-dimensional (2D) sections that can be stained afterwards.", "documentation": "## Macro Serial Blockface Fluorescence Imaging (S-BFI)\n---\n**Serial block face imaging (SFBI) is a method used to generate 3-dimensional (3D) reconstruction of a sample via serial image acquisition, here on a microtome. The system can detect the endogenous autofluorescence signal of paraffin-embedded samples. Optimization of quality section recovery offers the possibility to develop correlative approaches and multimodal analysis between the 3D dataset with the 2-dimensional (2D) sections that can be stained afterwards.**\n\n", "provider_node_ids": [ "2b34e271", "fc1893d4", "64543c53", "09122290" ], "abbr": "", "category": { "id": "88f6b6cb-b1e0-4b33-b15d-b32c118bac24", "name": "Mesoscopic Imaging" } }, { "id": "0d8de032", "name": "Magnetic Particle Imaging (MPI)*", "original_id": "eea0a9f5-57a7-47dc-90f4-7d1b7d2d103a", "description": "Real-time, high-resolution imaging using superparamagnetic nanoparticles.", "documentation": "## Magnetic Particle Imaging (MPI)\\*\n---\n**Magnetic particle imaging is a tomographic method based on detection of nonlinear response of superparamagnetic tracers (usually superparamagnetic Iron Oxide, SPIO) to alternating magnetic fields.**\nThe method detects the tracer only (i.e., it is a hot spot imaging). Therefore MPI images have no background signal, but require colocalization with an anatomical imaging method, such as [MRI](https://www.eurobioimaging.eu/service/Magnetic-Resonance-Imaging-MRI) or [CT](https://www.eurobioimaging.eu/service/micro-CT). At moderate spatial resolution, MPI provides high sensitivity and superb temporal resolution.\nCurrent main applications are in the preclinical field and include biodistribution of nanoparticles, cell tracking, detection of nanoparticles deployed for thermoablation.\n![](upload/mpict.png)\nMPI-CT image of a mouse: a representative MPI image visualizes SPIO tracer with high image contrast and no signal modulation by biological tissue. From \nMagnetic Particle Imaging is provided by the [Centre for Advanced Preclinical Imaging Prague (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n\n## AI Generated Documentation\n\n### Overview\nMagnetic Particle Imaging (MPI) is a cutting-edge imaging technology that utilizes superparamagnetic iron oxide nanoparticles (SPIONs) as tracers to create high-resolution, three-dimensional images of biological tissues. This non-invasive technique is distinguished by its unique ability to provide real-time imaging without ionizing radiation, setting it apart from conventional imaging modalities such as MRI and PET.\n\n### Key Capabilities\nMPI operates by detecting the magnetic signals emitted from SPIONs introduced into the body. The technology features a field-free region (FFR) within the MPI scanner, where the magnetic field strength is zero. As the scanner moves this FFR across the area of interest, the SPIONs become magnetized and demagnetized, generating a detectable electrical signal proportional to their concentration. This process allows MPI to achieve high spatial resolutions on the order of 1 mm and temporal resolutions capable of capturing up to 30 frames per second. The direct detection of the nanoparticle signal, rather than signals from surrounding tissues, results in a clear and accurate representation of the nanoparticle distribution.\n\n### Applications\nMPI has significant applications in various fields of biomedicine, including:\n- **Cancer Imaging**: Monitoring tumor response to therapies and tracking metastasis.\n- **Cardiovascular Imaging**: Assessing blood flow and vascular health.\n- **Drug Delivery Monitoring**: Evaluating the distribution and efficacy of therapeutic agents in real-time.\n- **Cell Tracking**: Visualizing the behavior of labeled cells within living organisms.\n\n### Advantages\nThe advantages of MPI include:\n- **Zero Endogenous Background Signal**: This feature minimizes noise and enhances image clarity, allowing for more precise imaging compared to traditional methods.\n- **Rapid Imaging**: With short scanning times, MPI facilitates dynamic studies and quick assessments of biological processes.\n- **Biocompatibility**: The SPIONs used in MPI are biocompatible and can be safely metabolized and excreted by the body, reducing the risk of adverse effects.\n- **High Spatial and Temporal Resolution**: MPI provides detailed imaging capabilities that are crucial for understanding complex biological processes in real-time.\n\nIn summary, Magnetic Particle Imaging represents a significant advancement in medical imaging technology, offering unique features and capabilities that enhance diagnostic practices and therapeutic monitoring in clinical medicine.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC9285659/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC8306580/\n3. https://biologyinsights.com/magnetic-particle-imaging-principles-and-applications/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "e0395c6a" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "b5cb68ca", "name": "MagnetoEncephaloGraphy (MEG)", "original_id": "06611baf-80f4-4e52-9902-32ccbe7c5ee6", "description": "Non-invasive, high temporal resolution, direct neuronal activity mapping.", "documentation": "## MagnetoEncephaloGraphy (MEG) \\*\n---\n**Magnetoencephalography (MEG) measures noninvasively minute magnetic fields produced by neuronal activity of the brain. In electroencephalography (EEG), a voltage distribution produced by neuronal currents is measured with scalp electrodes whereas in MEG neuronal activity is detected by superconducting sensors measuring the corresponding magnetic fields outside the head.**\nSource modelling is used in MEG to model, quantify, and localize sources contributing to the measured magnetic fields at ms temporal resolution and a few mm spatial resolution. Skull, cerebrospinal fluid, and scalp are transparent to magnetic fields. MEG is optimally suited for detecting neuronal dynamics in the cerebral cortex. The first whole-head commercial MEG systems were introduced in the early 90’s. At present, MEG systems are widely used in hospitals and academic research infrastructures.\nThe potential clinical and research uses include for example studies of the functions of neural oscillations, the nature of event-related brain activation, mechanisms of functional connectivity between regions and the emergence of modes of network communication in brain systems.\nMEG has two clinical applications related to the localizations of epileptic foci and mapping functionally important regions in the brain prior to surgery.\n**REFERENCES.**\n* S. Baillet, “Magnetoencephalography for brain electrophysiology and imaging”,\n* J. Gross, “Magnetoencephalography in Cognitive Neuroscience: A Primer”, \n* R. Haari et al., “IFCN-endorsed practical guidelines for clinical magnetoencephalography (MEG)”, \nMEG is available at the [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node).\n**MEG Use cases:**\n| Use cases | Node | DOI |\n| --- | --- | --- |\n| Assessment of the developmental vs progressive character of the impairment of spinocortical proprioceptive pathways in Friedreich ataxia | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| Study of the neural underpinnings of predictive processing in natural speech | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n![](upload/megfinland.png)\nMEG measurement at the FiBI Node (MEG Core, Aalto NeuroImaging, Aalto University, Espoo, Finland)\n\n## AI Generated Documentation\n\n### Overview\nMagnetoencephalography (MEG) is a non-invasive neuroimaging technique that measures the magnetic fields generated by neuronal electrical activity in the brain. It is particularly effective in clinical settings for localizing brain functions and planning surgeries, especially for epilepsy and tumor removal. MEG provides a unique combination of high temporal resolution and spatial accuracy, making it a critical tool in both clinical and research applications.\n\n### Key Capabilities\nMEG operates by detecting the extremely weak magnetic fields produced by groups of neurons firing synchronously. The technique utilizes superconducting quantum interference devices (SQUIDs) to measure these fields, which are a billionth of the strength of the Earth's magnetic field. The SQUID sensors are maintained at cryogenic temperatures (around -269 degrees Celsius) to enhance sensitivity. MEG can capture brain activity with millisecond precision, allowing for real-time monitoring of dynamic neural processes. \n\n### Applications\n1. **Clinical Applications**: MEG is primarily used for pre-surgical mapping of brain functions in patients with epilepsy, enabling surgeons to identify the precise locations of seizure foci. It is also used to assess brain responses to sensory stimuli, aiding in the diagnosis of various neurological conditions.\n2. **Research Applications**: In cognitive neuroscience, MEG is employed to investigate brain function related to sensory processing, language, and motor control. Its ability to provide both temporal and spatial information makes it invaluable for studying rapid cognitive processes and understanding brain dynamics.\n\n### Advantages\nMEG offers several distinct advantages over other neuroimaging techniques:\n- **Direct Measurement**: Unlike fMRI, which measures blood flow as an indirect indicator of neuronal activity, MEG directly measures the electrical activity of neurons, providing more accurate data on brain function.\n- **High Temporal Resolution**: With a temporal resolution on the order of milliseconds, MEG is capable of tracking fast cognitive processes that other imaging methods cannot capture.\n- **Spatial Resolution**: MEG provides better spatial resolution compared to EEG, allowing for precise localization of brain activity, which is crucial for both clinical diagnosis and research.\n\nIn conclusion, MEG is a powerful tool that combines high temporal and spatial resolution, making it essential for both clinical applications in neurology and advanced research in cognitive neuroscience. Its ability to provide direct measurements of neuronal activity sets it apart from other imaging modalities, enhancing our understanding of brain function and aiding in the treatment of neurological disorders.\n\n## References\n\n1. https://ilabs.uw.edu/what-magnetoencephalography-meg/\n2. https://my.clevelandclinic.org/health/diagnostics/17218-magnetoencephalography-meg\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "3850f7eb", "64543c53" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "4b561f4f", "name": "Mass spectrometry-based imaging - bio (MSI - bio)*", "original_id": "fa2ec13c-338f-4f0c-bcbe-2447618fef4a", "description": "Spatially resolved analysis of metabolites, proteins, lipids, peptides, glycans and even drugs has become feasible with the development of mass spectrometry-based imaging strategies. Development and application of these techniques has been pioneered in medicinal and pharmacological research. MSI has allowed, for instance, the detection of novel clinical markers for better diagnosis of cancer tissues and to follow the spatial-temporal patterns of drug molecules used for pharmacological studies at cellular resolution.", "documentation": "## Mass spectrometry-based imaging (MSI)\\*\n---\n**Spatially resolved analysis of metabolites, proteins, lipids, peptides, glycans and even drugs has become feasible with the development of mass spectrometry-based imaging strategies. Development and application of these techniques has been pioneered in medicinal and pharmacological research. MSI has allowed, for instance, the detection of novel clinical markers for better diagnosis of cancer tissues and to follow the spatial-temporal patterns of drug molecules used for pharmacological studies at cellular resolution.**\nDifferent versions of MSI approaches exist. All of them represent surface analysis techniques which are based on desorption and ionization of molecules followed by their subsequent MS data recording. After collecting a mass spectrum at one spot, the sample is moved to the neighboring spot, and the mass spectrum is sampled again, until the entire sample surface is scanned. By choosing a peak (a distinct m/z value) in the resulting spectra that corresponds to the compound of interest, the MS data is used to map its distribution across the sample. This results in pictures of the spatially resolved distribution of a compound pixel by pixel. Each data set contains a gallery of pictures because any peak in each spectrum can be spatially mapped. MSI therefore has the ability to detect thousands of different analytes in a single experiment. Furthermore, MSI can be applied to any kind of surface, polymers, metal or paper, and of course biological tissues, like histological sections or cells, for obtaining e.g. distribution maps of metabolites.\nThe most common technique applied for MSI of metabolites and peptides is MALDI MSI, involving the application of a suitable matrix substance on the surface. Spatial resolution achievable is depending on the chosen ionization technique and ranges from few nm (SIMS) to µm (MALDI, LA, DESI). Despite the fact that MSI has been generally considered a qualitative method, the signal generated by this technique is proportional to the relative abundance of the analyte and therefore, quantification is possible, but challenging.\nExample applications are described here:\n* M.J.J. Haartmans et al., “Mass Spectrometry-based Biomarkers for Knee Osteoarthritis: A Systematic Review”, \n* S.T.P. Mezger et al., “Trends in mass spectrometry imaging for cardiovascular diseases”, \n![](upload/Mass_spec.png)\nMALDI-MSI of mouse brain and rat retina slices. The localization of phosphatidic acid (PA), phosphatidyl choline (PtdCho), phosphatidyl serine (PtdSer), phosphatidyl ethanolamine (PE) is shown. Courtesy of the Facility of Multimodal Imaging - AMMI Maastricht Node\nMSI is available at:\n* [ALM Italian Node](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-italian-node)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Facility of Multimodal Imaging - AMMI Maastricht](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Advanced Microscopy Node](https://www.eurobioimaging.eu/nodes/finnish-alm-node---advanced-light-microscopy-finnish-node)\n* [NORMOLIM Node](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Swedish NMI Node](https://www.eurobioimaging.eu/nodes/swedish-national-microscopy-infrastructure-nmi)\n* [UK Node](https://www.eurobioimaging.eu/nodes/uk-node)\n**Use cases:**\n| **Use case** | **Node** | **DOI** |\n| --- | --- | --- |\n| Proteomics analysis of human intestinal organoids during hypoxia and reoxygenation as a model to study ischemia-reperfusion injury | [Facility of Multimodal Imaging - AMMI Maastricht](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht) | |\n\n", "provider_node_ids": [ "522e8aaa", "2b34e271", "9c8d648e", "46ccfb38", "3e52fd14", "64543c53", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "9c814a85", "name": "Mass spectrometry-based imaging - med (MSI - med)*", "original_id": "ce6c4f02-f677-4394-a67b-cf2fc62d6087", "description": "High-resolution MSI for spatial molecular mapping in tissues, untargeted analysis.", "documentation": "## Mass spectrometry-based imaging (MSI)\\*\n---\n**Spatially resolved analysis of metabolites, proteins, lipids, peptides, glycans and even drugs has become feasible with the development of mass spectrometry-based imaging strategies. Development and application of these techniques has been pioneered in medicinal and pharmacological research. MSI has allowed, for instance, the detection of novel clinical markers for better diagnosis of cancer tissues and to follow the spatial-temporal patterns of drug molecules used for pharmacological studies at cellular resolution.**\nDifferent versions of MSI approaches exist. All of them represent surface analysis techniques which are based on desorption and ionization of molecules followed by their subsequent MS data recording. After collecting a mass spectrum at one spot, the sample is moved to the neighboring spot, and the mass spectrum is sampled again, until the entire sample surface is scanned. By choosing a peak (a distinct m/z value) in the resulting spectra that corresponds to the compound of interest, the MS data is used to map its distribution across the sample. This results in pictures of the spatially resolved distribution of a compound pixel by pixel. Each data set contains a gallery of pictures because any peak in each spectrum can be spatially mapped. MSI therefore has the ability to detect thousands of different analytes in a single experiment. Furthermore, MSI can be applied to any kind of surface, polymers, metal or paper, and of course biological tissues, like histological sections or cells, for obtaining e.g. distribution maps of metabolites.\nThe most common technique applied for MSI of metabolites and peptides is MALDI MSI, involving the application of a suitable matrix substance on the surface. Spatial resolution achievable is depending on the chosen ionization technique and ranges from few nm (SIMS) to µm (MALDI, LA, DESI). Despite the fact that MSI has been generally considered a qualitative method, the signal generated by this technique is proportional to the relative abundance of the analyte and therefore, quantification is possible, but challenging.\nExample applications are described here:\n* M.J.J. Haartmans et al., “Mass Spectrometry-based Biomarkers for Knee Osteoarthritis: A Systematic Review”, \n* S.T.P. Mezger et al., “Trends in mass spectrometry imaging for cardiovascular diseases”, \n![](upload/Mass_spec.png)\nMALDI-MSI of mouse brain and rat retina slices. The localization of phosphatidic acid (PA), phosphatidyl choline (PtdCho), phosphatidyl serine (PtdSer), phosphatidyl ethanolamine (PE) is shown. Courtesy of the Facility of Multimodal Imaging - AMMI Maastricht Node\nMSI is available at:\n* [ALM Italian Node](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-italian-node)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Facility of Multimodal Imaging - AMMI Maastricht](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [NORMOLIM Node](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**MSI Use cases:**\n| Use cases | Node | DOI |\n| --- | --- | --- |\n| Proteomics analysis of human intestinal organoids during hypoxia and reoxygenation as a model to study ischemia-reperfusion injury | [Facility of Multimodal Imaging - AMMI Maastricht](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht) | |\n| An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue | [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure) | |\n| Lipid metabolism alterations in cancer | [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure) | |\n\n## AI Generated Documentation\n\n**Overview** \nMass Spectrometry-Based Imaging - Med (MSI - Med) is a cutting-edge analytical technique that integrates mass spectrometry with imaging to visualize the spatial distribution of biomolecules within biological samples. This technology is particularly significant in medical research, enabling the detailed molecular characterization of tissues, cells, and other biological materials. MSI - Med stands out due to its ability to perform untargeted analyses, allowing researchers to detect a wide array of molecular species without prior knowledge of their presence.\n\n**Key Capabilities** \nMSI - Med employs various ionization techniques, including Matrix-Assisted Laser Desorption/Ionization (MALDI), Desorption Electrospray Ionization (DESI), and Secondary Ion Mass Spectrometry (SIMS). These methods facilitate the imaging of thousands of molecules, such as metabolites, lipids, peptides, proteins, and glycans, in a single experiment. The spatial resolution of MSI can reach sub-10 micrometers, enabling the visualization of fine molecular distributions within complex tissues. The technique generates mass spectra from different regions of a sample, creating detailed molecular maps that can be analyzed for both qualitative and quantitative data.\n\n**Applications** \nMSI - Med is widely used in various fields, including: \n- **Cancer Research**: It aids in identifying tumor markers and understanding metabolic changes in cancerous tissues, contributing to the development of targeted therapies. \n- **Neuroscience**: Researchers utilize MSI to study the distribution of neurotransmitters and lipids in brain tissues, providing insights into neurological disorders. \n- **Pharmacology**: The technology tracks drug distribution within tissues, enhancing the understanding of pharmacokinetics and therapeutic efficacy.\n\n**Advantages** \nThe primary advantage of MSI - Med is its capability for untargeted molecular analysis, allowing for the simultaneous detection of numerous molecular species. This feature surpasses traditional methods like immunohistochemistry, which require specific antibodies and can only target known biomarkers. Additionally, MSI provides quantitative data, as the intensity of the signals correlates with the abundance of the analytes, although challenges in quantification must be addressed. Overall, MSI - Med represents a transformative approach in bioimaging, offering high-resolution, spatially resolved molecular insights crucial for advancing medical research and improving diagnostic capabilities.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC5959842/\n2. https://www.eurobioimaging.eu/news/technology/msi-mass-spectrometry-based-imaging/\n3. https://en.wikipedia.org/wiki/Mass_spectrometry_imaging\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "9c8d648e", "3e52fd14", "64543c53", "2103118f" ], "abbr": "", "category": { "id": "3b54df7f-9def-4570-8dcf-fc2eeb4ad891", "name": "ex-vivo and materials imaging using biomedical technologies\r\n\r\n" } }, { "id": "afeaed8d", "name": "Micro X-ray Fluorescence Spectrometry (XRF)*", "original_id": "76e2543c-d2bd-4062-a8c3-ddd2cdb0db0f", "description": "Micro-X-Ray Fluorescence Spectrometry (XRF) allows the qualitative analysis of the elemental composition of solid samples. The detected signal results from the emission of element-characteristic fluorescence X-rays from a sample bombarded with high-energy X-rays. The result is a spatially resolved distribution of elements represented in a 2D map. Possible applications include the investigation of element distribution in tissues, like bone, uptake of specific elements by tumorous tissue or foreign bodies within tissues and organs, e.g. implants.", "documentation": "## Micro X-ray Fluorescence Spectrometry (XRF)\n---\n**Micro-X-Ray Fluorescence Spectrometry (XRF) allows the qualitative analysis of the elemental composition of solid samples. The detected signal results from the emission of element-characteristic fluorescence X-rays from a sample bombarded with high-energy X-rays. The result is a spatially resolved distribution of elements represented in a 2D map.\nPossible applications include the investigation of element distribution in tissues, like bone, uptake of specific elements by tumorous tissue or foreign bodies within tissues and organs, e.g. implants.**\nDifferent XRF setups are available, which offer confocal (3D) or non-confocal (2D) modes. One setup uses polychromatic radiation from a Rhodium (20W) X-ray tube for excitation of low-, medium- and high-Z elements. Measurements can be performed in air or vacuum. The fluorescence signal is detected using a Si(Li) detector with an ultrathin window, which extends the detectable elements range from Uranium down to Magnesium or Sodium if in vacuo. Scans can be performed with spatial resolution of about 50 µm.\nA second micro-XRF setup uses focused monochromatic Mo-Ka radiation from a 2 kW Mo anode X-ray tube. The polycapillary optics produces a beam of 15 µm diameter. Measurements can be performed only under ambient conditions, so light elements are not accessible. The monochromatic excitation leads to lower detection limits than polychromatic excitation.\n![XRF_Image](upload/XRF_fig1.png \"XRF_image\")\n*Element distributions in bone carrying bioresorbable Mg implant.*\n![XRF_Image](upload/XRF_fig2.png \"XRF_image\")\n*2D Gd-Lα map from a gallbladder stone. The scan was conducted with a step size of 15\nμm and a counting time of 50 s/point.*\n\n", "provider_node_ids": [ "2b34e271", "64543c53" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "0a49ed44", "name": "Micro-Particle Induced X-ray Emmission (µ-PIXE)*", "original_id": "a852f3b2-31f3-43be-bc59-a87ce2f496ce", "description": "High-resolution (1µm), non-destructive elemental mapping for diverse samples.", "documentation": "## AI Generated Documentation\n\n### Overview\nMicro-Particle Induced X-ray Emission (µ-PIXE) is an advanced analytical technique that extends the capabilities of traditional Particle Induced X-ray Emission (PIXE) by employing a focused ion beam to achieve high spatial resolution. This technique is particularly effective for non-destructive elemental analysis, allowing researchers to determine the composition of materials with precision and detail.\n\n### Key Capabilities\nµ-PIXE utilizes an ion beam, typically protons accelerated to energies in the MeV range, to bombard a sample. The interaction causes inner-shell ionization of atoms, leading to the emission of characteristic X-rays as outer-shell electrons fill the vacancies. The focused beam can achieve a spatial resolution as fine as 1 µm, enabling detailed elemental mapping of samples. The detection limits are exceptional, with the ability to identify elemental concentrations down to 1 part per million (ppm). This high sensitivity makes µ-PIXE particularly suitable for trace element analysis in various materials.\n\n### Applications\nThe applications of µ-PIXE span multiple scientific fields:\n- **Geology**: Used for analyzing mineral compositions, understanding geological formations, and studying elemental distributions in rocks and sediments.\n- **Biology**: Valuable for investigating elemental concentrations in biological specimens, such as plant tissues, animal shells, and microfossils, providing insights into biological processes and environmental interactions.\n- **Environmental Science**: Employed to assess pollution levels and elemental distributions in environmental samples, aiding in monitoring and remediation efforts.\n- **Cultural Heritage**: Utilized in art conservation and archaeology to analyze the elemental composition of artifacts, helping to determine provenance and authenticity.\n\n### Advantages\nµ-PIXE offers several distinct advantages over other elemental analysis techniques:\n- **Non-destructive Nature**: Unlike many analytical methods, µ-PIXE preserves the integrity of the sample, allowing for further analysis or conservation.\n- **High Spatial Resolution**: The ability to focus the ion beam to 1 µm enables detailed mapping of elemental distributions, which is crucial for understanding complex materials.\n- **Versatile Sample Compatibility**: µ-PIXE can be applied to a wide range of materials, including solids, liquids, and biological samples, making it a versatile tool in various research contexts.\n\nIn summary, µ-PIXE stands out as a powerful technique for high-resolution, non-destructive elemental analysis, providing critical insights across diverse scientific disciplines.\n\n## References\n\n1. https://en.wikipedia.org/wiki/Particle-Induced_X-ray_Emission\n2. https://www.ansto.gov.au/micro-particle-induced-x-ray-emission\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2103118f" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "b5ef918c", "name": "Microdissection (µDis)*", "original_id": "276519bc-3dcf-4bbc-a6e8-203972022514", "description": "Laser microdissection is a useful technique that enables the precise isolation of cells or tissue regions out of a tissue specimen, allowing the isolation of high-purity biomolecules. The technique can be used on fixed samples (FFPE or frozen), for the isolation and comparison of specific cell types, or from live samples, for the generation of homogeneous cell colonies. \r\n\r\nIn laser microdissection, a high power laser is used to cut the tissue around the cell or tissue region of interest and the isolated cell then commonly drops into a receptacle placed below the sample.\r\nAlternatively, in Laser Microdissection and Pressure Catapulting (LMPC), which is a non-contact sampling technique, especially for RNA, DNA and protein studies but also for cloning/live cell culture the specimen is microdissected by a focused laser beam with a wavelength of 355 nm, which is not absorbed by nucleic acids or proteins. Then the same laser beam is defocused and a defined, but gentle, laser pulse transports the cut piece of the specimen out of the sample plane into a collection device. \r\n", "documentation": "", "provider_node_ids": [ "fcf6bac6", "e532f9cb", "b19711d3", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "fc6e9ebb", "name": "Minimal Photon Fluxes Microscopy (MINFLUX)*", "original_id": "4f084eac-fa80-49b5-89b9-f57c01045b3c", "description": "Sub-2nm resolution, minimal photon use, live-cell tracking, 3D imaging.", "documentation": "## Minimal Photon Fluxes Microscopy (MINFLUX)\n---\n**MINFLUX enables imaging of a broad range of biological samples with a spatial resolution in the single nanometer range. This allows to study the structure of large multimolecular protein complexes, such as nuclear pores with unprecedented 3D resolution.\nAdditionally, MINFLUX tracking allows to study movement of single molecules in living cells with up to 10 kHz sampling rate (one localisation each 100 µs, which is up to 100 x faster than conventional camera-based tracking).\nMINFLUX relies on localising individual photoswitchable fluorophores with a movable excitation beam with an intensity minimum, commonly in a donut shape.**\n\n## AI Generated Documentation\n\n**Overview** Minimal Photon Fluxes Microscopy (MINFLUX) is an advanced super-resolution microscopy technique that enables the localization of single fluorophores with exceptional precision and minimal photon emission. This method combines aspects of single-molecule localization microscopy (SMLM) and stimulated emission depletion (STED) microscopy, achieving spatial resolutions in the single-digit nanometer range. MINFLUX is particularly effective for imaging dynamic biological processes in live cells, providing insights into molecular interactions and structures at unprecedented detail.\n\n**Key Capabilities** MINFLUX utilizes a structured excitation beam, typically configured as a doughnut shape, which features a central intensity minimum. This configuration allows for the precise positioning of the excitation beam relative to the fluorophore. When the beam's intensity zero is aligned with the fluorophore, no photons are emitted, thus requiring fewer emitted photons to determine the fluorophore's location. The technique achieves localization precision of less than 2 nm in 2D and less than 3 nm in 3D imaging modes, with each localization event occurring in under 5 microseconds. This rapid imaging capability allows for the tracking of fast molecular movements and interactions over extended periods.\n\n**Applications** MINFLUX is particularly valuable in the fields of structural biology and biophysics, where it can be used to visualize and track protein complexes, nucleic acids, and other molecular structures in live cells. The high spatiotemporal resolution enables researchers to study dynamic processes such as protein folding, molecular interactions, and cellular signaling pathways in real-time. Additionally, the technique supports multi-color imaging, allowing for the simultaneous observation of multiple targets within the same specimen.\n\n**Advantages** The primary advantages of MINFLUX include its high resolution, minimal photon requirement, and compatibility with standard fluorescence microscopy setups. By reducing phototoxicity and photobleaching, MINFLUX is well-suited for live-cell imaging, making it a preferred choice for researchers studying dynamic biological systems. Its integration into existing fluorescence microscopy systems enhances its accessibility, allowing researchers to leverage this advanced technology without extensive reconfiguration. Overall, MINFLUX represents a significant advancement in microscopy, providing powerful tools for exploring molecular dynamics with unprecedented detail and efficiency.\n\n## References\n\n1. https://www.nature.com/articles/s41566-025-01625-0\n2. https://abberior.rocks/knowledge-base/minflux/\n3. https://en.wikipedia.org/wiki/Minflux\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "b19711d3", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "3ba9fb09", "name": "Multiplexing imaging (MXI)*", "original_id": "3cd385cd-b8d8-42e2-8a6a-e3471ea7a86a", "description": "Multiplexing is the ability to stain the same sample many times. Today we are limited to 7 stains on the same slide but researchers want to go further and to be able to use more than 50 dyes to map their samples. The multiplexed imaging solution is an integrated system for imaging 50+ biomarkers from one tissue sample at a single-cell level. The solution consists of a fully customizable assay design with tissue-preserving staining protocol and a precision-engineered imager with intuitive, scalable acquisition and analysis software. The most important aspect of this technique is the use of few samples. Often samples come from surgical parts or scarce sources and they need to be handled with care and sliced with parsimony. Multiplexing helps getting the most information out of the rare samples.", "documentation": "## Multiplexing Imaging\\* (MXI)\n---\n**Multiplexing is the ability to stain the same sample many times. Today we are limited to 7 stains on the same slide but researchers want to go further and to be able to use more than 50 dyes to map their samples. The multiplexed imaging solution is an integrated system for imaging 50+ biomarkers from one tissue sample at a single-cell level. The solution consists of a fully customizable assay design with tissue-preserving staining protocol and a precision-engineered imager with intuitive, scalable acquisition and analysis software. The most important aspect of this technique is the use of few samples. Often samples come from surgical parts or scarce sources and they need to be handled with care and sliced with parsimony. Multiplexing helps getting the most information out of the rare samples**\n\n", "provider_node_ids": [ "90c8b0d6", "fc1893d4", "64543c53" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "a7c09ccd", "name": "Objective-coupled planar illumination (OCPI)", "original_id": "6dea9f79-5d6a-4b98-92da-e527e792b5d4", "description": "High-speed, low-phototoxicity 3D imaging of large biological samples.", "documentation": "## OBJECTIVE-COUPLED PLANAR ILLUMINATION (OCPI)\n---\n**An Objective-coupled planar illumination (OCPI) microscope is a microscope that rapidly sections a three-dimensional volume using a thin illumination sheet whose position is rigidly coupled to the objective and aligned with its focal plane. This method offers superior sensitivity and temporal resolution over laser-scanning microscopy for imaging rapid events in large populations of neurons. The reduced photobleaching associated with the method also allows optical recordings to be made over long periods of time.**\n\n## AI Generated Documentation\n\n**Objective-Coupled Planar Illumination (OCPI) Microscopy**\n\n**Overview** \nObjective-Coupled Planar Illumination (OCPI) microscopy is an innovative optical imaging technique that combines the principles of light sheet fluorescence microscopy with a unique objective-coupled illumination approach. This method facilitates high-speed, three-dimensional imaging of biological specimens while minimizing phototoxicity, making it particularly suitable for observing dynamic processes in living tissues.\n\n**Key Capabilities** \nOCPI is distinguished by its ability to achieve imaging rates of up to 40 Hz for 700 μm-thick volumes, depending on the camera's capabilities. The technique employs Distributed Planar Imaging (DPI), which allows for parallel image acquisition across multiple cameras, effectively overcoming the limitations of traditional point-scanning methods. This configuration enables researchers to capture rapid biological events, such as neuronal activity, with high temporal resolution. The system also supports low phototoxicity imaging, crucial for long-term studies of live samples without causing significant damage.\n\n**Applications** \nOCPI is primarily utilized in neuroscience for real-time imaging of neuronal dynamics, such as calcium signaling in the larval zebrafish brain. Its ability to visualize large volumes of tissue at high speeds allows for the exploration of complex biological interactions and processes, including developmental biology and cellular communication. The technique is also applicable in various fields requiring high-resolution imaging of biological samples, such as developmental biology, cell biology, and tissue engineering.\n\n**Advantages** \nThe main advantages of OCPI over traditional microscopy techniques include its high-speed imaging capabilities, which can be millions of times faster than point-scanning methods like two-photon microscopy. The low phototoxicity associated with light sheet illumination reduces the risk of damaging live samples, enabling prolonged observation periods. Moreover, the three-dimensional imaging capability provides comprehensive insights into the spatial organization and interactions within biological tissues, making OCPI a powerful tool for researchers aiming to understand complex biological systems.\n\n## References\n\n1. https://opg.optica.org/ol/abstract.cfm?uri=ol-33-20-2302&origin=search\n2. https://www.nature.com/articles/s41467-019-12340-0\n3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775063/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "fc1893d4", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "17dd34eb", "name": "Optical projection tomography (OPT)", "original_id": "133032ad-8fff-4ef7-9279-13c8a04e3d64", "description": "Optical projection tomOptical projection tomography (OPT) is in many ways the optical equivalent of x-ray computed tomography (CT) or the medical CT scan. OPT differs in the way that it often uses ultraviolet, visible, and near-infrared photons as opposed to X-ray photons. However, essential mathematics and reconstruction algorithms used for CT and OPT are similar; for example, radon transform or iterative reconstruction, based on projection data are used in both medical CT scan and OPT for 3D reconstruction. OPT has a few advantages. It typically allows the 3D imaging or samples larger than those that can be imaged with light-sheet, while producing truly isometric 3D datasets. It also allows 3D imaging of samples that are not fluorescently labelled. However, OPT typically does not provide cellular or sub-cellular resolution. ography (OPT)", "documentation": "## OPTICAL PROJECTION TOMOGRAPHY (OPT)\n---\n**Optical projection tomography (OPT) is in many ways the optical equivalent of x-ray computed tomography (CT) or the medical CT scan. OPT differs in the way that it often uses ultraviolet, visible, and near-infrared photons as opposed to X-ray photons. However, essential mathematics and reconstruction algorithms used for CT and OPT are similar; for example, radon transform or iterative reconstruction, based on projection data are used in both medical CT scan and OPT for 3D reconstruction.**\n\n", "provider_node_ids": [ "90c8b0d6", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "e5f30cac", "09122290" ], "abbr": "", "category": { "id": "88f6b6cb-b1e0-4b33-b15d-b32c118bac24", "name": "Mesoscopic Imaging" } }, { "id": "a9c43bba", "name": "PET", "original_id": "743a7862-7e42-4d20-a266-b283aaa47d0f", "description": "High-resolution metabolic imaging; oncology, neurology, cardiology applications.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n**Overview** \nPositron Emission Tomography (PET) is a cutting-edge imaging technology that provides detailed insights into metabolic processes within the body. Utilizing radioactive tracers, PET captures gamma rays emitted from positron-electron annihilation events, allowing for the visualization of physiological functions. This technology is particularly valuable in clinical settings for diagnosing and monitoring various diseases, including cancer, neurological disorders, and cardiac conditions.\n\n**Key Capabilities** \nPET scanners are equipped with a ring of detectors that measure the gamma radiation emitted from the body after the administration of a radiolabeled tracer, commonly fluorodeoxyglucose (FDG). The technology achieves a spatial resolution of approximately 4 to 6 mm, enabling precise imaging of metabolic activity. The sensitivity of PET systems typically ranges from 1-2%, allowing for the detection of low levels of radioactivity, which is crucial for identifying early-stage diseases. PET can be combined with CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) to provide anatomical context to the functional data, enhancing diagnostic accuracy.\n\n**Applications** \nPET is predominantly used in:\n- **Oncology**: It is essential for tumor detection, staging, and monitoring treatment response. PET scans can reveal areas of increased glucose metabolism, indicative of malignant growth.\n- **Neurology**: PET assists in diagnosing conditions such as Alzheimer’s disease, epilepsy, and brain tumors by evaluating cerebral blood flow and glucose utilization.\n- **Cardiology**: The technology is employed to assess myocardial perfusion and viability, aiding in the diagnosis of coronary artery disease and guiding therapeutic decisions.\n\n**Advantages** \nPET offers several distinct advantages over other imaging modalities:\n- **Functional Imaging**: Unlike CT or MRI, PET provides metabolic and physiological information, allowing for early disease detection.\n- **Reproducibility**: PET scans are consistent and reliable, making them useful for longitudinal studies and treatment monitoring.\n- **Non-invasive**: The procedure is generally well-tolerated, with minimal discomfort for patients.\n\nIn conclusion, PET stands out as a vital tool in both clinical and research settings, offering unique capabilities in metabolic imaging that enhance diagnostic and therapeutic strategies across various medical disciplines.\n\n## References\n\n1. https://omnexus.specialchem.com/selection-guide/polyethylene-terephthalate-pet-plastic/key-applications\n2. https://kbdelta.com/blog/what-is-pet-material-exploring-properties-applications/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "6e382796", "3850f7eb", "cf8f008b", "d2be2f9c", "64543c53" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "3a2f2c38", "name": "PET-MRI", "original_id": "95dd764b-ac3c-4352-9ca7-82036b0681b1", "description": "Hybrid imaging: combines PET's metabolic data with MRI's high-resolution anatomy.", "documentation": "## Positron Emission Tomography–Magnetic Resonance Imaging (PET-MRI)\n---\n**Positron Emission Tomography–Magnetic Resonance Imaging (PET-MRI) is a hybrid imaging technology that incorporates Magnetic Resonance Imaging ([MRI](/service/Magnetic-Resonance-Imaging-MRI)****) soft tissue morphological imaging, and Positron Emission Tomography ([PET](/service/Nuclear-Medicine))****molecular imaging. The technology combines the exquisite structural and functional characterization of tissue provided by MRI with the extreme sensitivity of PET imaging for the determination of receptor density/biological reaction rates/detection of radiolabelled drugs or vectors.**\nMR and PET acquisition can be made either separately or inline on individual MR and PET scanners, or simultaneously on bimodal machines. MR and PET images are then superimposed to provide single images with the characteristics of both technologies.\nRead more on applications and used PET tracers [here](/service/Nuclear-Medicine)\n### Preclinical PET-MRI is provided by the following nodes:\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM (NO)](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n### Human PET-MRI is provided by the following nodes:\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n**Use cases**\n| Use cases | Preclinical or human | Node | DOI |\n| --- | --- | --- | --- |\n| [11C]-tracers, investigation of the potential link between availability of specific neuroreceptors and transporters and gray matter density | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [11C]-carfentanil, association of endogenous μ-opioid receptor (MOR) and neuronal rewards response to food picture | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [11C](R)-PK11195, Evaluation of widespread Multiple Sclerosis | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [18F]FDG, Monitoring the side effects of radiation therapy in mice | Animal | [HU Med & Preclinical Node](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary) | |\n| [18F]FDG, spinal cord | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n| [18F]FDG, cancer | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n| [18F]FDG, injured brain imaging | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n\n## AI Generated Documentation\n\n**Overview** \nPositron Emission Tomography-Magnetic Resonance Imaging (PET-MRI) is a cutting-edge hybrid imaging technology that integrates the functional imaging capabilities of PET with the high-resolution anatomical imaging provided by MRI. This combination allows for simultaneous acquisition of metabolic and structural information, enhancing diagnostic accuracy and treatment planning across various medical fields. \n\n**Key Capabilities** \nModern PET-MRI systems typically utilize time-of-flight (TOF) PET technology alongside high-field (3 Tesla) MRI systems, which significantly improves image quality and sensitivity. The PET component detects gamma rays emitted from positron-emitting radiotracers, while the MRI component employs strong magnetic fields and radiofrequency pulses to generate detailed images of soft tissues. This technology can achieve spatial resolutions of approximately 1-2 mm, enabling precise localization of lesions and metabolic activity within anatomical structures. \n\n**Applications** \nThe primary applications of PET-MRI span several clinical fields, including: \n- **Oncology**: PET-MRI is instrumental in assessing tumor metabolism and morphology, aiding in diagnosis, treatment planning, and monitoring therapeutic responses. \n- **Neurology**: It is used to evaluate brain disorders such as tumors, epilepsy, and neurodegenerative diseases, providing insights into both structural and functional changes. \n- **Cardiology**: The technology helps investigate myocardial viability and perfusion, crucial for managing heart disease. \n- **Neuroscience**: PET-MRI is employed in research to explore brain function and structure in various conditions, enhancing our understanding of complex neurological disorders. \n\n**Advantages** \nPET-MRI offers several distinct advantages over traditional imaging modalities: \n1. **Comprehensive Data**: The integration of functional and anatomical imaging provides a holistic view of the patient's condition, facilitating more informed clinical decisions. \n2. **Reduced Radiation Exposure**: Compared to PET-CT, PET-MRI typically involves lower radiation doses, making it a safer option for sensitive populations, including pediatric patients. \n3. **Enhanced Diagnostic Accuracy**: The simultaneous acquisition of images allows for precise localization of metabolic activity within anatomical structures, improving diagnostic confidence. \n4. **Convenience**: Patients benefit from undergoing a single imaging session, which reduces the time and stress associated with multiple appointments. \n\nOverall, PET-MRI represents a significant advancement in medical imaging, providing clinicians with powerful tools for diagnosis and treatment planning while ensuring patient safety and comfort.\n\n## References\n\n1. https://radiology.ucsf.edu/patient-care/services/pet-mri\n2. https://en.wikipedia.org/wiki/PET%E2%80%93MRI\n3. https://stanfordhealthcare.org/medical-tests/p/pet-mri-scan.html\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "6e382796", "3850f7eb", "0c8677f6", "cf8f008b", "d2be2f9c", "64543c53", "6d068cfb" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "0f1e5f18", "name": "PET/CT *", "original_id": "a74dcaa4-a565-411d-bc6c-9a5711b36a74", "description": "Hybrid imaging combining metabolic PET with anatomical CT for precise diagnostics.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n**Overview** \nPositron Emission Tomography/Computed Tomography (PET/CT) is a hybrid imaging technology that integrates the functional imaging capabilities of PET with the anatomical detail provided by CT. This combination allows for enhanced diagnostic accuracy and is particularly valuable in oncology, cardiology, and neurology. By providing both metabolic and structural information in a single examination, PET/CT has become a critical tool in modern medical imaging.\n\n**Key Capabilities** \nPET/CT systems utilize radiotracers, such as 18F-fluorodeoxyglucose (FDG), which are injected into the patient to visualize metabolic processes. The PET component detects gamma rays emitted by the radiotracer, yielding quantitative images of regional in vivo biology. The CT component employs X-ray technology to produce high-resolution anatomical images, typically with a spatial resolution of 1-2 mm. The integration of these modalities allows for precise localization of metabolic abnormalities within anatomical structures, facilitating accurate diagnosis and treatment planning.\n\n**Applications** \n1. **Oncology:** PET/CT is predominantly used for tumor detection, staging, and monitoring treatment response. It enables differentiation between benign and malignant lesions and provides insights into tumor metabolism, aiding in the assessment of disease progression and therapeutic efficacy.\n \n2. **Cardiology:** In cardiology, PET/CT is utilized to evaluate myocardial perfusion and viability, helping to identify areas of the heart that may benefit from revascularization procedures. It provides critical information on blood flow and metabolic activity in cardiac tissues.\n \n3. **Neurology:** This technology is also applied in the assessment of neurological disorders, including Alzheimer’s disease and epilepsy, by visualizing brain metabolism and identifying areas of dysfunction.\n\n**Advantages** \n- **Comprehensive Imaging:** The combination of functional and anatomical imaging provides a holistic view of disease processes, enhancing diagnostic confidence and treatment planning.\n- **Single Examination Efficiency:** PET/CT allows for a single examination to yield both metabolic and structural information, reducing the need for multiple imaging studies and improving patient comfort.\n- **Quantitative Analysis:** The ability to provide quantitative data on metabolic activity makes PET/CT invaluable in clinical research, particularly in evaluating new therapies and understanding disease mechanisms.\n\nIn conclusion, PET/CT stands out in the field of medical imaging due to its unique ability to combine metabolic and anatomical insights, making it an essential tool for accurate diagnosis and effective treatment planning across various medical disciplines.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC4921358/\n2. https://www.siemens-healthineers.com/molecular-imaging/pet-ct\n3. https://acsjournals.onlinelibrary.wiley.com/doi/full/10.1002/cncr.28860\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "6e382796", "3850f7eb", "0c8677f6", "cf8f008b", "d2be2f9c", "64543c53" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "413a548d", "name": "Phase Contrast Imaging (PCI)", "original_id": "2977e68f-4f59-4681-88cd-80f0c2726780", "description": "High-resolution imaging of soft tissues via X-ray phase shifts, enhancing diagnostics.", "documentation": "## AI Generated Documentation\n\n**Overview** \nPhase Contrast Imaging (PCI) is a sophisticated X-ray imaging technique that enhances the visualization of soft tissues and low-contrast materials by utilizing the phase shifts of X-rays as they pass through different media. Unlike conventional X-ray imaging, which primarily relies on differential absorption, PCI captures phase information, allowing for superior contrast in imaging soft tissues, which are often difficult to distinguish in standard X-ray images.\n\n**Key Capabilities** \nPCI employs various methods, including propagation-based, analyzer-based, and grating interferometry techniques. The propagation-based technique, for instance, analyzes changes in the wavefront of X-rays as they traverse a sample, enabling high-resolution imaging of biological soft tissues. This method can achieve spatial resolutions in the range of micrometers to sub-micrometers, making it suitable for detailed structural analysis. PCI can be implemented in laboratory settings using microfocus X-ray sources and CCD detectors, facilitating its application in both preclinical and clinical environments.\n\n**Applications** \nThe applications of PCI are extensive and span multiple fields. In the medical domain, it significantly enhances the visualization of soft tissues, aiding in early detection and precise characterization of tumors, detailed imaging of vascular structures, and improved visualization of cartilage and other soft tissues. Furthermore, PCI is invaluable in materials science, where it is used to analyze the microstructure of polymers and composite materials, providing insights into their properties and behaviors. Its capability to visualize intricate details within low-Z materials positions PCI as a critical tool in biological research and industrial applications.\n\n**Advantages** \nThe primary advantage of PCI lies in its ability to produce high-contrast images of soft tissues, which is crucial for accurate diagnosis and treatment planning. By overcoming the limitations of conventional X-ray techniques, PCI provides clearer differentiation between tissues that are otherwise indistinguishable. Additionally, PCI opens new avenues in research, allowing scientists to observe fine anatomical details that were previously obscured by traditional imaging methods. As the technology continues to evolve, its integration into routine clinical practice and research is expected to expand, further enhancing its impact across various scientific and medical fields.\n\n## References\n\n1. https://diversedaily.com/phase-contrast-imaging-methods-in-x-ray-imaging-enhancing-soft-tissue-contrast-and-anatomical-visualization/\n2. https://pubmed.ncbi.nlm.nih.gov/23220766/\n3. https://www.sciencedirect.com/science/article/pii/S0030402613011510\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "64543c53", "d14abc55" ], "abbr": "", "category": { "id": "3b54df7f-9def-4570-8dcf-fc2eeb4ad891", "name": "ex-vivo and materials imaging using biomedical technologies\r\n\r\n" } }, { "id": "47c84335", "name": "Phosphorescence Lifetime imaging (PLIM)*", "original_id": "2ca3bc30-2dd6-47f7-a632-adf1762b73d2", "description": "Phosphorescence Lifetime Imaging works on a similar principle as fluorescence lifetime imaging (FLIM), but rather makes use of the phosphorescence induced by the excitation rather than the fluorescence. In PLIM the sample is excited for a certain time and the phosphorescence photons coming from the sample are collected, measuring how long the sample remains in an excited state. The common time range in which phosphorescence photons are collected is up to milliseconds.", "documentation": "## Phosphorescence Lifetime imaging\\* (PLIM)\n---\n**Phosphorescence Lifetime Imaging works on a similar principle as fluorescence lifetime imaging (FLIM), but rather makes use of the phosphorescence induced by the excitation rather than the fluorescence. In PLIM the sample is excited for a certain time and the phosphorescence photons coming from the sample are collected, measuring how long the sample remains in an excited state. The common time range in which phosphorescence photons are collected is up to milliseconds.**\n\n", "provider_node_ids": [ "90c8b0d6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "d54d34a2", "name": "PhotoAcoustic Imaging (PAI) - med", "original_id": "ac8af431-6694-4003-bc61-6a455feec1de", "description": "Non-invasive imaging combining optical and ultrasound for high-res tissue analysis.", "documentation": "## PhotoAcoustic Imaging (PAI) \\*\n---\n**PhotoAcoustic (or optoacoustic) Imaging (PAI) is a novel but well-established technology that combines optical and ultrasound imaging. Briefly, the technique detects endogenous or exogenous chromophores that are excited through an illumination carried out with pulsed laser light, typically in the Red-NIR range. The non-radiative release of the absorbed energy produces a microheating and a thermoelastic expansion in the chromophore close surrounding, which can generate ultrasound. The acoustic waves are detected by a transducer and transformed into an image.**\nPAI combines the advantages of optical and US imaging technologies. The detection of the US signal makes it possible to achieve an increase of both spatial resolution (micrometric) and penetration depth with respect to optical imaging and reduces scattering phenomena. Other advantages include good sensitivity (comparable to that of optical imaging), safety, cheapness and ease of use.\nA very large number of chromophores can be used to generate PAI contrast: endogenous molecules (e.g. oxy- and deoxy-hemoglobin, myoglobin, melanin), exogenous probes (e.g. organic dyes like fluorescein and ICG), nanosystems (e.g. noble metals-containing nanoparticles, quantum dots, carbon nanotubes, etc.) and also fluorescent proteins and gene reporters. Detection of different types of chromophores in the same anatomical region is also feasible.\nAs any tomographic technique, PAI allows to get 3D-high resolution images of soft tissues which provide anatomical, functional, and molecular information. Due to the not optimal penetration depth, PAI is particularly useful for preclinical imaging, whereas in humans it’s use is limited to superficial organs analysis (e.g. palmar vessels detection, breast analysis).\n![](upload/paimed.png)\nPhotoacoustic imaging of palmar vessels (left) and of breast tissue (right). Adapted from Matsumotu Y. et al., [https://doi.org/10.1038/s41598...](https://doi.org/10.1038/s41598-018-33255-8)\nThe most important in vivo application of PAI is the detection of blood hemoglobin, which provides a different PA signal depending on its deoxy- or oxy-state, allowing it to evaluate the vascular volume and pO2 in normal and hypoxic conditions.\nOther applications in the preclinical biomedical field include, but are not limited to:\n* oncology (cancer detection, assessment of vascular volume and hypoxia, targeting experiments, assessment of drug distribution and therapy outcome)\n* neurobiology (stroke, brain cancer, intracranial injection of drugs, functional imaging)\n* cardiovascular biology (heart attack, detection of atherosclerotic plaques, hemodynamic and O2 perfusion)\n* in developmental biology (vascular volume and oxygenation of placenta, image-guided embryo injection, fetal analysis)\n* abdomen analysis (kidney diseases as renal microcirculation flow, renal obstruction analysis, gastrointestinal motility, organs’ perfusion)\n* skin analysis (mainly detection of melanin in melanoma cells)\n* image-guided injection of drug\n![](upload/PAI_1.png)\n3D Photoacoustic imaging of a tumour vasculature after treatment with Combrastatin, a vascular disrupting agent. Adapted from Laufer et al., [https://doi.org/10.1117/1.jbo....](https://doi.org/10.1117/1.jbo.17.5.056016)\n![](upload/PAI_2.jpg)\nPhotoacoustic multispectral imaging of a mouse tumour coregistered with ultrasound detection and administered with gold nanoparticles (yellow). Red: oxy-hemoglobin, Blue: deoxy-hemoglobin. Courtesy of Visualsonics\nWithin Euro-BioImaging, preclinical PhotoAcoustic Imaging is provided by the following Nodes:\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM (NO)](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n### Use cases\nClick here for\n[Use Cases](/content/use-cases/#PAI)from our Nodes.\n## Single wavelength regime (2D, 3D) PAI\nIn Single Wavelength regime, a tunable near infrared laser is used to\nilluminate the subject at the desired wavelength in order to visualize\nspecific chromophores such as hemoglobin, melanin, dyes and\nnanoparticles. The simultaneous acquisition of high-resolution\nultrasound images allows the localization of the chromophores’ signals\nto specific anatomical regions.\n**Available at:**\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n## Multi-wavelength Mode (2D, 3D) PAI\nIn Multi-Wavelength PAI,  photoacoustic data are acquired at\nmultiple wavelengths in 2D and 3D. The main advantage of multispectral\nimaging is the ability to distinguish optically differing signals from\neach other.\nMulti-Wavelenght PAI can be successfully used to detect multiple dyes\n(e.g. in  nanoparticles) and to monitor accumulation at target\nsites and drug release.\n**Available at:**\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n## Spectro Mode PAI\nSpectro Mode consists in the rapid collection of photoacoustic data\nacross the entire wavelength range (680-970 and 1200-2000\\* nm) to\ndetermine the spectral characteristics of a given contrast agent. This\nallows to detect contrast agents in vivo and to distinguish them from\nendogenous absorbers. The \"spectral fingerprint\" collected by this\nmodality can also be saved and used for spectral unmixing in\nsubsequent acquisitions.\nSee for example Bui DT, et al., “Multimodal Contrast Agent Enabling pH\nSensing Based on Organically Functionalized Gold Nanoshells with Mn-Zn\nFerrite Cores”,\n\n## Oxy-Hemo Mode (2D, 3D) PAI\nThis PAI modality is used for the determination of the oxygen\nsaturation in blood. It is based on the fact that oxy- and\ndeoxyhemoglobin absorb light at different wavelengths, thus allowing\nto generate high resolution parametric maps of the oxygen saturation.\nThese maps can be superimposed to high resolution anatomical images\nand used e.g. for studying hypoxia, ischemia and other functional\nprocesses.\n**Available at:**\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n## Photoacoustic ECG-gated Kilohertz Visualization (EKV Mode PAI)\nIn EKV Mode,multiple cardiac cycles are averaged. This allows to\nincrease temporal resolution for photoacoustic imaging, with frame\nrates being increased from about 5 to hundreds of frames/sec. This\nmakes it useful for cardiovascular applications, with the\nvisualization of dynamic changes in the photoacoustic signal over the\nentire cardiac cycle.\n## PAI - Volumetric analysis\nVolumetric analysis is used to quantify the amount of the drug or\ncontrast agent in the specific organ volume. A 3D scan is used for\nthis purpose.\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n\n## AI Generated Documentation\n\n### Overview\nPhotoAcoustic Imaging (PAI) is a cutting-edge biomedical imaging technique that merges the principles of optical illumination and ultrasound detection to provide detailed visualizations of biological tissues. Utilizing the photoacoustic effect, where absorbed light energy is converted into ultrasound waves, PAI offers a unique approach to imaging that is both non-invasive and capable of delivering real-time insights into tissue characteristics.\n\n### Key Capabilities\nPAI systems typically consist of a pulsed laser source, ultrasound transducers, and a signal processing unit. The pulsed laser emits light at specific wavelengths that are absorbed by endogenous chromophores such as hemoglobin and melanin, or by exogenous contrast agents. This absorption leads to a rapid thermal expansion, generating ultrasound waves that are detected by transducers. The imaging resolution can reach submillimeter levels at depths of several centimeters, and with adjustments, it can achieve submicrometer resolution for detailed cellular imaging. \n\n### Applications\nPAI is particularly valuable in various medical fields, especially oncology, where it is employed to:\n- **Monitor Blood Flow**: Assessing hemodynamics in tumors and surrounding tissues.\n- **Evaluate Oxygen Saturation**: Measuring blood oxygen levels to understand tumor metabolism.\n- **Visualize Tumor Vasculature**: Producing angiograms to map blood vessel networks in tumors.\n- **Molecular Imaging**: Tracking molecular probes to visualize cancer pathology and response to therapies.\n- **Thermal Monitoring**: Non-invasively mapping temperature changes during thermal therapies, enhancing treatment planning and monitoring.\n\n### Advantages\nThe distinct advantages of PAI include its high spatial resolution combined with the ability to penetrate deeper tissues, making it superior to traditional optical imaging methods. Unlike X-ray or CT imaging, PAI is non-ionizing, reducing patient exposure to harmful radiation. Furthermore, it leverages existing ultrasound technology, making it a cost-effective and portable solution for clinical settings. The integration of functional and structural imaging capabilities allows for comprehensive assessments of tissue health, paving the way for improved diagnostic and therapeutic strategies in medicine. \n\nIn summary, PhotoAcoustic Imaging stands out as a versatile and powerful tool in the biomedical imaging landscape, offering unique insights into tissue characteristics that are critical for advancing medical diagnostics and treatment outcomes.\n\n## References\n\n1. https://openmedscience.com/photoacoustic-imaging-a-revolutionary-approach-in-biomedical-imaging/\n2. https://www.sciencedirect.com/topics/medicine-and-dentistry/photoacoustic-imaging\n3. https://pmc.ncbi.nlm.nih.gov/articles/PMC6595011/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "6e382796", "e0395c6a", "9beefd47", "d2be2f9c", "3e52fd14", "64543c53" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "f4eef350", "name": "Photoacoustic imaging (PAI - bio)*", "original_id": "b01c0297-2315-4d1a-88a6-ea4b1386ab5d", "description": "Non-invasive imaging with sub-mm resolution, real-time vascular and tumor analysis.", "documentation": "## PhotoAcoustic Imaging (PAI) \\*\n---\n**PhotoAcoustic (or optoacoustic) Imaging (PAI) is a novel but well-established technology that combines optical and ultrasound imaging. Briefly, the technique detects endogenous or exogenous chromophores that are excited through an illumination carried out with pulsed laser light, typically in the Red-NIR range. The non-radiative release of the absorbed energy produces a microheating and a thermoelastic expansion in the chromophore close surroundings, which can generate ultrasound. The acoustic waves are detected by a transducer and transformed into an image.**\nPAI combines the advantages of optical and US imaging technologies. The detection of the US signal makes it possible to achieve an increase of both spatial resolution (micrometric) and penetration depth with respect to optical imaging and reduces scattering phenomena. Other advantages include good sensitivity (comparable to that of optical imaging), safety, cheapness and ease of use.\nA very large number of chromophores can be used to generate PAI contrast: endogenous molecules (e.g. oxy- and deoxy-hemoglobin, myoglobin, melanin), exogenous probes (e.g. organic dyes like fluorescein and ICG), nanosystems (e.g. noble metals-containing nanoparticles, quantum dots, carbon nanotubes, etc.) and also fluorescent proteins and gene reporters. Detection of different types of chromophores in the same anatomical region is also feasible.\nAs any tomographic technique, PAI allows to get 3D-high resolution images of soft tissues which provide anatomical, functional, and molecular information. Due to the not optimal penetration depth, PAI is particularly useful for preclinical imaging, whereas in humans it’s use is limited to superficial organs analysis (e.g. palmar vessels detection, breast analysis). The most important in vivo application of PAI is the detection of blood hemoglobin, which provides a different PA signal depending on its deoxy- or oxy-state, allowing it to evaluate the vascular volume and pO2 in normal and hypoxic conditions.\nOther applications in the preclinical biomedical field include, but are not limited to:\n* oncology (cancer detection, assessment of vascular volume and hypoxia, targeting experiments, assessment of drug distribution and therapy outcome)\n* neurobiology (stroke, brain cancer, intracranial injection of drugs, functional imaging)\n* cardiovascular biology (heart attack, detection of atherosclerotic plaques, hemodynamic and O2 perfusion)\n* in developmental biology (vascular volume and oxygenation of placenta, image-guided embryo injection, fetal analysis)\n* abdomen analysis (kidney diseases as renal microcirculation flow, renal obstruction analysis, gastrointestinal motility, organs’ perfusion)\n* skin analysis (mainly detection of melanin in melanoma cells)\n* image-guided injection of drug\n\n## AI Generated Documentation\n\n**Overview** \nPhotoacoustic Imaging (PAI) is a hybrid imaging modality that combines the high spatial resolution of ultrasound with the rich optical contrast of light absorption in biological tissues. This technique utilizes pulsed laser light to induce thermal expansion in tissues, generating ultrasound waves that are then detected to create detailed images of tissue structures. PAI is particularly valuable in biomedical research and clinical diagnostics due to its ability to visualize functional and molecular information in vivo without the use of ionizing radiation.\n\n**Key Capabilities** \nPAI operates primarily in the near-infrared spectrum, allowing for deeper tissue penetration while maintaining high resolution. The imaging system can achieve submillimeter resolution at depths of several centimeters, with the potential for enhanced resolution down to submicrometer levels by sacrificing depth. This capability enables the visualization of fine structures such as microvasculature and cellular components. The technique can also be adapted for various imaging modalities, including 3D imaging and real-time monitoring, making it versatile for different research needs.\n\n**Applications** \nPAI has a broad range of applications in both preclinical and clinical settings:\n- **Tumor Imaging**: It provides insights into tumor vascularization and metabolic activity by mapping blood oxygenation levels, which is crucial for assessing tumor response to therapies.\n- **Angiography**: PAI allows for detailed imaging of blood vessels, facilitating the diagnosis and treatment of vascular diseases.\n- **Thermal Therapy Monitoring**: The modality can noninvasively track temperature changes during thermal treatments, such as laser ablation, enhancing treatment efficacy.\n- **Molecular Imaging**: By employing specific contrast agents, PAI can visualize molecular pathways and disease processes, aiding in early diagnosis and personalized medicine.\n\n**Advantages** \nThe non-invasive nature of PAI, combined with its ability to provide real-time imaging, makes it a powerful tool for continuous monitoring of disease progression and treatment response. Unlike traditional imaging techniques that may expose patients to ionizing radiation, PAI utilizes light and sound, offering a safer alternative for repeated imaging. Additionally, the integration of optical and ultrasound imaging enhances tissue characterization, providing critical information for accurate diagnosis and treatment planning. Overall, Photoacoustic Imaging represents a significant advancement in the field of biomedical imaging, offering unique capabilities that bridge the gap between functional and structural imaging.\n\n## References\n\n1. https://www.sciencedirect.com/topics/medicine-and-dentistry/photoacoustic-imaging\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC6595011/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "64543c53", "09122290" ], "abbr": "", "category": { "id": "88f6b6cb-b1e0-4b33-b15d-b32c118bac24", "name": "Mesoscopic Imaging" } }, { "id": "b5333ef4", "name": "Photomanipulation (Pmanip)", "original_id": "182db29a-bf27-41a7-b4b2-b72d4a28ef3b", "description": "Photomanipulation includes a variety of techniques in which lasers (or other light sources) are used to interact with the sample in a targeted fashion. This includes laser ablation to induce cellular injuries and measure physical properties, photoconversion or photobleaching of fluorescent proteins for tracking of protein movements, uncaging of probes or different compounds in the cell etc. Photomanipulation is key in using optogenetics approaches.", "documentation": "## Photomanipulation (Pmanip)\n---\n**Photomanipulation includes a variety of techniques in which lasers (or other light sources) are used to interact with the sample in a targeted fashion. This includes laser ablation to induce cellular injuries and measure physical properties, photoconversion or photobleaching of fluorescent proteins for tracking of protein movements, uncaging of probes or different compounds in the cell etc. Photomanipulation is key in using optogenetics approaches.**\n\n", "provider_node_ids": [ "90c8b0d6", "e532f9cb", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "3ef7ea02", "name": "Plant Phenotyping (PHENOPlant)*", "original_id": "d471728c-208a-4d95-9036-ffb74946d5c1", "description": "High-throughput, multi-sensor phenotyping for crops, Arabidopsis, stress studies.", "documentation": "## Plant Phenotyping\n---\n**Plant Phenotyping is designed for non-invasive, morphometric and physiological high-throughput phenotyping of small plants (e.g. Arabidopsis) and mid-size crop plants (e.g. wheat, barley).**\nThe system available at PHENOPlant at the Austria BioImaging Node can process samples on agar-plates and different type of pots ranging from 250mL up to 5L and is fully integrated into a state-of-the-art walk-in phytotron providing highly controlled plant growth conditions. Furthermore, the platform facilitates precise environmental (live) simulations across different climate zones as well as controlled plant stress experiments (cold- or heat stress).\nPlants are transported on conveyor belts from the growth area to the imaging cabinets equipped with a wide range of sensors, including multi-excitation PAM kinetic chlorophyll fluorescence imaging, RGB, hyperspectral imaging (VNIR & SWIR), thermal imaging and 3D scanning.\nFollowing the imaging process, the soil water content is adjusted by an automated, gravimetric watering system, facilitating highly controlled drought stress experiments.\nPotential applications are basic and applied plant research questions where objective, reproducible and high-throughput phenotype assessment (morphology and physiology) is requested.  This includes abiotic- and biotic stress response (e.g. drought, cold, heat light, salt, pathogens), plant breeding, but also testing of e.g. fertiliser, biostimulants, herbicides.\nFor a  360 degree plant point of view of Plant Phenotyping, check out this video \n![](upload/mpi.png)\nView from inside the PHENOPlant facility at the Vienna BioCenter Core Facilities\n\n## AI Generated Documentation\n\n**Overview** \nPHENOPlant is a state-of-the-art high-throughput plant phenotyping platform located at the Vienna BioCenter. It is specifically designed for the non-invasive assessment of morphological and physiological traits in small plants, such as Arabidopsis, and mid-size crops, including wheat and barley. The facility is fully integrated into a sophisticated walk-in phytotron that provides highly controlled growth conditions, enabling precise simulations of various environmental scenarios and stress conditions.\n\n**Key Capabilities** \nPHENOPlant boasts an array of advanced imaging technologies that set it apart from other phenotyping systems:\n- **Multi-Sensor Imaging:** The platform utilizes multiple sensors, including:\n - Multi-excitation PAM kinetic chlorophyll fluorescence for assessing photosynthetic efficiency.\n - RGB imaging for capturing detailed plant morphology from multiple angles.\n - Hyperspectral imaging (VNIR and SWIR) for analyzing plant biochemical properties.\n - Thermal imaging to monitor plant temperature and stress responses.\n - 3D laser scanning for precise structural analysis.\n- **Environmental Control:** The phytotron maintains optimal growth conditions with:\n - Temperature range: 0°C to 40°C.\n - Humidity control: 40% to 80% relative humidity.\n - Adjustable LED light spectrum up to 1000 µmol m⁻² s⁻¹.\n - CO2 levels adjustable from ambient to 2000 ppm.\n- **Automated Systems:** The platform features automated watering and weighing systems, allowing for precise control of soil moisture and facilitating drought stress experiments.\n\n**Applications** \nPHENOPlant is invaluable for researchers studying:\n- Plant responses to environmental stresses, such as drought, heat, and cold.\n- Morphological and physiological trait assessment in plant breeding programs.\n- Basic plant biology, including growth dynamics and stress physiology.\n- High-throughput screening of genetic variants for improved resilience and productivity.\n\n**Advantages** \nThe unique design of PHENOPlant allows for the parallel processing of samples, significantly enhancing throughput and sensor utilization. Its integration of automated environmental adjustments and precise imaging technologies provides researchers with reliable, reproducible data that is critical for advancing our understanding of plant responses to varying conditions. This comprehensive approach to phenotyping makes PHENOPlant a leading facility in plant research, supporting both academic and industrial applications.\n\n## References\n\n1. https://www.viennabiocenter.org/vbcf/plant-sciences/phenoplant/\n2. https://www.eurobioimaging.eu/news/phenoplant-high-throughput-phenotyping-capability-for-plant-research/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "4ba07d0c", "name": "Polarization microscopy (PM)", "original_id": "3a0a0bfe-1645-446a-8b8b-801b49f1c7c1", "description": "Polarization Microscopy or Polarized Light Microscopy involve the use of polarized light in illuminating the sample and make use of the samples optically anisotropic character to generate contrast. ", "documentation": "## Polarization Microscopy (PM)\n---\n**Polarization Microscopy or Polarized Light Microscopy involve the use of polarized light in illuminating the sample and make use of the samples optically anisotropic character to generate contrast.**\n\n", "provider_node_ids": [ "90c8b0d6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "fd0e8053", "name": "Population imaging (PI data)", "original_id": "bda7dbdc-9625-4b38-b972-199da4a0731f", "description": "Advanced imaging for large cohorts: AI analysis, biomarker tracking, multi-modal.", "documentation": "## Population Imaging (PI)\n---\n**Population Imaging relies on the application of advanced image analysis tools to large numbers of medical images related to population cohorts. The aim is the identification and monitoring of specific imaging biomarkers which can provide information about diseases at the population level, allowing early diagnosis, early identification of people at risk and preventive measures.**\nExamples:\n* In a population based study of people with asymptomatic carotid wall thickening, it was shown that carotid intraplaque hemorrhage has the potential to be used as marker of systemic plaque vulnerability in clinical practice, particularly among women, and thus carries promise for cardiovascular disease prevention (J.E. van der Toorm et al., “Carotid Plaque Composition and Prediction of Incident Atherosclerotic Cardiovascular Disease”, )\n* A CT and MRI population based study showed that a larger burden of carotid and vertebrobasilar  arteries was associated with an increase of cerebral small vessel disease markers accelerating over time, but not with accelerated brain atrophy. Identifying pathophysiological mechanisms of intracranial arteriosclerosis could help to lower the vascular burden in the brain and eventually prevent stroke, cognitive impairment and dementia. (E.J. Vinke et al., “Intracranial arteriosclerosis is related to cerebral small vessel disease: a prospective cohort study”, )\n**Population imaging is available at:**\n* [Brain Imaging Network](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [DIMP Neuromed](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam)\n* [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n**Use cases:**\n| **Use case** | **Node** | **DOI** |\n| --- | --- | --- |\n| Carotid plaques study | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Relation of intracranial atherosclerosis and cerebral small vessel disease from MR and CT images | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Combined molecular subtyping, grading, and segmentation of glioma using multi-task deep learning | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Differential diagnosis and molecular stratification of gastrointestinal stromal tumors on CT images using a radiomics approach | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Predicting symptomatic mesenteric mass in small intestinal neuroendocrine tumors using radiomics | [Population Imaging Node Rotterda](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| EASE: clinical implementation of automated tumor segmentation and volume quantification for adult low-grade glioma | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Distinguishing pure histopathological growth patterns of colorectal liver metastases on CT using deep learning and radiomics | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Deep and conventional machine learning for MRI-based diagnosis and prediction of Alzheimer’s disease | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Automated differentiation of malignant and benign primary solid liver lesions on MRI | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| A machine learning approach to distinguish between knees without and with osteoarthritis using MRI-based radiomic features from tibial bone | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Differential diagnosis and mutation stratification of desmoid-type fibromatosis on MRI using radiomics | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Radiomics approach to distinguish between well differentiated liposarcomas and lipomas on MRI | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma Detection and Segmentation in MR Image | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.3390/cancer...](https://doi.org/10.3390/cancers15051622) |\n| Artificial Intelligence on FDG PET Images Identifies Mild Cognitive Impairment Patients with Neurodegenerative Disease | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1007/s10916...](https://doi.org/10.1007/s10916-022-01836-w) |\n| | | |\n| MR Denoising Increases Radiomic Biomarker Precision and Reproducibility in Oncologic Imaging | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1007/s10278...](https://doi.org/10.1007/s10278-021-00512-8) |\n| A Confidence Habitats Methodology in MR Quantitative Diffusion for the Classification of Neuroblastic Tumors | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.3390/cancer...](https://doi.org/10.3390/cancers12123858) |\n| Machine Learning-Based Integration of Prognostic Magnetic Resonance Imaging Biomarkers for Myometrial Invasion Stratification in Endometrial Cancer | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1002/jmri.2...](https://doi.org/10.1002/jmri.27625) |\n| | | |\n\n## AI Generated Documentation\n\n**Overview** \nPopulation Imaging (PI data) is a cutting-edge technology designed for the comprehensive analysis of medical images from large population cohorts. It utilizes advanced image processing techniques and artificial intelligence (AI) to identify and monitor imaging biomarkers that provide critical insights into diseases at the population level. This technology is instrumental in facilitating early diagnosis, risk assessment, and preventive healthcare strategies. \n\n**Key Capabilities** \n1. **Data Management and Storage**: PI data supports secure storage and preparation of medical images, including anonymization and data curation to ensure compliance with ethical standards. \n2. **Advanced Image Processing**: The technology employs sophisticated algorithms for the analysis of extensive datasets, including tasks such as Common Data Model (CDM) mapping and feature extraction. \n3. **AI and Machine Learning Integration**: By leveraging AI/ML tools, Population Imaging enhances the accuracy and efficiency of data analysis, enabling the identification of subtle imaging biomarkers that may indicate disease progression or risk factors. \n4. **Custom Software Development**: Tailored imaging software solutions can be developed to meet specific research needs, allowing for flexibility in application and analysis. \n5. **Multi-Center Collaboration Support**: PI data facilitates collaborative research efforts across multiple institutions, providing a framework for data sharing and joint analysis of imaging studies. \n\n**Applications** \nPopulation Imaging is widely applicable in various fields, including: \n- **Epidemiological Studies**: Tracking disease prevalence and progression in large populations. \n- **Clinical Trials**: Assessing treatment efficacy and safety through imaging biomarkers. \n- **Public Health Research**: Identifying at-risk populations and informing preventive measures. \n- **Neuroimaging**: Utilizing modalities such as MRI and EEG to study brain health and disorders. \n\n**Advantages** \n- **Scalability**: Capable of processing vast amounts of diverse data, making it suitable for extensive population studies. \n- **Enhanced Precision**: The integration of AI/ML tools improves the reliability of biomarker identification and data analysis. \n- **Resource Efficiency**: Supports effective resource allocation in research projects, optimizing study design and execution. \n- **Robust Collaboration**: Enables multi-center studies, enhancing the quality and generalizability of research findings. \n\nIn summary, Population Imaging (PI data) stands out as a powerful tool for analyzing medical imaging data at the population level, significantly contributing to advancements in public health and clinical research.\n\n## References\n\n1. https://github.com/neurospin/piws\n2. https://www.eurobioimaging-access.eu/service/population-imaging-pi\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "6e382796", "6319df36", "64543c53", "84334573", "6d068cfb" ], "abbr": "", "category": { "id": "b73300b1-0934-4e73-86be-a829aa06ee16", "name": "Medical Image Data services" } }, { "id": "1fe88685", "name": "Population imaging (PI)", "original_id": "7265d9e1-ee0f-4144-88e5-2805422b1592", "description": "Large-scale imaging of populations for early disease detection and prevention.", "documentation": "## Population Imaging (PI)\n---\n**Population Imaging relies on the application of advanced image analysis tools to large numbers of medical images related to population cohorts. The aim is the identification and monitoring of specific imaging biomarkers which can provide information about diseases at the population level, allowing early diagnosis, early identification of people at risk and preventive measures.**\nExamples:\n* In a population based study of people with asymptomatic carotid wall thickening, it was shown that carotid intraplaque hemorrhage has the potential to be used as marker of systemic plaque vulnerability in clinical practice, particularly among women, and thus carries promise for cardiovascular disease prevention (J.E. van der Toorm et al., “Carotid Plaque Composition and Prediction of Incident Atherosclerotic Cardiovascular Disease”, )\n* A CT and MRI population based study showed that a larger burden of carotid and vertebrobasilar  arteries was associated with an increase of cerebral small vessel disease markers accelerating over time, but not with accelerated brain atrophy. Identifying pathophysiological mechanisms of intracranial arteriosclerosis could help to lower the vascular burden in the brain and eventually prevent stroke, cognitive impairment and dementia. (E.J. Vinke et al., “Intracranial arteriosclerosis is related to cerebral small vessel disease: a prospective cohort study”, )\n**Population imaging is available at:**\n* [Brain Imaging Network](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [DIMP Neuromed](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam)\n* [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n**Use cases:**\n| **Use case** | **Node** | **DOI** |\n| --- | --- | --- |\n| Carotid plaques study | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Relation of intracranial atherosclerosis and cerebral small vessel disease from MR and CT images | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Combined molecular subtyping, grading, and segmentation of glioma using multi-task deep learning | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Differential diagnosis and molecular stratification of gastrointestinal stromal tumors on CT images using a radiomics approach | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Predicting symptomatic mesenteric mass in small intestinal neuroendocrine tumors using radiomics | [Population Imaging Node Rotterda](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| EASE: clinical implementation of automated tumor segmentation and volume quantification for adult low-grade glioma | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Distinguishing pure histopathological growth patterns of colorectal liver metastases on CT using deep learning and radiomics | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Deep and conventional machine learning for MRI-based diagnosis and prediction of Alzheimer’s disease | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Automated differentiation of malignant and benign primary solid liver lesions on MRI | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| A machine learning approach to distinguish between knees without and with osteoarthritis using MRI-based radiomic features from tibial bone | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Differential diagnosis and mutation stratification of desmoid-type fibromatosis on MRI using radiomics | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Radiomics approach to distinguish between well differentiated liposarcomas and lipomas on MRI | [Population Imaging Node Rotterdam](https://www.eurobioimaging.eu/nodes/population-imaging-flagship-node-rotterdam) | |\n| Independent Validation of a Deep Learning nnU-Net Tool for Neuroblastoma Detection and Segmentation in MR Image | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.3390/cancer...](https://doi.org/10.3390/cancers15051622) |\n| Artificial Intelligence on FDG PET Images Identifies Mild Cognitive Impairment Patients with Neurodegenerative Disease | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1007/s10916...](https://doi.org/10.1007/s10916-022-01836-w) |\n| | | |\n| MR Denoising Increases Radiomic Biomarker Precision and Reproducibility in Oncologic Imaging | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1007/s10278...](https://doi.org/10.1007/s10278-021-00512-8) |\n| A Confidence Habitats Methodology in MR Quantitative Diffusion for the Classification of Neuroblastic Tumors | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.3390/cancer...](https://doi.org/10.3390/cancers12123858) |\n| Machine Learning-Based Integration of Prognostic Magnetic Resonance Imaging Biomarkers for Myometrial Invasion Stratification in Endometrial Cancer | [Population Imaging Node Valencia](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia) | [https://doi.org/10.1002/jmri.2...](https://doi.org/10.1002/jmri.27625) |\n| | | |\n\n## AI Generated Documentation\n\n**Overview** \nPopulation Imaging (PI) is a cutting-edge imaging technology that enables the large-scale acquisition, analysis, and interpretation of medical images across defined population cohorts. This approach integrates advanced imaging modalities such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), and Positron Emission Tomography (PET) to visualize and quantify biological changes associated with health and disease. By leveraging sophisticated computational techniques, including machine learning, PI facilitates the extraction of significant patterns and biomarkers from complex datasets, enhancing our understanding of disease mechanisms and progression.\n\n**Key Capabilities** \nPopulation Imaging is distinguished by its ability to handle high-resolution imaging data from diverse modalities, allowing for detailed anatomical and functional assessments. The technology supports the analysis of longitudinal data, enabling researchers to track changes over time within the same individuals or populations. This capability is crucial for identifying subclinical disease stages, understanding disease trajectories, and evaluating the effectiveness of interventions. Furthermore, PI promotes data integration from various sources, including genetic, environmental, and lifestyle factors, which enriches the analysis and interpretation of health outcomes.\n\n**Applications** \nThe applications of Population Imaging are extensive and include: \n- **Neuroepidemiology**: PI is particularly valuable in studying neurological diseases, where it helps visualize brain changes that occur before clinical symptoms manifest. This aids in identifying at-risk individuals and understanding the progression of diseases such as Alzheimer's and Parkinson's. \n- **Public Health Research**: By assessing the impact of social determinants on health, PI informs public health strategies aimed at reducing disease prevalence and improving health outcomes across populations. \n- **Clinical Trials**: In clinical research, PI supports the identification of biomarkers for disease prediction and progression, enhancing the design and evaluation of therapeutic interventions.\n\n**Advantages** \nPopulation Imaging offers several advantages over traditional imaging approaches: \n- **Early Detection**: The ability to visualize subclinical changes allows for earlier diagnosis and intervention, which can significantly improve patient outcomes. \n- **Comprehensive Data Analysis**: The integration of diverse data types provides a holistic view of health determinants, facilitating more effective public health interventions. \n- **Standardization and Collaboration**: The push for harmonization in imaging protocols enhances the reliability and comparability of findings across studies, fostering collaborative research efforts and improving the overall quality of epidemiological data. \nIn summary, Population Imaging stands out as a transformative approach in medical research, offering unique capabilities that enhance our understanding of health and disease dynamics within populations.\n\n## References\n\n1. https://bmcmethods.biomedcentral.com/articles/10.1186/s44330-024-00010-7\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC11706584/\n3. https://www.sciencedirect.com/science/article/pii/B9780128029732000057\n4. https://www.sciencedirect.com/science/article/pii/S295034772500012X\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "6e382796", "6319df36", "64543c53", "84334573", "6d068cfb" ], "abbr": "", "category": { "id": "17cfa36f-2c2b-4ce7-9ec8-ce84eb82d56d", "name": "Human Imaging\t\t\t\t\t\t" } }, { "id": "f6b01df1", "name": "Quantitative Phase Imaging (QPI)*", "original_id": "6333c3d2-7607-4b05-83c4-6fb52631b8c7", "description": "Label-free imaging of live cells with nanoscale resolution and quantitative analysis.", "documentation": "## Quantitative Phase Imaging \\*\n---\n**Quantitative Phase Imaging (QPI) has emerged as a valuable method for investigating cells and tissues. QPI operates on unlabelled specimens and, as such, is complementary to established fluorescence microscopy, exhibiting lower phototoxicity and no photobleaching. QPI is a label-free technique in which various methods (for example off-axis digital holography, wavefront sensing, spatial light interference, ptychography) are used to retrieve the phase information of light passing through the cell. In contrast to traditional qualitative label-free techniques such as phase contrast or DIC, QPI measures the absolute phase delay and is high-contrast. In 2D acquisitions the images represent quantitative maps of optical path length delays introduced by the specimen, which correspond to differences between refractive index of the cellular components and medium, and the length of the optical path within the cell. The phase delay can be directly converted into a dry mass of the cell. In 3D acquisition a spatial distribution of refractive indices is obtained, giving a three-dimensional shape of the cell and its compartments.**\nQPI provides an objective measure of morphology and dynamics, free of variability due to contrast agents not used. QPI data are suitable for image segmentation, making label-free cell counting and tracking easy.\nApplication areas:\nThe interpretation of the phase signal has proven to deliver novel parameters for studying physiological processes in living cells, such as transmembrane fluid flux, dry mass and water content changes, intracellular transport as well as tissue structure and density changes. Protein concentrations, growth and cell motility can be precisely quantified. The morphologies of cells and organelles can be established by phase tomography. Their studies provide information on the biomechanical characteristics of cell structures and membranes. These data are indicative of biomolecular activity, which can be affected by pathology.\n\n## AI Generated Documentation\n\n### Overview\nQuantitative Phase Imaging (QPI) is a cutting-edge optical imaging technique that provides label-free, quantitative assessments of biological specimens by measuring the phase shift of light as it passes through transparent materials. This method is particularly advantageous for imaging live cells, as it allows researchers to observe cellular dynamics in real-time without the interference of fluorescent markers or other contrast agents.\n\n### Key Capabilities\nQPI utilizes digital holography and interferometric techniques to achieve high-resolution imaging with nanoscale sensitivity, typically in the range of 100 nm. The technology captures phase delays that correlate with variations in the refractive index of biological samples, enabling detailed morphological and dynamic analyses. QPI can produce quantitative maps of cell thickness, density, and refractive index, making it a powerful tool for studying cellular structures and behaviors over time. The technique is capable of monitoring live cells over various temporal scales, from milliseconds to days, providing insights into processes such as cell division, migration, and response to stimuli.\n\n### Applications\nQPI has a wide array of applications across various fields:\n- **Biomedicine**: It is extensively used for live cell imaging, allowing for the study of cellular processes like proliferation, apoptosis, and motility without disrupting the cells. Researchers can analyze the effects of drugs or environmental changes on cell behavior in real-time.\n- **Material Science**: QPI is employed to investigate the structural properties of materials at the microscopic level, including surface topography and refractive index mapping of optical waveguides. This capability is crucial for developing advanced materials and nanotechnology applications.\n- **Nanotechnology**: The technique is useful for studying nanoplasmonics and photothermal effects in nanomaterials, facilitating the development of novel nanostructures for various applications.\n\n### Advantages\nThe distinct advantages of QPI include:\n- **Label-Free Imaging**: This eliminates the need for fluorescent or other contrast agents, reducing potential artifacts and cellular stress, which is particularly beneficial for live cell studies.\n- **Quantitative Analysis**: QPI provides objective measurements of biological specimens, enhancing the reliability and reproducibility of research data.\n- **High Sensitivity and Resolution**: The ability to detect subtle changes in cellular morphology and dynamics is crucial for understanding complex biological processes, making QPI a valuable tool in both research and clinical settings. \n\nOverall, QPI stands out as a versatile and powerful imaging modality, offering unique capabilities that enhance our understanding of biological systems and materials science.\n\n## References\n\n1. https://www.phasics.com/en/wavefront-mtf-quantitative-phase-imaging-solutions/quantitative-phase-imaging/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC10112851/\n3. https://link.springer.com/chapter/10.1007/978-3-030-21722-8_1\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "fcf6bac6", "638ca876", "90c8b0d6", "fc1893d4", "64543c53", "09122290" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "dcb85d5e", "name": "Raman Spectroscopy (RS)", "original_id": "346c0634-5360-47db-a0d8-a89e581d1ea4", "description": "Non-destructive molecular fingerprinting, high sensitivity, rapid analysis.", "documentation": "##\n## RAMAN SPECTROSCOPY\n---\n**Raman spectroscopy is a spectroscopic technique based on inelastic scattering of monochromatic light, usually from a laser source. Inelastic scattering means that the frequency of photons in monochromatic light changes upon interaction with a sample.**\n\n## AI Generated Documentation\n\n### Overview\nRaman Spectroscopy (RS) is a non-invasive analytical technique that exploits the inelastic scattering of monochromatic light, typically from a laser, to provide detailed information about the molecular composition and structure of materials. The technique is based on the Raman effect, where a small fraction of light scattered by a sample experiences a shift in wavelength corresponding to the vibrational modes of the molecules within the sample. This results in a unique spectral fingerprint that can be used for identification and characterization of substances.\n\n### Key Capabilities\nRaman spectroscopy is distinguished by its ability to:\n- **Detect Trace Amounts**: It can analyze very low concentrations of substances, making it suitable for applications in forensic science and environmental monitoring.\n- **Provide Molecular Fingerprints**: Each material has a unique Raman spectrum, allowing for precise identification of chemical compounds without the need for extensive sample preparation.\n- **Analyze Various States**: RS can be applied to solids, liquids, and gases, and can even analyze samples through transparent containers, such as glass or plastic.\n- **Rapid Data Acquisition**: The technique allows for quick analysis, often providing results in seconds, which is crucial for time-sensitive applications.\n\n### Applications\nRaman spectroscopy is utilized across a wide range of fields:\n- **Biomedical Research**: It is employed to study cellular environments, monitor drug interactions, and analyze tissue samples for diagnostic purposes.\n- **Pharmaceutical Industry**: RS is used for process validation, quality control, and formulation analysis, ensuring the consistency and safety of drug products.\n- **Material Science**: The technique aids in characterizing polymers, nanomaterials, and other advanced materials, providing insights into their structural properties.\n- **Environmental Analysis**: RS is effective in detecting pollutants and hazardous substances in air, water, and soil samples.\n- **Forensic Science**: It assists in identifying unknown substances and analyzing evidence from crime scenes.\n\n### Advantages\nRaman spectroscopy offers several notable advantages:\n- **Non-Destructive**: Samples remain intact post-analysis, allowing for further testing or use.\n- **Minimal Sample Preparation**: Unlike techniques such as FTIR (Fourier Transform Infrared Spectroscopy), RS often requires little to no sample preparation, streamlining the analysis process.\n- **High Specificity**: The unique spectral fingerprints enable precise identification of materials, even in complex mixtures.\n- **Versatile Applications**: Its ability to analyze a wide range of materials and states makes it applicable in diverse scientific and industrial fields.\n\nIn conclusion, Raman spectroscopy is a powerful and versatile tool that provides critical insights into molecular structures and compositions, making it invaluable in research, quality control, and environmental monitoring.\n\n## References\n\n1. https://wiki.anton-paar.com/us-en/basics-of-raman-spectroscopy/raman-spectroscopy-applications/\n2. https://scienceinfo.com/raman-spectroscopy-instrumentation/\n3. https://www.sciencedirect.com/science/article/pii/S0924203111001111\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "2b34e271", "1fa342de", "161021f6", "23f7a2fd", "fc1893d4", "e5f30cac", "09122290" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "b51478b1", "name": "Random Illumination Microscopy (RIM)*", "original_id": "180cdd02-b022-4bfe-88b7-54b5c95c5d36", "description": "Speckled illumination, super-resolution, fast imaging of thick biological samples.", "documentation": "## Random Illumination Microscopy (RIM)\n---\n**Random Illumination Microscopy is a powerful super-resolution method using the natural speckle of laser wide field illumination to acquire sequences of random illumination for blindSIM reconstruction. The main advantage is its potential on thick samples as speckle are invariant through diffusion and its power in z sectioning.**\n\n## AI Generated Documentation\n\n### Overview\nRandom Illumination Microscopy (RIM) is a cutting-edge imaging technique that enhances fluorescence microscopy by utilizing random speckled illumination patterns. This method allows for high-resolution imaging of thick biological samples while minimizing phototoxicity and imaging time. RIM stands out due to its robustness against optical aberrations, making it particularly suitable for imaging complex three-dimensional (3D) structures such as tissues and organoids.\n\n### Key Capabilities\nRIM employs a unique approach where multiple speckled illuminations are used to capture images, allowing for the reconstruction of super-resolved images through variance data processing. This technique effectively doubles the resolution compared to conventional microscopy methods. The Extended Depth of Field (EDF) variant of RIM further enhances its capabilities by providing aberration-insensitive imaging, which is crucial for visualizing samples with varying depths. The ability to capture entire volumes in a single image significantly accelerates the imaging process, making RIM ideal for dynamic studies in live cells.\n\n### Applications\nRIM is particularly useful in biological research where observing dynamic processes at the subcellular level is essential. It has been successfully applied to live-cell imaging, enabling researchers to monitor molecular events in real-time. The technique is advantageous for studying larger and thicker samples, such as embryos and organoids, where traditional imaging methods may struggle due to their sequential acquisition processes. RIM's robustness allows for clearer imaging of samples that scatter light, providing valuable insights into cellular dynamics and tissue architecture.\n\n### Advantages\nThe primary advantages of Random Illumination Microscopy include:\n- **High Resolution**: Achieves super-resolution imaging without the need for structured illumination setups.\n- **Speed**: Captures entire volumes in a single image, significantly reducing acquisition times and enabling real-time imaging of dynamic processes.\n- **Low Phototoxicity**: Minimizes light exposure to living samples, making it suitable for long-term imaging studies without damaging the specimens.\n- **Robustness**: Less affected by optical aberrations, allowing for clearer imaging of thick biological tissues and complex structures.\n\nIn summary, RIM represents a significant advancement in fluorescence microscopy, combining speed, resolution, and robustness to facilitate the study of complex biological systems in real-time, setting it apart from traditional imaging techniques.\n\n## References\n\n1. https://www.nature.com/articles/s41377-024-01612-0\n2. https://www.azooptics.com/News.aspx?newsID=30002\n3. https://www.nature.com/articles/s41377-024-01687-9\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "fc1893d4", "64543c53" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "a42333c3", "name": "Reversible optical fluorescence transitions (RESOLFT)", "original_id": "8cd290ad-e26a-4928-a24e-162809ef8252", "description": "Sub-100nm resolution, live cell imaging, reversible fluorescent switching.", "documentation": "## AI Generated Documentation\n\n### Overview\nReversible Optical Fluorescence Transitions (RESOLFT) is a cutting-edge microscopy technique that enables imaging with resolutions significantly below the diffraction limit, achieving spatial resolutions down to 100 nm or less. This method leverages the principles of reversible saturable optical fluorescence transitions, allowing researchers to visualize intricate biological structures and processes that are otherwise undetectable with conventional microscopy techniques.\n\n### Key Capabilities\nRESOLFT microscopy operates by utilizing fluorescent molecules that can be switched between a bright state, which emits fluorescence, and a dark state, which does not. This reversible switching is accomplished through the application of specific light patterns, enabling selective excitation of fluorescent markers. The technique allows for high-resolution imaging by rasterizing the sample and controlling the illumination, effectively overcoming the diffraction limit associated with traditional optical microscopy.\n\nRecent advancements in RESOLFT have introduced multi-sheet imaging capabilities, which employ parallelized light sheets to enhance imaging speed and resolution. This innovation allows for rapid volumetric imaging at rates of 1-2 Hz, facilitating the observation of dynamic cellular processes in real-time. The use of reversibly switchable fluorescent proteins (RSFPs) further enhances the technique's versatility, accommodating various fluorescent markers with minimal switching cycles.\n\n### Applications\nRESOLFT microscopy is particularly valuable in biological research, where it is used to study live cells and complex multicellular systems. It enables detailed observation of subcellular structures, cellular dynamics such as cell division and actin motion, and the behavior of virus-like particles in three dimensions. The ability to visualize these processes in real-time makes RESOLFT an essential tool for researchers investigating cellular mechanisms and interactions.\n\n### Advantages\nThe primary advantage of RESOLFT is its ability to achieve high-resolution imaging without the need for electron microscopy, which often requires extensive sample preparation and can induce damage. By utilizing standard far-field optics and fluorescent markers, RESOLFT provides a less invasive approach to high-resolution imaging, significantly reducing photodamage to live samples. This capability makes it an invaluable tool for real-time studies in cellular biology and nanoscience, distinguishing it from other imaging techniques such as STED and STORM, which may not offer the same level of flexibility and ease of use in live-cell applications.\n\n## References\n\n1. https://en.wikipedia.org/wiki/RESOLFT\n2. https://www.nature.com/articles/s41592-024-02196-8\n3. https://www.microscopyu.com/references/the-resolft-concept\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "161021f6", "b19711d3", "fc1893d4", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "995a6055", "name": "STEM tomography (STEM)", "original_id": "d1846502-489a-4dbd-8971-04b9cece9599", "description": "Scanning transmission electron microscopy (STEM) is a type of transmission electron microscopy in which the focussed electron beam is rastered or scanned across the samples. \r\n\r\nIn STEM tomography, similar to TEM tomography, sections are placed on EM grids and are tilted in the electron beam to +/- 70 degrees. At each tilt angle, a 2D image is acquired and the series of images are later computed to reconstruct the 3D volume: the tomogram. In STEM tomography thicker sections in the μm range can be used.\r\n", "documentation": "## STEM Tomography (STEM)\n---\n**Scanning transmission electron microscopy (STEM) is a type of transmission electron microscopy in which the focussed electron beam is rastered or scanned across the samples.\nIn STEM tomography, similar to TEM tomography, sections are placed on EM grids and are tilted in the electron beam to +/- 70 degrees. At each tilt angle, a 2D image is acquired and the series of images are later computed to reconstruct the 3D volume: the tomogram. In STEM tomography thicker sections in the μm range can be used.**\n\n", "provider_node_ids": [ "d039b533", "fc1893d4", "64543c53", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } }, { "id": "c60b4a73", "name": "Scanning Electron Microscopy (SEM)", "original_id": "d9f3d1b5-a8e0-46f0-9fa4-25186a551f18", "description": "In Scanning Electron Microscopy, a focussed beam of accelerated electrons is scanned across the surface of the sample and the scanned and secondary electrons are used to generate the SEM image.\r\nSEM can be used to automatically acquire serial images of different samples, and can be operated under cryo conditions (see cryo-SEM), at room temperature or under heated conditions. SEM only provides images of the surface of the sample, but through methods such as freeze-fracturing, an internal view of the sample can also be revealed in SEM.\r\n", "documentation": "## Scanning Electron Microscopy (SEM)\n---\n**In Scanning Electron Microscopy, a focussed beam of accelerated electrons is scanned across the surface of the sample and the scanned and secondary electrons are used to generate the SEM image.\nSEM can be used to automatically acquire serial images of different samples, and can be operated under cryo conditions (see cryo-SEM), at room temperature or under heated conditions. SEM only provides images of the surface of the sample, but through methods such as freeze-fracturing, an internal view of the sample can also be revealed in SEM.**\n\n", "provider_node_ids": [ "fcf6bac6", "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "fc1893d4", "9beefd47", "64543c53", "e5f30cac", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "71c66bf5-90db-427e-8ddc-5bc0e722c489", "name": "Scanning Electron Microscopy (SEM)" } }, { "id": "d52b6d15", "name": "Second/Third Harmonic Generation (SHG/THG)", "original_id": "f78b39ca-3b2a-49f4-99eb-a7f241640bf2", "description": "SHG is a label free technique to visualize specific structures e.g. fibrillar collagen, muscle myosin, and microtubules in vitro and in vivo. THG shows interfaces having local transitions of the refractive index e.g. between water-lipid molecules in cellular membranes and surroundings, and water-protein interfaces in protein-rich regions. SHG and THG are not fluorescence, but coherent scattering processes instead, so there is no photobleaching and triplet state induced phototoxicity, and they are well suited especially for live sample imaging. SHG is also a very sensitive method to detect trace amounts of crystallinity e.g. in pharmaceutical materials.\r\n\r\nSHG/THG are often available in multi-photon systems (2PM using pulsed NIR lasers) which allows imaging of unlabelled samples containing aligned fibrous. \r\nSome of the systems available at Euro-BioImaging Nodes can also perform polarized second harmonic microscopy and third harmonic microscopy.\r\n", "documentation": "## Second/Third Harmonic Generation (SHG/THG)\n---\n**SHG is a label free technique to visualize specific structures e.g. fibrillar collagen, muscle myosin, and microtubules in vitro and in vivo. THG shows interfaces having local transitions of the refractive index e.g. between water-lipid molecules in cellular membranes and surroundings, and water-protein interfaces in protein-rich regions. SHG and THG are not fluorescence, but coherent scattering processes instead, so there is no photobleaching and triplet state induced phototoxicity, and they are well suited especially for live sample imaging. SHG is also a very sensitive method to detect trace amounts of crystallinity e.g. in pharmaceutical materials.\nSHG/THG are often available in multi-photon systems (2PM using pulsed NIR lasers) which allows imaging of unlabelled samples containing aligned fibrous.\nSome of the systems available at Euro-BioImaging Nodes can also perform polarized second harmonic microscopy and third harmonic microscopy.**\n\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "e532f9cb", "1fa342de", "161021f6", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "c1a46958", "name": "Secondary Ion Mass Spectrometry with MeV ions (MeV-SIMS)*", "original_id": "d96e8c06-8e7d-43b8-9d41-91771635762a", "description": "High-resolution imaging of large biomolecules using MeV ions, low fragmentation.", "documentation": "## AI Generated Documentation\n\n**Overview** \nSecondary Ion Mass Spectrometry with MeV ions (MeV-SIMS) is an advanced mass spectrometry technique that utilizes high-energy (1-10 MeV) heavy ions to desorb secondary ions from a sample surface. This method significantly enhances the yield of large molecular ions while minimizing fragmentation, making it particularly suitable for detailed molecular analysis and imaging. The technique employs a dual-polarity Time-of-Flight (TOF) mass spectrometer, which allows for the simultaneous detection of all charged secondary particles resulting from a single ion impact, thus providing comprehensive mass spectral data.\n\n**Key Capabilities** \nMeV-SIMS is characterized by its ability to achieve high spatial resolution, often down to sub-micrometer levels, allowing for precise imaging of biological tissues and complex materials. The electronic sputtering process, which dominates at MeV energies, leads to higher yields of intact secondary ions compared to traditional keV SIMS techniques. This is crucial for applications requiring the analysis of large biomolecules, as it reduces the likelihood of fragmentation that can obscure mass spectral information. The technique also allows for the investigation of unexplored energy deposition ranges, providing insights into the physical processes involved in desorption and ionization.\n\n**Applications** \nMeV-SIMS has found applications in various fields, particularly in biomedical research, where it is used to study the distribution of biomolecules in plant and animal tissues. Its ability to maintain the integrity of large organic molecules makes it ideal for proteomic and metabolomic studies. Additionally, MeV-SIMS is employed in materials science for the analysis of thin films and coatings, providing valuable information on composition and structure at the nanoscale.\n\n**Advantages** \nThe primary advantages of MeV-SIMS include enhanced ion yields, reduced fragmentation of large molecules, and high spatial resolution. These features make it a powerful tool for detailed molecular imaging and analysis, setting it apart from conventional SIMS techniques. Furthermore, the versatility of MeV-SIMS allows it to be applied to a wide range of materials, from biological samples to advanced materials, making it an essential technique in modern analytical chemistry and materials science. Overall, MeV-SIMS represents a significant advancement in mass spectrometry, enabling researchers to explore complex molecular landscapes with unprecedented detail and accuracy.\n\n## References\n\n1. https://link.springer.com/article/10.1007/s13361-019-02258-8\n2. https://www.irb.hr/eng/Divisions/Division-of-Experimental-Physics/Laboratory-for-Ion-Beam-Interactions/Articles/Experimental-end-stations/Capillary-MeV-TOF-SIMS\n3. https://ams.ethz.ch/research/ion-beam-physics/mev-sims.html\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2103118f" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "c9ddc22b", "name": "Serial Blockface SEM (SBF-SEM)", "original_id": "f6bcf804-2506-491d-988c-b8a2b535af8b", "description": "A full understanding of the fine organization of cells and tissues requires their high-resolution visualization in three dimensions (3D). In this technique a miniaturized ultramicrotome, embedded in the chamber of the SEM, removes thin layers of the resin block (down to 25 nm) exposing a cross-section of the sample. The newly exposed surface of the block is then imaged with the SEM, before being removed by the ultramicrotome again. The sequential imaging and sectioning enables automated acquisition of serial images. This method is particularly adapted for voluminous samples, such as small model organisms and tissues.", "documentation": "## Serial Blockface SEM (SBF-SEM)\n---\n**A full understanding of the fine organization of cells and tissues requires their high-resolution visualization in three dimensions (3D). In this technique a miniaturized ultramicrotome, embedded in the chamber of the SEM, removes thin layers of the resin block (down to 25 nm) exposing a cross-section of the sample. The newly exposed surface of the block is then imaged with the SEM, before being removed by the ultramicrotome again. The sequential imaging and sectioning enables automated acquisition of serial images. This method is particularly adapted for voluminous samples, such as small model organisms and tissues.**\n\n", "provider_node_ids": [ "fcf6bac6", "90c8b0d6", "ca2e3748", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } }, { "id": "d3d66a1d", "name": "Single Molecule localization microscopy (SMLM)", "original_id": "ffbfe7cf-ebb2-4e8b-80c0-267ecd4a60fe", "description": "Achieves 20-50nm resolution, enabling detailed imaging of molecular dynamics.", "documentation": "## Single Molecule Localisation Microscopy (SMLM)\n---\n**There are a variety of widely used implementations of single molecule localization microscopy that are offered at the Euro-BioImaging Nodes. The unifying principle behind them is that a large series of individual images is acquired, in each of which only a small subset of the fluorescent labels in the sample are fluorescing. This sparse nature of the signal allows the computational calculation of the exact position of each of the emitting fluorophores. By combining the large number of images with precise locations, an image with very high resolution can be formed.\nBelow are descriptions of some of the common SMLM techniques.\nThe fundamental principle behind stochastic optical reconstruction microscopy (STORM) is that the activated state of a photo-switchable molecule must lead to the consecutive emission of sufficient photons to enable precise localization before it enters a dark state or becomes deactivated by photobleaching. Additionally, the sparsely activated fluorescent molecules must be separated by a distance that exceeds the Abbe diffraction limit (in effect, greater than approximately 250 nanometers) to enable the parallel recording of many individual emitters, each having a distinct set of coordinates in the lateral image plane.\nPhoto activated localization microscopy (PALM) is a widefield fluorescence microscopy imaging methods that allow obtaining images with a resolution beyond the diffraction limit. PALM is based on collecting a large number of images each containing just a few active isolated fluorophores. The imaging sequence allows for the many emission cycles necessary to stochastically activate each fluorophore from a non-emissive state to a bright state, and back to a bleached state. During each cycle, the density of activated molecules is kept low enough that the molecular images of individual fluorophores do not typically overlap.\nGround state depletion microscopy followed by individual molecule return (GSDIM or GSD for short) is a super-resolution technique based on single molecule localization. To precisely localize single molecules and create a high-resolution image the ensemble of overlapping fluorophores are temporally \"separated\". This can be achieved by using high power lasers to transfer fluorophores into long-lived \"off states\" – a non-fluorescent molecule state. Single fluorophores return stochastically from the off state and emit bursts of photons, which are recorded. The position of the fluorophore is determined using a software algorithm. Based on this list of coordinates a super-resolution image is reconstructed.**\n\n## AI Generated Documentation\n\n**Overview** \nSingle Molecule Localization Microscopy (SMLM) is a super-resolution imaging technique that surpasses the diffraction limit of conventional microscopy, allowing for the visualization of biological structures at the molecular level. By utilizing the stochastic switching of fluorescent probes, SMLM can localize individual molecules with high precision, achieving resolutions of 20-50 nanometers. This capability is particularly valuable for studying complex biological systems where understanding molecular interactions and arrangements is crucial. \n\n**Key Capabilities** \nSMLM operates by capturing a series of images where only a sparse number of fluorescent molecules are activated at any given time. This allows for the precise localization of these molecules based on their emission patterns. The technique can reconstruct super-resolution images from the accumulated data of thousands to millions of localized molecules. SMLM can be performed in both fixed and live cells, making it versatile for various experimental setups. Additionally, advancements in multicolor SMLM enable simultaneous imaging of multiple targets, providing insights into the spatial relationships and interactions between different biomolecules. \n\n**Applications** \nSMLM is widely used in cell biology, biophysics, and neuroscience to study protein dynamics, receptor interactions, and the organization of cellular structures. It has been instrumental in elucidating the mechanisms of synaptic transmission, understanding the dynamics of membrane proteins, and visualizing the architecture of cellular organelles. The ability to resolve structures at the nanoscale has opened new avenues for research in areas such as drug delivery, disease pathology, and cellular signaling. \n\n**Advantages** \nThe primary advantage of SMLM over traditional microscopy techniques lies in its ability to provide unprecedented spatial resolution, allowing researchers to visualize molecular details that were previously inaccessible. The technique's reliance on fluorescent probes also enables specific labeling of target molecules, enhancing the specificity of the imaging. Furthermore, the ability to perform multicolor imaging expands its utility in studying complex biological systems, facilitating a more comprehensive understanding of molecular interactions and cellular processes. Despite some limitations, such as sensitivity to sample preparation and the need for sophisticated data analysis, SMLM remains a powerful tool in modern biological research, continually evolving with advancements in imaging technology and fluorescent probe development.\n\n## References\n\n1. https://link.springer.com/article/10.1186/s43074-024-00147-2\n2. https://www.nature.com/articles/s43586-021-00038-x\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "7add3aac", "name": "Single Particle Tracking (SPT)*", "original_id": "35a1cf8f-78bb-4ab2-8505-f1d9467130ab", "description": "Real-time tracking of individual particles with nanometer precision in live cells.", "documentation": "## AI Generated Documentation\n\n**Overview** \nSingle Particle Tracking (SPT) is a cutting-edge microscopy technique that allows researchers to monitor the motion of individual particles, such as proteins, vesicles, and other biomolecules, in real-time within complex biological environments, including living cells. This method provides unprecedented insights into the dynamic behaviors of these particles, revealing their interactions and the microenvironments they inhabit.\n\n**Key Capabilities** \nSPT employs high-resolution imaging techniques, often utilizing fluorescent labeling to visualize particles. The tracking process typically involves capturing images at high frame rates (up to milliseconds), enabling the precise determination of particle positions over time. Advanced image processing algorithms are used to analyze the trajectories of these particles with nanometer precision. SPT can differentiate various motion types, including free diffusion, confinement, and directed motion, which are indicative of underlying cellular processes and interactions.\n\n**Applications** \nSPT has a broad range of applications in biological research, including: \n- **Intracellular Dynamics**: Understanding the movement of proteins and nucleic acids within the cytoplasm and nucleus. \n- **Membrane Dynamics**: Analyzing the behavior of lipids and proteins in cellular membranes, crucial for understanding membrane fluidity and protein interactions. \n- **Vesicle and Viral Particle Movement**: Tracking the transport of vesicles and viral particles, essential for studying processes like endocytosis and viral infection. \n- **Drug Delivery Mechanisms**: Evaluating how drugs or genetic materials are internalized by cells, providing insights into therapeutic strategies.\n\n**Advantages** \nThe primary advantages of SPT include: \n- **High Spatial and Temporal Resolution**: Enables the observation of rapid movements and interactions at the molecular level. \n- **Direct Observation**: Unlike ensemble methods, SPT allows for the analysis of individual particles, providing a more nuanced understanding of heterogeneity in biological systems. \n- **Versatility**: Applicable to a variety of biological contexts, from cellular mechanics to the dynamics of complex biomolecular interactions. \n\n**Challenges and Future Directions** \nDespite its strengths, SPT faces challenges such as experimental noise and the complexity of data interpretation. Future developments are focused on improving analytical tools to better handle these challenges, enhancing the accuracy and reliability of SPT data. \n\nIn summary, Single Particle Tracking is a powerful tool that significantly enhances our understanding of molecular dynamics in biological systems, paving the way for advancements in cell biology, pharmacology, and materials science.\n\n## References\n\n1. https://oni.bio/nanoimager/super-resolution-microscopy/single-particle-tracking/\n2. https://pubmed.ncbi.nlm.nih.gov/33533163/\n3. https://www.nature.com/articles/s43586-024-00341-3\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "0c8677f6", "09122290" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "931ee18e", "name": "Single molecule FRET (smFRET)*", "original_id": "c2fcc0eb-e1e4-4163-a26a-855f338f56c8", "description": "Single molecule FRET allows the measurement of distances and distance changes between two fluorescent molecules in a biomolecular complexes, down to the Angstrom and the microsecond timescales. smFRET measurement can be performed on diffusing molecules, in a confocal geometry, to measure distances and fast conformational changes or on immobilized molecules to measure association dissociation kinetics and conformational changes in the seconds timescales.", "documentation": "## Single molecule FRET \\* (smFRET)\n---\n**Single molecule FRET allows the measurement of distances and distance changes between two fluorescent molecules in a biomolecular complexes, down to the Angstrom and the microsecond timescales. smFRET measurement can be performed on diffusing molecules, in a confocal geometry, to measure distances and fast conformational changes or on immobilized molecules to measure association dissociation kinetics and conformational changes in the seconds timescales.**\n\n", "provider_node_ids": [ "90c8b0d6", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "02c9e1e3", "name": "Spatial Transcriptomics (ST)*", "original_id": "2d65deee-89c0-4a88-9a58-e056660c0a18", "description": "High-resolution spatial gene expression mapping in tissues, enabling cell interaction insights.", "documentation": "## AI Generated Documentation\n\n### Overview\nSpatial Transcriptomics (ST) is a cutting-edge technology that integrates transcriptomic analysis with spatial localization, allowing researchers to visualize and quantify gene expression within the complex architecture of tissues. This approach provides unprecedented insights into cellular interactions and the microenvironment, which are critical for understanding various biological processes and disease mechanisms.\n\n### Key Capabilities\nSpatial Transcriptomics encompasses several methodologies, primarily divided into imaging-based and sequencing-based techniques. Imaging-based methods, such as MERFISH and seqFISH, allow for direct visualization of RNA molecules in situ, achieving resolutions down to the sub-cellular level. Sequencing-based platforms, like 10x Genomics' Visium and GeoMx DSP, utilize spatially barcoded oligonucleotides to capture RNA from tissue sections, followed by high-throughput sequencing. These methods can analyze thousands of genes simultaneously while retaining spatial context, making ST distinct from traditional transcriptomics that lacks spatial resolution.\n\n### Applications\nThe applications of Spatial Transcriptomics are vast and impactful. In neuroscience, ST is instrumental in mapping brain regions, understanding neurodevelopment, and investigating neurodegenerative diseases, such as Alzheimer's. In cancer research, it elucidates tumor microenvironments, revealing how different cell types interact and contribute to tumor progression. Additionally, ST is employed in developmental biology to study tissue differentiation and organization, providing insights into embryonic development and regenerative medicine.\n\n### Advantages\nThe primary advantage of Spatial Transcriptomics is its ability to maintain the spatial organization of tissues while providing comprehensive transcriptomic data. This spatial context is essential for deciphering the complex interactions between different cell types and understanding the functional implications of gene expression patterns. Moreover, ST enables the identification of biomarkers and therapeutic targets with greater accuracy, facilitating the development of targeted therapies. By bridging the gap between gene expression analysis and tissue architecture, Spatial Transcriptomics significantly enhances our understanding of biological processes and disease mechanisms, paving the way for innovative research and therapeutic strategies.\n\n## References\n\n1. https://www.sciencedirect.com/science/article/pii/S0888754323001155\n2. https://pubmed.ncbi.nlm.nih.gov/39760243/\n3. https://pmc.ncbi.nlm.nih.gov/articles/PMC11562938/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "0c8677f6", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "3cf0830c", "name": "Spinning disk confocal microscopy (SDCM)", "original_id": "88287b12-592a-486c-84a4-03cf19f9dd62", "description": "Spinning disc confocal microscopy is one of the solutions for routine and high-performance fluorescence live-cell imaging applications. SDCM uses a series of moving pinholes on a disc to scan spots of light, in combination with a high-sensitivity camera to acquire instantaneous optical slices. Since a series of pinholes scans an area in parallel, each pinhole is allowed to hover over a specific area for a longer amount of time than on laser scanning confocals (CLSM) thereby reducing the excitation energy needed to illuminate a sample . Furthermore, cameras (often EMCCDs or sCMOS), typically have quantum efficiencies 2-3x higher than PMTs, so much less laser excitation energy is necessary and that reduces photo-toxicity and photo-bleaching of a sample, making it the preferred system for imaging live cells or organisms when optical slicing is necessary. However, optical sectioning in depth is more limited than in CLSM. This technology can be improved with image scanning mic/pixel reassignment to allow non-diffraction limited images which provide resolutions 100-200nm (check with the lab where these improvements are available).", "documentation": "## Spinning Disk Confocal Microscopy (SDCM)\n---\n**Spinning disc confocal microscopy is one of the solutions for routine and high-performance fluorescence live-cell imaging applications. SDCM uses a series of moving pinholes on a disc to scan spots of light, in combination with a high-sensitivity camera to acquire instantaneous optical slices. Since a series of pinholes scans an area in parallel, each pinhole is allowed to hover over a specific area for a longer amount of time than on laser scanning confocals (CLSM) thereby reducing the excitation energy needed to illuminate a sample . Furthermore, cameras (often EMCCDs or sCMOS), typically have quantum efficiencies 2-3x higher than PMTs, so much less laser excitation energy is necessary and that reduces photo-toxicity and photo-bleaching of a sample, making it the preferred system for imaging live cells or organisms when optical slicing is necessary. However, optical sectioning in depth is more limited than in CLSM. This technology can be improved with image scanning mic/pixel reassignment to allow non-diffraction limited images which provide resolutions 100-200nm (check with the lab where these improvements are available).**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "e532f9cb", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "e480e528", "name": "Stimulated Raman Scattering (SRS)*", "original_id": "734d9e9d-c0a3-4935-8f09-3669bcc91ffa", "description": "High-speed, label-free imaging with sub-10 nm resolution for live cells.", "documentation": "## Stimulated Raman Scattering (SRS)\n---\n**Stimulated Raman scattering (SRS) microscopy is a fast, label-free, and sensitive contrast method, able to image the distribution of a vibrational species. SRS is a nonlinear optical process that utilizes two ultrafast laser pulses (the pump and the Stokes pulses) to stimulate the excitation of a molecule into a vibrational excited state with much higher efficiency than a spontaneous Raman experiment. SRS is closely related to coherent anti-Stokes Raman scattering (CARS), because both techniques utilize the same excitation sources and provide similar chemical contrast.**\n\n## AI Generated Documentation\n\n**Overview** \nStimulated Raman Scattering (SRS) microscopy is a cutting-edge nonlinear optical imaging technique that enhances the Raman scattering signal, achieving amplification by up to 10^8 times. This technology allows for high-resolution imaging of molecular vibrations, making it a powerful tool for both biomedical and materials science applications. SRS microscopy operates by using two synchronized laser beams—the pump and Stokes beams—where the energy difference between them matches the vibrational energy of specific molecular bonds, enabling selective imaging of chemical structures without the need for fluorescent labels.\n\n**Key Capabilities** \nSRS microscopy is distinguished by its exceptional capabilities: \n- **High Chemical Sensitivity:** Capable of detecting low concentrations of analytes, making it suitable for complex biological systems. \n- **Fast Imaging Speed:** The technique allows for rapid acquisition of images, facilitating the observation of dynamic processes in real-time. \n- **Label-Free Imaging:** Unlike traditional fluorescence microscopy, SRS does not require labeling, preserving the native state of biological samples. \n- **Sub-10 nm Resolution:** SRS can achieve spatial resolutions below 10 nm, enabling detailed visualization of cellular structures and chemical compositions. \n- **3D Imaging:** The technology supports three-dimensional imaging, providing comprehensive spatial information about the sample.\n\n**Applications** \nSRS microscopy has a wide range of applications across various fields: \n- **Biomedical Imaging:** Used to visualize biological tissues, cellular components, and dynamic processes such as drug delivery and cellular metabolism. \n- **Materials Science:** Increasingly utilized for characterizing materials, studying ion transport, and analyzing the properties of nanoparticles (NPs) in diverse systems. \n- **Chemical Analysis:** Allows for quantitative imaging, providing insights into the concentration and distribution of chemical species within a sample.\n\n**Advantages** \nThe primary advantages of SRS over traditional Raman microscopy include enhanced sensitivity, speed, and the ability to perform quantitative analysis. These features make SRS microscopy a valuable tool in both research and clinical settings, paving the way for advancements in understanding complex biological and material systems. As the technology continues to evolve, its integration into various fields is expected to expand, offering new insights and capabilities in chemical imaging.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC10521017/\n2. https://www.sciencedirect.com/science/article/pii/S2590238521000680\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "64543c53" ], "abbr": "", "category": { "id": "34fb4c18-d759-423c-a670-d982f3e0955b", "name": "Label-free Imaging" } }, { "id": "f1f735b6", "name": "Stimulated emission depletion microscopy (STED)", "original_id": "a7794e81-9a6c-47fe-889d-515b60c655c8", "description": "Sub-50nm resolution, live cell imaging, selective fluorophore deactivation", "documentation": "##\n## STIMULATION EMISSION DEPLETION MICROSCOPY (STED)\n---\nStimulated emission depletion microscopy (STED) is one of the techniques that allows super-resolution microscopy. It is similar to confocal microscopy, in that is uses laser scanning imaging, however it creates super-resolved images by the selective deactivation/depletion of fluorophores in the peripheral area of the illumination PSF, minimizing the area of illumination at the focal point, and thus enhancing the achievable resolution for a given system. STED can provide 3D datasets of samples, often with resolutions down to 50 nm or less.\n\n## AI Generated Documentation\n\n**Overview** \nStimulated Emission Depletion Microscopy (STED) is a super-resolution imaging technique that enables the visualization of biological structures at resolutions below the diffraction limit of light, achieving details as fine as 50 nanometers. Developed by Stefan W. Hell and Jan Wichmann in the mid-1990s, STED has become a pivotal tool in cell biology, allowing researchers to observe dynamic processes within living cells with unprecedented clarity.\n\n**Key Capabilities** \nSTED microscopy employs two laser beams: an excitation beam that activates fluorophores and a depletion beam that selectively deactivates them in a spatially controlled manner. This dual-beam approach minimizes the effective area of fluorescence, enhancing the achievable resolution significantly. The technique can utilize a variety of standard fluorophores, such as Alexa 488 and eGFP, making it adaptable for different experimental setups. Recent advancements include the use of continuous wave lasers (CW-STED) and temporal gating techniques (gSTED), which further improve resolution while reducing phototoxicity to samples. STED is capable of both 2D and 3D imaging, allowing for comprehensive studies of cellular structures and interactions.\n\n**Applications** \nSTED microscopy is widely used in biological research to investigate cellular dynamics, protein localization, and molecular interactions. Its ability to visualize subcellular structures, such as synapses, organelles, and protein complexes, has provided critical insights into various biological processes. The technique is particularly valuable in live-cell imaging, where it can capture real-time changes in cellular morphology and function. Additionally, STED has applications in materials science for studying nanoscale structures and interactions in synthetic materials.\n\n**Advantages** \nThe primary advantage of STED over conventional microscopy techniques, such as confocal microscopy, is its ability to achieve resolutions that surpass the diffraction limit, enabling the observation of fine structural details that are otherwise invisible. This capability is crucial for advancing our understanding of complex biological systems. Furthermore, STED's compatibility with a wide range of fluorescent labels enhances its versatility, making it a preferred choice for researchers seeking to explore the intricacies of cellular architecture and dynamics. Overall, STED microscopy stands out as a powerful tool for high-resolution imaging in both biological and materials sciences, driving significant advancements in research and discovery.\n\n## References\n\n1. https://www.nature.com/articles/s43586-024-00335-1\n2. https://en.wikipedia.org/wiki/STED_microscopy\n3. https://pmc.ncbi.nlm.nih.gov/articles/PMC3635273/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "161021f6", "ca2e3748", "23f7a2fd", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "e5f30cac", "151b4761", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "ff8ab803", "name": "Structured illumination microscopy* (SIM)", "original_id": "a87d8054-b017-4bbd-8795-c3424f72d88a", "description": "Spinning disc confocal microscopy is one of the solutions for routine and high-performance fluorescence live-cell imaging applications. SDCM uses a series of moving pinholes on a disc to scan spots of light, in combination with a high-sensitivity camera to acquire instantaneous optical slices. Since a series of pinholes scans an area in parallel, each pinhole is allowed to hover over a specific area for a longer amount of time than on laser scanning confocals (CLSM) thereby reducing the excitation energy needed to illuminate a sample . Furthermore, cameras (often EMCCDs or sCMOS), typically have quantum efficiencies 2-3x higher than PMTs, so much less laser excitation energy is necessary and that reduces photo-toxicity and photo-bleaching of a sample, making it the preferred system for imaging live cells or organisms when optical slicing is necessary. However, optical sectioning in depth is more limited than in CLSM. This technology can be improved with image scanning mic/pixel reassignment to allow non-diffraction limited images which provide resolutions 100-200nm (check with the lab where these improvements are available).", "documentation": "## Structured Illumination Microscopy (SIM) \\*\n---\n**SIM belongs to the family of super-resolution microscopy techniques that allow to acquire images with higher spatial resolution than with conventional fluorescence microscopy. SIM is a camera based widefield fluorescence microscope employing a patterned illumination, e.g. stripes, to excite the fluorescence in the sample. The diffraction limited structured illumination pattern is the key element that allows to extract higher frequencies from the sample and thus achieve the improved spatial resolution. To obtain one super-resolution image, several images with shifted and rotated illumination patterns projected on the sample are acquired. The set of acquired images is then mathematically processed to reconstruct the super-resolution image. The reachable resolution improvement, both laterally and axially, is twice as better as with conventional widefield microscopy for the same wavelength. Data acquisition for one super-resolution SIM image takes from hundreds of milliseconds to seconds.**\nSIM is a versatile super-resolution technique used for a detailed imaging of cellular structures within cell monolayers or thin tissue sections. The strength of the method lies in the compatibility with a high number of standard fluorophores allowing relatively simple multi-color imaging, and in live-cell imaging friendliness in terms of acquisition speed and used laser powers (phototoxicity) . The downside of SIM compared to other super-resolution techniques (STED, SMLM) is a moderate resolution improvement and proneness to image artifacts formation.\nThere are different realizations of SIM microscopes. Euro-BioImaging nodes offer 2D-SIM, 3D-SIM and TIRF-SIM modalities on commercial setups including DeltaVision OMX, Nikon N-SIM and Carl Zeiss Elyra PS1 systems, which all use sinusoidal striped illumination.\n![](upload/SIM1.png)\n**The principle of conventional light microscopy and structurally illuminated microscopy.** To collect sufficient information, 15 structurally illuminated images in 3 angles and 5 translations per angle are acquired for 1 final reconstructed image in one particular Z-position. The reconstruction of the super-resolution (SR) image is performed in Fourier space (after Fourier transformation (Ft)) when the SR contribution from all 15 images are extracted and aligned back to the newly formed Fourier information. Then, the reverse Fourier transform (rFt) gives the final SR image.\n![](upload/SIM2.png)\n**Examples of images obtained by conventional widefield fluorescence microscopy (left) and structured illumination microscopy (right).** SIM image clearly shows improved resolution. The images of actin (green) and mitochondria (red) are presented as maximum intensity projections and were acquired on DeltaVision OMX microscope (Institute of Molecular Genetics, Czech Republic).\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "23f7a2fd", "4f1ca4db", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "a44edc42", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "f45daf6b", "name": "Super-resolution radial fluctuations (SRRF)*", "original_id": "ea7da384-0e36-432c-a4e2-89aefefd132e", "description": "Sub-100nm resolution for live-cell imaging, low phototoxicity, accessible.", "documentation": "## AI Generated Documentation\n\n**Overview** \nSuper-resolution Radial Fluctuations (SRRF) is a cutting-edge computational imaging technique that enables super-resolution microscopy, achieving lateral resolutions of 50-100 nm. This technology is particularly notable for its compatibility with live-cell imaging, allowing researchers to visualize dynamic biological processes in real-time while minimizing phototoxicity and hardware complexity. Unlike traditional super-resolution methods, SRRF does not require specialized fluorophores or high-intensity illumination, making it accessible to a broader range of laboratories. \n\n**Key Capabilities** \nSRRF operates by analyzing fluorescence intensity fluctuations in time-series images, calculating local gradient convergence (termed \"radiality\") to reconstruct sub-diffraction structures. This approach allows for the generation of super-resolution images from standard wide-field microscopy data, which is a significant advantage over other techniques such as STED or SMLM that often require complex setups. The open-source NanoJ-SRRF platform facilitates the implementation of SRRF, enabling users to optimize parameters like ring radius and radiality magnification to enhance resolution and suppress noise. Recent advancements, including enhanced SRRF (eSRRF) and variance reweighted radial fluctuations (VeSRRF), address limitations in axial resolution and artifacts in high-density structures, further expanding the capabilities of SRRF. \n\n**Applications** \nSRRF is versatile and applicable in various fields, including cell biology, neuroscience, and clinical pathology. It allows for the dynamic visualization of subcellular processes such as mitochondrial dynamics, microtubule behavior, and chromatin organization. The ability to conduct multicolor imaging in real-time opens new avenues for studying complex biological systems and interactions. \n\n**Advantages** \nThe primary advantages of SRRF include its low phototoxicity, which is crucial for live-cell imaging, and its compatibility with conventional fluorescent dyes, allowing researchers to utilize existing equipment and methods. Its accessibility through open-source software democratizes super-resolution imaging, enabling a wider range of laboratories to engage in advanced cellular imaging research. Overall, SRRF represents a significant advancement in the field of microscopy, providing powerful tools for understanding dynamic biological processes at unprecedented resolutions.\n\n## References\n\n1. https://pubmed.ncbi.nlm.nih.gov/35218543/\n2. https://link.springer.com/article/10.1007/s00418-025-02396-z\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "0c8677f6", "09122290" ], "abbr": "", "category": { "id": "c3ff3572-d01f-4f4f-abf1-ccea9cb12dfd", "name": "Fluorescence Nanoscopy" } }, { "id": "af33ff84", "name": "TEM of chemical fixed samples (TEM)", "original_id": "1fc35beb-7903-4f77-9788-59ffb0bcc6b6", "description": "In transmission electron microscopy (TEM) the accelerated beam of electrons is transmitted through the sample and collected to form an image. To achieve this the specimen is usually sectioned into ultrathin sections less than 100 nm thick. \r\nIn this particular method, the samples are fixed chemically first to prepare them for sectioning. Following chemical fixation, the samples are commonly embedded in resin \r\n", "documentation": "## Transmission EM of chemically fixed samples (TEM)\n---\n**In transmission electron microscopy (TEM) the accelerated beam of electrons is transmitted through the sample and collected to form an image. To achieve this the specimen is usually sectioned into ultrathin sections less than 100 nm thick.\nIn this particular method, the samples are fixed chemically first to prepare them for sectioning. Following chemical fixation, the samples are commonly embedded in resin blocks which are then sectioned.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "ca2e3748", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "10c95db7-304f-4c1c-9428-fe5662aa4437", "name": "Ultrastructural analysis in 2D " } }, { "id": "4ae7143c", "name": "TEM of cryo-immobilized samples (TEM cryo samples)*", "original_id": "b5c2ac56-03ec-4e59-8428-00a70446b869", "description": "In transmission electron microscopy (TEM) the accelerated beam of electrons is transmitted through the sample and collected to form an image. To achieve this the specimen is usually sectioned into ultrathin sections less than 100 nm thick. \r\nIn this method, the samples are cryo-immobilising by means of high-pressure freezing to fix them in their \"close to native\" state. Specimens then go through a process of freeze substitution where they will be stained and eventually embedded into a resin for thin sectioning and imaging in the TEM.\r\n", "documentation": "## Transmission EM of cryo-immobilized samples \\* (TEM cryo samples)\n---\n**In transmission electron microscopy (TEM) the accelerated beam of electrons is transmitted through the sample and collected to form an image. To achieve this the specimen is usually sectioned into ultrathin sections less than 100 nm thick.\nIn this method, the samples are cryo-immobilising by means of high-pressure freezing to fix them in their \"close to native\" state. Specimens then go through a process of freeze substitution where they will be stained and eventually embedded into a resin for thin sectioning and imaging in the TEM.**\n\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "d039b533", "23f7a2fd", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "2103118f", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "10c95db7-304f-4c1c-9428-fe5662aa4437", "name": "Ultrastructural analysis in 2D " } }, { "id": "ae6d3c51", "name": "TEM of immobilized particles (TEM neg stain)*", "original_id": "9f9fbf01-eb70-43ad-9e06-3f0500d48773", "description": "High-resolution TEM negative staining for biomolecules, viruses, and complexes.", "documentation": "## AI Generated Documentation\n\n**Overview** \nTransmission Electron Microscopy (TEM) using negative staining is a critical technique for visualizing biological macromolecules, viruses, and other nanoscale structures. This method enhances contrast in electron microscopy images by utilizing electron-dense stains, such as uranyl acetate, ammonium molybdate, or phosphotungstic acid, which provide high-resolution imaging of specimens that are typically challenging to visualize. \n\n**Key Capabilities** \nThe negative staining technique allows for the imaging of samples at nanometer resolution, making it suitable for a wide range of biological applications. The process involves applying a small volume of sample suspension to a glow-discharged electron microscopy grid, which is then treated with heavy metal salts to create a contrasting background. This method is particularly effective for larger proteins, protein aggregates, filaments, fibers, membrane vesicles, bacteria, and viruses. The typical resolution achieved can be around 1-2 nm, depending on the sample and staining conditions. \n\n**Applications** \nNegative staining is extensively used in structural biology to study: \n- Purified subcellular components (e.g., ribosomes, mitochondria) \n- Isolated macromolecules and protein complexes (e.g., cytoskeletal components) \n- In vitro reconstituted complexes and assemblies \n- Viruses and bacteriophages \n- Filaments such as actin and microtubules \nAdditionally, negative staining can be combined with immunostaining techniques to identify specific antigens on the specimen surface, allowing for detailed studies of biological interactions and structures. \n\n**Advantages** \nThe primary advantages of TEM negative staining include its simplicity and speed, making it one of the quickest methods for specimen preparation. It provides high-contrast images essential for analyzing the structural details of biological macromolecules at nanometer resolution. Compared to other techniques like cryo-electron microscopy, negative staining is less technically demanding and more accessible, making it a preferred choice for many researchers in the field of structural biology. Overall, the TEM negative staining technique is a powerful tool that enhances our understanding of cellular processes and molecular interactions.\n\n## References\n\n1. https://caic.bio.cam.ac.uk/electron-microscopy/tem/tem-applications/transmission-electron-microscopy-tem-applications\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC2978762/\n3. https://www.unige.ch/medecine/pfmu/en/techniques/techniques-and-methods/negative-staining-tem\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "0c8677f6", "2103118f" ], "abbr": "", "category": { "id": "10c95db7-304f-4c1c-9428-fe5662aa4437", "name": "Ultrastructural analysis in 2D " } }, { "id": "b4d963a5", "name": "Terahertz Plant Imaging (THzI)*", "original_id": "cdaf4b67-111d-4cb4-b14b-7a9822baf5b6", "description": "Non-invasive THz imaging for plant hydration, quality assessment, high resolution.", "documentation": "## TeraHertz Plant Imaging\n---\n**TeraHertz Imaging consists in illuminating an object with a pulsed terahertz radiation and capturing the response through an array of sensors in the same spectral region.**\nIn the THz region, a photon carries a very small energy when compared with the ionization energy of atoms, which is why it is a totally safe technology that poses no risk to biological organisms. In addition, the very long wavelength (a fraction of a millimeter) makes it possible to strongly limit scattering processes due to the presence of small particles in the sample.\nIn contrast, this radiation is strongly absorbed by some molecules and, in particular, by water. This is why it is an ideal technology for observing both dry objects and very thin objects. Plant leaves are elements that are very well observed in this region.\nThis method makes it possible to monitor the amount of water in the leaves or major leaf districts, even on the same leaf as a function of time. This allows, for example, early detection of any signs of leaf water stress to enable precision irrigation. See for example: “[Non-invasive absolute measurement of leaf water content using terahertz quantum cascade lasers](https://doi.org/10.1186/s13007-017-0197-z)”\nIn addition, the method is suitable, for example, to study the effect of the presence of ozone in the air on the plants or the interaction with hormones such as abscisic acid (ABA).\nMoreover, it has been used for the quality assessment of dry fruits like chestnuts and hazelnuts. See for example “[Detection of fungal infections in chestnuts: a terahertz imaging-based approach](https://doi.org/10.1016/j.foodcont.2020.107700)“\nTeraHertz Plant Imaging is provided by the [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) and by [Flanders BioImaging Node](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node).![](upload/Teraherz.png)\n*THz leaf measurement method; B) THz transmission measurement setup. From* *[https://doi.org/10.3390/s19224...](https://doi.org/10.3390/s19224838)*\n\n## AI Generated Documentation\n\n**Overview** \nTerahertz Plant Imaging (THzI) is an innovative imaging technology that utilizes terahertz (THz) radiation to non-invasively analyze plant materials. Operating within the frequency range of 0.1 to 10 THz, THzI leverages the unique properties of THz waves, which are non-ionizing and safe for biological specimens. This makes it particularly suitable for studying living organisms without causing any harm. \n\n**Key Capabilities** \nTHzI employs pulsed terahertz radiation to illuminate plant samples, capturing the response through an array of sensors. The imaging system typically includes high-efficiency antennas such as planar patch, photoconductive, and dielectric-resonator types, designed for optimal performance in the THz range. Image reconstruction algorithms, including back-projection and compressed sensing techniques, enhance spatial resolution and image quality. The technology is capable of achieving high-resolution imaging, allowing researchers to observe fine details in plant structures, with lateral dimensions of a few centimeters. \n\n**Applications** \nTHzI has a diverse range of applications in plant research, including: \n- **Monitoring Leaf Water Stress**: The technology can assess the hydration status of plants, which is vital for understanding their health and stress responses. \n- **Quality Assessment of Dried Fruits**: THzI can differentiate between healthy and defective dried fruits, such as chestnuts and hazelnuts, by detecting internal moisture levels and structural integrity. \n- **Real-Time Imaging**: The rapid acquisition capabilities of THzI allow for its integration into industrial production lines, facilitating continuous quality control. \n\n**Advantages** \nThe advantages of THzI include: \n- **Non-invasive Nature**: As a non-ionizing technique, THzI poses no risk to living tissues, making it ideal for biological applications. \n- **High Spatial Resolution**: The technology can achieve high-resolution imaging, allowing researchers to observe fine details in plant structures. \n- **Minimal Scattering**: The long wavelengths of THz radiation reduce scattering effects from small particles, enhancing image clarity. \n\nIn summary, Terahertz Plant Imaging represents a cutting-edge approach in plant biology, combining safety, efficiency, and high-resolution capabilities to advance research and applications in agriculture and food quality assessment. Its ongoing development promises to unlock further potential in understanding plant physiology and improving crop management practices.\n\n## References\n\n1. https://link.springer.com/article/10.1007/s11468-022-01775-9\n2. https://www.nature.com/collections/cgidgbfcjc\n3. https://www.eurobioimaging.eu/news/terahertz-imaging-portable-plant-imaging/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "d2be2f9c" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "f05d797c", "name": "Tissue Clearing (TC)*", "original_id": "b04dba6f-7eb1-43d9-9761-e9f5e99ec138", "description": "The restitution of 3D images from samples becomes a major challenge for visualizing, exploring, analyzing and quantifying. The major problem with samples is their intrinsic composition which prevents correct observation. Tissue clearing is a set of chemical procedures to render biological tissues transparent (as opposed to translucent), reducing light scattering and thereby allowing imaging in depths which would otherwise be impossible with fresh or live tissues. Tissue clearing is most commonly used on large \"mesoscopic\" samples (>1mm) which are then imaged with lightsheet microscopy, but can also be used to great advantage for smaller samples, such as those used in confocal or two-photon microscopy. \r\n\r\nA wide variety of different protocols for tissue clearing exist and are offered by the Euro-BioImaging Nodes, such as CUBIS, Rapiclear, X-Clarity, BABB, and SCALE. The Nodes offering these techniques provide access to the required chemicals and materials for the clearing protocol, as well as expertise in the protocols.", "documentation": "## Tissue Clearing\\* (TC)\n---\n**The restitution of 3D images from samples becomes a major challenge for visualizing, exploring, analyzing and quantifying. The major problem with samples is their intrinsic composition which prevents correct observation. Tissue clearing is a set of chemical procedures to render biological tissues transparent (as opposed to translucent), reducing light scattering and thereby allowing imaging in depths which would otherwise be impossible with fresh or live tissues. Tissue clearing is most commonly used on large \"mesoscopic\" samples (>1mm) which are then imaged with lightsheet microscopy, but can also be used to great advantage for smaller samples, such as those used in confocal or two-photon microscopy.**\nA wide variety of different protocols for tissue clearing exist and are offered by the Euro-BioImaging Nodes, such as CUBIS, Rapiclear, X-Clarity, BABB, and SCALE. The Nodes offering these techniques provide access to the required chemicals and materials for the clearing protocol, as well as expertise in the protocols.\n\n", "provider_node_ids": [ "522e8aaa", "638ca876", "90c8b0d6", "1fa342de", "9c8d648e", "0c8677f6", "fc1893d4", "64543c53", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "8399c5a7", "name": "Total internal reflection fluorescence microscopy (TIRF)", "original_id": "37e7478b-3725-481f-bec3-07ea6a0bd4b2", "description": "Total internal reflection fluorescence microscopy (TIRF) is a microscopy technique with which a thin region of the cell, usually less than 200nm can be observed. A TIRF microscope uses an evanescent wave to selectively illuminate and excite fluorophores in a restricted region of the specimen immediately adjacent to the glass-water interface. The evanescent wave is generated only when the incident light is totally internally reflected at the glass-water interface. The evanescent electromagnetic field decays exponentially from the interface, and thus penetrates to a depth of only approximately 100 nm into the sample medium. Thus the TIRF microscope enables a selective visualization of surface regions such as the basal plasma membrane (which are about 7.5 nm thick) of cells. This technique is often used also for observing molecular dynamics in vitro, or study the details of cell locomotion or adhesion to substrata.", "documentation": "## TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY (TIRF)\n---\nTotal internal reflection fluorescence microscopy (TIRF) is a microscopy technique with which a thin region of the cell, usually less than 200nm can be observed. A TIRF microscope uses an evanescent wave to selectively illuminate and excite fluorophores in a restricted region of the specimen immediately adjacent to the glass-water interface. The evanescent wave is generated only when the incident light is totally internally reflected at the glass-water interface. The evanescent electromagnetic field decays exponentially from the interface, and thus penetrates to a depth of only approximately 100 nm into the sample medium. Thus the TIRF microscope enables a selective visualization of surface regions such as the basal plasma membrane (which are about 7.5 nm thick) of cells. This technique is often used also for observing molecular dynamics in vitro, or study the details of cell locomotion or adhesion to substrata.\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "638ca876", "90c8b0d6", "2b34e271", "e532f9cb", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "a44edc42", "e5f30cac", "2103118f", "151b4761", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "0534020c", "name": "Traction Force Microscopy (TFM)*", "original_id": "ba698105-938d-4a8e-a6d8-a1fe602fe506", "description": "Traction Force Microscopy (TFM) has been extremely useful in the field of mechanobiology where it is applied to locally track the forces that cells exert on a particular substrate. Experiments can be performed in many cell types and even as a function of time where we can track the effects of drugs, mutations, etc.\r\nTo perform TFM small beads are commonly embedded in the substrate that the cells are plated on and the displacement of the beads due to the forces the cells exert is traced. Combining this displacement with data on the substrate, such as its stiffness as measured by AFM, allows the calculation of total forces produced. \r\nIn high or super-resolution mode, TFM can provide detailed force maps with sub-cellular resolution.\r\n", "documentation": "## Traction Force Microscopy (TFM)\\*\n**Traction Force Microscopy (TFM) has been extremely useful in the field of mechanobiology where it is applied to locally track the forces that cells exert on a particular substrate. Experiments can be performed in many cell types and even as a function of time where we can track the effects of drugs, mutations, etc.**\nTo perform TFM small beads are commonly embedded in the substrate that the cells are plated on and the displacement of the beads due to the forces the cells exert is traced. Combining this displacement with data on the substrate, such as its stiffness as measured by AFM, allows the calculation of total forces produced.\nIn high or super-resolution mode, TFM can provide detailed force maps with sub-cellular resolution.\n\n", "provider_node_ids": [ "46ccfb38", "fc1893d4", "64543c53" ], "abbr": "", "category": { "id": "d3c4396b-8a19-4414-b4a8-a08477ce23bb", "name": "Sample characterisation" } }, { "id": "2fa1c4a2", "name": "Two-photon microscopy (2P)", "original_id": "5aa5d287-4bba-404e-8d4a-28c4d6848b12", "description": "Multiphoton microscopy - most commonly in the form of two-photon microscopy - is a fluorescence imaging technique that allows observation of living tissue up to about one millimeter in depth. It uses pulsed red-shifted excitation laser light, which can also excite visible fluorescent dyes. However, for each excitation, two (or three) photons of low energy infrared light are absorbed “simultaneously” to provide the required energy for electrons in the fluorophore to reach the excited state. Using infrared light minimizes scattering in the tissue and allows imaging deeper than is possible with common confocal microscopes. Due to the localized multiphoton absorption effect, the background signal is strongly suppressed and a pinhole is not required in front of the detector (PMTs). Both effects lead to an increased penetration depth for these microscopes. Two-photon microscopy is often used to image intravitally, and it may facilitate imaging of unlabelled tissues, using autofluorescence or SHG (second harmonic generation).", "documentation": "## Two-photon microscopy (2P)\n---\n**Multiphoton microscopy - most commonly in the form of two-photon microscopy - is a fluorescence imaging technique that allows observation of living tissue up to about one millimeter in depth. It uses pulsed red-shifted excitation laser light, which can also excite visible fluorescent dyes. However, for each excitation, two (or three) photons of low energy infrared light are absorbed “simultaneously” to provide the required energy for electrons in the fluorophore to reach the excited state. Using infrared light minimizes scattering in the tissue and allows imaging deeper than is possible with common confocal microscopes. Due to the localized multiphoton absorption effect, the background signal is strongly suppressed and a pinhole is not required in front of the detector (PMTs). Both effects lead to an increased penetration depth for these microscopes. Two-photon microscopy is often used to image intravitally, and it may facilitate imaging of unlabelled tissues, using autofluorescence or SHG (second harmonic generation).**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "e532f9cb", "1fa342de", "161021f6", "ca2e3748", "23f7a2fd", "4f1ca4db", "b19711d3", "9c8d648e", "46ccfb38", "0c8677f6", "fc1893d4", "9beefd47", "64543c53", "e5f30cac", "f1099f78", "09122290", "c4b25263", "66b1f7ec" ], "abbr": "", "category": { "id": "d7736e6e-52c6-4311-b304-dc70b8aa6431", "name": "Fluorescence Microscopy" } }, { "id": "a6cee2e2", "name": "Voltage/pH/Ion Imaging *", "original_id": "b3cba508-6160-43ca-9731-a26e9042447e", "description": "Real-time imaging of voltage, pH, and ions in live cells with high sensitivity.", "documentation": "## Voltage PH-Ion Imaging\nContent coming soon....\n\n## AI Generated Documentation\n\n**Overview** \nVoltage/pH/Ion Imaging is a cutting-edge bioimaging technology designed to visualize and quantify electrical activity, pH levels, and ion concentrations in living cells. This technology leverages advanced fluorescent dyes and genetically encoded sensors that respond to specific ionic changes or voltage fluctuations, providing critical insights into cellular dynamics and physiological processes.\n\n**Key Capabilities** \nThe technology employs ratiometric imaging techniques, which allow for precise quantification of ion concentrations by measuring fluorescence intensity ratios across different wavelengths. This method enhances accuracy compared to non-ratiometric approaches, enabling researchers to obtain absolute measurements of intracellular ions such as calcium, sodium, and potassium, as well as pH levels. Voltage-sensitive dyes, often derived from engineered rhodopsins, facilitate the monitoring of membrane potential changes with high temporal resolution, making it possible to track rapid electrical events in neurons and other excitable cells.\n\n**Applications** \nVoltage/pH/Ion Imaging finds extensive applications across various fields of biological research. In neuroscience, it is instrumental in mapping neuronal activity and understanding synaptic transmission dynamics. In pharmacology, it aids in investigating the effects of drugs on cellular ion homeostasis and pH regulation, providing insights into mechanisms of action and potential side effects. Additionally, this technology is crucial in cancer research, where it helps elucidate the ionic imbalances within tumor microenvironments and their implications for disease progression and treatment efficacy. Furthermore, advancements in pH-sensitive fluorescent proteins have expanded its use in monitoring organelle-specific pH changes, particularly in mitochondria, which are essential for understanding metabolic processes.\n\n**Advantages** \nThe distinct advantages of Voltage/pH/Ion Imaging include its non-invasive nature, allowing for real-time monitoring of live cells without disrupting cellular integrity. The high sensitivity and specificity of the fluorescent probes enable the detection of subtle changes in ion concentrations and pH levels, which are critical for understanding various physiological and pathological processes. Recent advancements have also improved the photostability and multiplexing capabilities of these sensors, allowing simultaneous imaging of multiple ions or parameters, thus enhancing the depth of analysis in complex biological systems. Overall, Voltage/pH/Ion Imaging is a powerful tool that significantly contributes to our understanding of cellular function and disease mechanisms, paving the way for innovative therapeutic strategies.\n\n## References\n\n1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10375888/\n2. https://probes.bocsci.com/resources/ion-imaging-definition-principles-benefits-dyes-and-uses.html\n3. https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2023.1339518/full\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "0c8677f6", "fc1893d4", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "f1991fd9-386e-43ff-b968-81a55df3af19", "name": "Functional Imaging and specialised methodologies" } }, { "id": "c83c6c2b", "name": "ex-vivo micro-CT", "original_id": "83943538-8a06-4e80-888f-3ff98b741c9f", "description": "High-resolution 3D imaging of excised tissues, sub-10µm resolution, vascular studies.", "documentation": "## X-rays Computed Tomography (CT)\n---\n**X-rays Computed Tomography (CT) makes use of X-ray images (projections) taken from different angles and image reconstruction techniques to produce anatomic cross-sectional (tomographic) 3D  images. CT contrast agents (usually based on Iodine, Barium, Gold) can be used to enhance the contrast.**\nIn microCT, the instrumentation is implemented with accessories or with a technical set-up which provides optimum resolution and sensitivity for small animal studies.\nThe spatial resolution of microCT is higher with respect to clinical CT and typically the voxel size is lower than 100 mm for *in vivo* imaging and even smaller (less than 10 mm) for *ex-vivo* sample imaging. In order to achieve high spatial resolution a microfocus X-ray source is installed on microCT scanners.\nAnother difference with respect to clinical CT scanners is the use of flat panel detectors (FPD) with small pixel sizes (less than 100 mm) instead of curved detectors arrays. The use of a FPD results in a cone beam acquisition geometry. In this case, dedicated image reconstruction algorithms, such as the Feldkamp filtered back projection (FBP) algorithm, are needed.\nPreclinical microCT systems can be stand alone or integrated with other modalities like optical or nuclear medicine imaging in order to perform multimodal imaging.  microCT devices can be also found in small animal radiotherapy systems for animal positioning and treatment planning.\n**At Euro-BioImaging, preclinical and ex-vivo CT is provided by the following Nodes:**\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Hungary: Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n### Use cases\nClick here for\n[Use Cases](/content/use-cases/#CT) from our Nodes.\n## Dual energy CT\nDual energy CT (DECT) was firstly introduced in 1976 with the main\ngoal of obtaining the photoelectric and Compton components of the\nabsorption coefficients using a polychromatic x-ray beam with\ndifferent energies. These two components are respectively proportional\nto atomic number (Z) and density of the material (r) (R.E. Alvarez and\nE. Macovski, “Energy-selective reconstructions in X-ray computerized\ntomography”,\n).\nBy using DECT acquisitions it is thus possible to obtain rZ maps to\ngain material-specific information at each voxel as shown in the\nfigure below.\n![](upload/microCT.png)\nDECT imaging enables quantitative, 3D mapping of extrinsic contrast\nagents (iodine, red; gold, green) and soft tissues (gray) (from\n).\nA significant boost of DECT came in 2006 with the introduction of dual\nsource CT. In this case two x-ray tubes operating at different tension\nare orthogonally mounted in the gantry and both high and low tension\nimages are acquired (axial or spiral mode) at the same time, reducing\nartifacts induced by movement (T.G. Flohr et al. “First performance\nevaluation of a dual-source CT (DSCT) system”,\n).\n## Photon counting CT\nCurrent CT scanners are mostly based on scintillator energy\nintegrating detectors and it is thus not possible to gain information\nabout the energy of the detected x-ray photons. Photons counting\ndetectors (PCD) were firstly introduced for nuclear medicine imaging\nmodalities and their application for x-ray CT was limited by the low\ndetector rate PCD can handle.  However, considering also the\ndevelopments of DECT, there has been a significant research interest\nin improving their material composition and reading electronics.\nA PCD is made of a semiconductor (e.g. Cadmium Telluride) where the\ninteraction with the incoming x-ray generates positive and negative\ncharges proportional to the energy of the incoming photons. Different\nsignal thresholds corresponding to different energy values can be set\nin order to divide the detected transmitted x-ray spectrum into\ndifferent energy bins.\nThe use of PCD is particularly important for DECT as shown in the\nfigure below, where DECT imaging of a mouse using PCD is presented. In\nthis example, material decomposition into three basis materials was\nperformed.\n![](upload/microCT1.png)\nExample of photon-counting CT in a mouse. Material decomposition was\nperformed into iodine (red), photoelectric effect (PE, green), and\nCompton scattering (gray) (from\n)\n## K-Edge subtraction CT\nIn subtraction X-ray imaging, tissue structures or organs are\nvisualized using a contrast medium and measuring the changes in the\nattenuation between the contrasted structure and the surrounding\ntissue. In K-edge subtraction (KES) imaging, two X-ray images are\ntaken at different mean energies, slightly below and a bit above the\nK-edge of the contrast agent photoelectric absorption. Their\nsubtraction generates an image only displaying the contrasted\nstructure.\nSo far, this method mostly relies on monochromatic X-rays produced at\nlarge synchrotron facilities.\nKES allows to differentiate similarly absorbing substances in contrast\nenhanced CT, such as for example commonly used iodine contrast agents\nand calcium which is typically seen in calcifications, kidney stones\nand bones.\n## Phase contrast CT\nOne of the main limitations of CT is the poor contrast of low Z\nmaterials, e.g. soft tissues, because of similar X-ray absorption. In\norder to solve this problem the diffraction and refraction of the\nX-rays can be exploited to obtain more information about the structure\nof the object. This technique is called Phase Contrast Imaging. See\nPhase Contrast CT Imaging for more information\n[here](/service/phase-contrast-imaging-PCI).\n\n## AI Generated Documentation\n\n**Ex-Vivo Micro-CT: Detailed Overview** \nEx-vivo micro-computed tomography (micro-CT) is a sophisticated imaging technology designed for high-resolution, three-dimensional visualization of biological samples that have been excised from living organisms. This technique is particularly valuable in biomedical research, where it facilitates the detailed study of tissue architecture, vascular structures, and biomaterials without the limitations imposed by live imaging. \n\n**Key Capabilities** \nEx-vivo micro-CT systems are characterized by their ability to achieve voxel resolutions as fine as 1-10 micrometers, enabling researchers to capture intricate details of biological structures. These systems operate with longer scan times, allowing for higher radiation doses that improve signal-to-noise ratios and overall image quality. Notable systems, such as Bruker’s Skyscan 1272 and 1273, utilize higher energy X-rays to effectively image denser biological materials, including bone and soft tissues, while specialized techniques like microangioCT employ novel contrast agents to visualize microvascular networks in unprecedented detail. \n\n**Applications** \nThe applications of ex-vivo micro-CT are extensive and include: \n- **Tissue Analysis**: Endpoint studies of excised organs (e.g., lungs, tumors) to assess pathological changes or treatment effects. \n- **Vascular Imaging**: Utilizing advanced contrast agents for detailed visualization of blood vessels, enabling studies of angiogenesis and vascular integrity. \n- **Material Studies**: Evaluation of biomaterials and implants, assessing integration and structural performance in biological environments. \n\n**Advantages** \nEx-vivo micro-CT offers several distinct advantages over in-vivo imaging techniques: \n- **Higher Spatial Resolution**: The ability to achieve finer imaging details makes it ideal for studying small anatomical features and complex structures. \n- **Flexibility in Sample Preparation**: Researchers can manipulate and prepare samples extensively without the constraints of maintaining life functions, allowing for more complex experimental designs. \n- **Correlative Analysis**: The imaging data can be integrated with subsequent morphological studies, providing a comprehensive understanding of the sample’s structure and function. \n\nIn conclusion, ex-vivo micro-CT is an essential tool in preclinical research, enabling detailed insights into biological structures and processes, with broad applications in tissue engineering, regenerative medicine, and material science.\n\n## References\n\n1. https://www.bruker.com/en/news-and-events/webinars/2020/ex-vivo-microangioct-advances-in-microvascular-imaging.html\n2. https://www.microphotonics.com/what-is-the-difference-between-in-vivo-micro-ct-and-ex-vivo-micro-ct-scanning/\n3. https://www.raycisionglobal.com/products/ex-vivo-micro-ct-imaging-system/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "23f7a2fd", "6319df36", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "cf8f008b", "d2be2f9c", "64543c53", "706cb740", "2103118f", "f1099f78" ], "abbr": "", "category": { "id": "3b54df7f-9def-4570-8dcf-fc2eeb4ad891", "name": "ex-vivo and materials imaging using biomedical technologies\r\n\r\n" } }, { "id": "4e2f1176", "name": "immunolabeling on immobilized particles (immunolocal)*", "original_id": "19b3c78b-8991-4054-acba-3a5c370f4f9c", "description": "High-resolution immunolocalization via oriented antibody immobilization for diagnostics.", "documentation": "## AI Generated Documentation\n\n**Overview** \nImmunolabeling on immobilized particles, or immunolocal, is a cutting-edge technique that enhances the localization and quantification of specific proteins within biological samples. This method involves the strategic immobilization of antibodies onto solid substrates or particles, which allows for precise detection and analysis of target antigens in various biological contexts. By ensuring optimal orientation of the antibodies, immunolocal maximizes binding efficiency and sensitivity, making it a powerful tool in both research and clinical diagnostics.\n\n**Key Capabilities** \nThe primary technical capability of immunolocal is its ability to achieve high specificity and sensitivity in immunoassays. The technique employs site-specific conjugation methods that allow antibodies to be immobilized in a manner that preserves their functional integrity. This is crucial for maintaining the antigen-binding sites in an accessible orientation, which significantly enhances the performance of immunoassays. Additionally, the use of heterofunctional matrices provides a versatile platform that can be tailored for different applications, allowing for the detection of a wide range of analytes.\n\n**Applications** \nImmunolocal is utilized across various fields, including: \n- **Biomedical Research**: For studying protein localization in cells and tissues, which is essential for understanding cellular functions and disease mechanisms. \n- **Clinical Diagnostics**: In the detection of biomarkers related to diseases such as cancer and infectious diseases, facilitating early diagnosis and treatment monitoring. \n- **Biosensing**: Development of immunosensors that can detect food contaminants, pathogenic bacteria, and other critical analytes with high specificity and sensitivity.\n\n**Advantages** \nThe advantages of immunolocal include: \n- **Enhanced Sensitivity**: The controlled orientation of antibodies leads to improved binding efficiency, allowing for the detection of low-abundance targets. \n- **Versatility**: The technique can be adapted for various types of analytes and integrated into different imaging modalities, including fluorescence and electron microscopy. \n- **Cost-Effectiveness**: The use of heterofunctional matrices allows for the creation of economical immuno-platforms while maintaining high performance. \nIn summary, immunolabeling on immobilized particles is a distinct and valuable technology that significantly advances the capabilities of protein detection and localization in both research and clinical settings.\n\n## References\n\n1. https://www.sciencedirect.com/science/article/pii/S0003267021007339\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC8836139/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "0c8677f6", "2103118f" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "59a33aed", "name": "in vivo optical imaging (OI)", "original_id": "023df2e2-aff0-419e-a099-7252852ebe9d", "description": "Non-invasive, high-resolution imaging of live biological processes using light.", "documentation": "## In vivo optical imaging (OI)\n---\n**Optical Imaging uses non ionizing radiation such as visible, ultraviolet, and infrared light to obtain detailed images of organs and tissues as well as smaller structures including cells and even molecules. A variety of bioluminescent and/or fluorescent probes can be used, each targeted to a specific tissue or molecular or cellular event.**\nOptical Imaging is particularly useful for visualizing cells that have been engineered to express reporter genes, provided that they are located not too deep in the body.\nMost preclinical applications are in oncology and neuroscience research, but optical imaging is also used for cardiovascular studies and to monitor gene therapy, infectious diseases, inflammation, metabolic diseases and drug metabolism.\nBioluminescence Imaging of a lung tumor mouse model (courtesy of San Raffaele Hospital, Molecular Imaging Italian Node)\nWithin Euro-BioImaging, preclinical in vivo optical Imaging is provided by the following Nodes:\n[• Austria BioImaging Node / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n[• Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n[• Center for Advanced Preclinical Imaging, CAPI (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n[• Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n[• Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n[• Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n[• Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n[• DIMP Neuromed Node (IT)](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n[• Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n[• Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n[• NORMOLIM (NO)](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n[• PRIME Node (NL)](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/content/use-cases/#OI) from our Nodes.\n## Fluorescence in vivo Imaging (NIR I, NIR II)\nIn vivo Fluorescence imaging is based on the detection of fluorescence\nemitted by fluorescent reporters either in Near InfraRed I (NIR I,\nwavelength range 700-900 nm) or in Near InfraRed II (NIR II, or SWIR -\nShort Wave InfraRed - wavelength in the range 1000-2000 nm) in living\nlaboratory animals, most usually mice.\nThe NIR I \"optical window\" covers regions where light is not much\nabsorbed by hemoglobin and water, thus allowing the signal coming from\ninner organs to be detected. The low autofluorescence of skin and\nurine results in a good ratio of signal to background.\nFluorescence is usually emitted by NIR I dyes linked to tracked\nmolecules or particles but NIR I proteins have also been developed.\nThe optical window for in vivo optical imaging in NIR II can even\nincrease the benefits with respect to imaging in NIR I. In fact,\nalthough absorption of light by water is higher than in NIR I, lower\nscattering and lower autofluorescence enable the visualization of fine\nstructures such as e.g. blood vessels with a better quality. The\ndrawback of NIR II in vivo imaging is the small number of\nbiocompatible fluorophores and commercially available optical imagers.\nSee also: M. Hassan and B.A. Klaunberg, “Biomedical applications of\nfluorescence imaging in vivo”, [https://www.ingentaconnect.com/content/aalas/cm/2004/00000054/00000006/art00006](https://www.ingentaconnect.com/content/aalas/cm/2004/00000054/00000006/art00006#)\n**Available at:**\n[• CAPI Node](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n[• Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n[• Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n[• Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n[• NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n[• Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Bioluminescence Imaging (BLI)\nBioluminescence Imaging is based on the detection of light emitted by\nenzymes (e.g. luciferase) transfected (or transducted) to laboratory\ncell lines or animals from other organisms, for example fireflies.\nInteraction of the enzymes with their substrates is needed for light\nemission: for this reason, substrates are injected into the animal or\nadded to cultivation media before the imaging session.\nThe bioluminescence signal is relatively low compared to fluorescence,\nbut the background is limited to digital noise and therefore the signal\nto noise ratio can be excellent. Example applications of BLI are the\ntracking of stem cells or viability of tissues transplanted from animals\nexpressing bioluminescent enzymes into non-luminescent animals, in vivo\nstudies of infection (with bioluminescent pathogens) and cancer\nprogression (e.g. using bioluminescent cancer cell lines).\nSee for example: P.E. Almeida et al., “In vivo bioluminescence for\ntracking cell fate and function”,\n; M. Hutchens and G.D. Luker “Applications of bioluminescence imaging\nto the study of infectious diseases”,\n; N. Alsawaftah et al., “Bioluminescence Imaging Applications in\nCancer: A Comprehensive Review”,\n\nLight can also be produced by chemical reactions in living bodies\n(chemiluminescence). An example is the reaction of luminol with hydrogen\nperoxide which can be used in vivo for the localization of infiltrated\nneutrophils by monitoring the activity of myeloperoxidase ().\n**Available at:**\n* [CAPI Node](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Flanders BioImaging Node](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Cerenkov Radiation Imaging and Radio Luminescence Imaging\nCerenkov radiation is a blue light emitted when charged particles (e.g. electrons) move through dielectric materials faster than light. Sensitive optical imagers can localize therapeutic isotopes emitting Cerenkov radiation, for example Yttrium-90 or Terbium-161, in small animals. No significant changes in imaging procedures are required for Cerenkov Imaging, other than replacing injection of a bioluminescent substrate with that of a radiotracer.\nCerenkov and RadioLuminescence Imaging can be used to image the spatial distribution and concentration of therapeutic radionuclides, visualize gene expression, imaging guided surgery at preclinical level.\nSee also:\n* D.L.J. Thorek et al., “Cerenkov imaging - a new modality for molecular imaging” \n* Spinelli AE, Boschi F. “Novel biomedical applications of Cerenkov radiation and radioluminescence imaging” \n* F. Boschi et al., “Optical emission of 223Radium: in vitro and in vivo preclinical applications” \n![](upload/ivoi1.png)\nExample of whole body CLI image reconstructed using the multi spectral Cerenkov luminescence tomography approach. As shown on the picture on the right, it is possible to clearly distinguish the internal organs in the animal abdomen. \n**Available at:**\n- [CAPI Node](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n- [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Optical Coherence Tomography (OCT)\nOptical Coherence Tomography (OCT) uses scattering contrast. When light impinges upon layered structures, backscattered light from interfaces in the sample interferes with a reference light beam, forming modulated interferogram, which can in turn lead to the reconstruction of inner structures of biological samples in vivo. By using wideband low coherence light sources, OCT can achieve subcellular spatial resolution as well as high temporal resolution. In addition to structural imaging, an extension of OCT, namely OCT angiography (OCTA), can produce contrast based on speckle or phase variance, which has seen increasing applications in ophthalmology () and dermatology ().\n![](upload/ivoi2.png)\nmicro-OCT Imaging of corneal scar in an animal model ()\nAvailable at:\n* [Austrian BioImaging / CMI](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Imaging guided surgery\nDuring tumor resection, clear differentiation between normal and cancerous tissues is critical for increasing the negative margin rates. The difference in fluorescence intensity between the normal and cancer tissues can be enhanced by the use of fluorescent probes targetting the tumor of interest, making it easier to distinguish cancer tissue from normal tissue during intervention.\nSee for example:\n* K. Teranishi, “Near-Infrared Fluorescence Imaging of Renal Cell Carcinoma with ASP5354 in a Mouse Model for Intraoperative Guidance” \n* A.Pagoto et al. “Novel Gastrin-Releasing Peptide Receptor Targeted Near-Infrared Fluorescence Dye for Image-Guided Surgery of Prostate Cancer” \n\n## AI Generated Documentation\n\n**Overview:** In vivo optical imaging (OI) is a cutting-edge, non-invasive imaging technology that utilizes light to visualize biological processes in real time within living organisms. This technique is particularly advantageous in preclinical research, allowing for the monitoring of disease progression, therapeutic efficacy, and molecular interactions in small animal models. OI encompasses various modalities, including fluorescence and bioluminescence imaging, which provide unique insights into cellular and molecular dynamics.\n\n**Key Capabilities:** In vivo OI employs advanced techniques such as fluorescence imaging, which utilizes fluorescent probes that emit light upon excitation, and bioluminescence imaging, which relies on naturally occurring light from biochemical reactions. These methods can achieve high spatial resolution and depth penetration, enabling detailed observations of biological structures and functions. Technologies like two-photon microscopy and multispectral imaging further enhance the capabilities of OI, allowing researchers to visualize complex interactions at the cellular level with minimal invasiveness.\n\n**Applications:** The applications of in vivo OI are extensive and include cancer research, neurobiology, and cardiovascular studies. For example, it is used to track tumor growth, assess drug delivery mechanisms, and monitor the biological effects of therapies in real time. In neuroscience, OI enables the visualization of hemodynamic changes and neuronal activity, providing insights into brain function and disorders. Additionally, OI is increasingly applied in studies of infectious diseases, allowing for the observation of pathogen dynamics in live models.\n\n**Advantages:** One of the primary advantages of in vivo OI is its high sensitivity and specificity without the use of ionizing radiation, making it a safer alternative to other imaging modalities like MRI or PET. The technology is also relatively cost-effective and allows for longitudinal studies, enabling researchers to image the same subjects over time to observe changes and responses to treatment. Overall, in vivo optical imaging is a versatile and essential tool in modern biomedical research, offering unique insights into the dynamic processes of living organisms while maintaining a non-invasive approach.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC6776895/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC2435254/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "6e382796", "ca2e3748", "e0395c6a", "23f7a2fd", "6319df36", "3850f7eb", "0c8677f6", "fc1893d4", "9beefd47", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53", "706cb740" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "3744dad8", "name": "intravital microscopy (IVM-med)", "original_id": "1633170f-80fe-42cb-943b-8c2771644601", "description": "Real-time in vivo imaging with dual-mode confocal/two-photon, 100 fps.", "documentation": "## Intravital microscopy (IVM)\n---\n**Intravital imaging covers a range of microscopy modalities used for the long term imaging of living animal models (e.g. zebrafish larvae, mice, rats), in various organs or tissues, or as a whole for smaller models. Intravital Imaging can be performed using 2-photon microscopy, light-sheet microscopy or others. The choice is usually made based on the required penetration depth and resolution. These techniques can be combined with optical manipulation systems, such as laser ablation or optogenetic manipulation systems, and also with a range of e.g. neurological or behavioral stimuli especially when awake, immobilized animals are imaged.**\nIntravital imaging allows the real-time visualization of cellular processes in their native environment in the living organism. It can be performed as repetitive imaging on the same animal, allowing biological processes to be tracked over long periods of time, or as acute experiments.\nSome Euro-BioImaging Nodes offer Intravital Imaging in direct association with animal houses, which is required especially for chronic or repeated imaging.\nIntravital microscopy is used for a wide variety of applications where dynamic processes in intact tissue environments need to be understood (see the review articles below for a range of examples). These include various analyses of vascular function, following the migration and cell-cell or cell-matrix interactions of e.g. immune cells or invasive/metastatic tumor cells in different tissues, and changes in e.g. neuronal or astrocyte morphology in response to stimulus or injury. Intravital brain imaging is increasingly done in awake rodents, which allows the integration of e.g. sensory cues for analysis of behavioral responses. A constantly increasing variety of functional probes can also be used for intravital microscopy, including calcium indicators, environmental sensors, FRET probes and enzyme-activated probes.\n**REFERENCES.**\n* Pittet M.J., Weissleder R. “Intravital imaging”, \n* Secklehner J. et al. “Intravital microscopy in historic and contemporary immunology”, \n* Coste A. et al. “Intravital Imaging Techniques for Biomedical and Clinical Research”, \n* Murphy K.J. et al. “Quantifying and visualising the nuances of cellular dynamics in vivo using intravital imaging”\n![](upload/ivmright.png)\n![](upload/ivmleft.png)\n*2-photon intravital microscopy images of living mouse ear skin, captured at the Biomedicum Imaging Unit In Vivo Imaging (BIU-IVI), part of Helsinki In Vivo Animal Imaging Platform (HAIP) in the Finnish Biomedical Imaging (FiBI) EuBI Node.*\n**IVM is available at the following Nodes:**\n* [Advanced Light and Electron Microscopy Node Prague CZ](https://www.eurobioimaging.eu/nodes/advanced-light-and-electron-microscopy-node-prague-cz)\n* [EMBL Node](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-facility-embl)\n* [Facility of Multimodal Imaging - AMMI Maastricht](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [French BioImaging Node](https://www.eurobioimaging.eu/nodes/french-bioimaging-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Portuguese Platform of BioImaging PPBI](https://www.eurobioimaging.eu/nodes/portuguese-platform-of-bioimaging-ppbi)\n* [PRIME Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [Swedish National Microscopy Infrastructure NMI](https://www.eurobioimaging.eu/nodes/swedish-national-microscopy-infrastructure-nmi)\n| Use cases | Node | DOI |\n| --- | --- | --- |\n| Longitudinal two-photon imaging in somatosensory cortex of behaving mice reveals dendritic spine formation enhancement by subchronic administration of low-dose ketamine | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n\n## AI Generated Documentation\n\n**Overview** \nIntravital microscopy (IVM-med) is a cutting-edge imaging technology designed for real-time visualization of biological processes within living organisms. It combines the capabilities of both confocal and two-photon microscopy, allowing researchers to observe dynamic cellular events in their natural physiological environments. This technology is particularly valuable in preclinical research, providing insights into cellular behavior, interactions, and responses in fields such as immunology, cancer research, and neuroscience.\n\n**Key Capabilities** \nThe IVM systems, such as the All-in-One IVM Series from IVIM Technology, are equipped with several advanced features that distinguish them from traditional microscopy techniques:\n- **Dual-Mode Functionality**: The ability to switch between confocal and two-photon imaging modes allows for versatile applications and enhanced imaging capabilities.\n- **High Imaging Speed**: Capable of ultra-high-speed imaging at up to 100 frames per second (fps) with a resolution of 512x512 pixels, enabling the tracking of fast-moving cellular events.\n- **Motion Compensation**: Advanced motion compensation technology automatically adjusts for movements caused by respiration or cardiac activity, ensuring high-quality images of dynamic organs.\n- **Label-Free Imaging**: The systems support non-linear second and third harmonic generation imaging, facilitating label-free visualization of cellular structures and processes.\n- **Integrated Animal Welfare Systems**: Features such as body temperature regulation and anesthesia management ensure the well-being of animal subjects during imaging sessions.\n\n**Applications** \nIntravital microscopy is utilized in various research applications, including:\n- **Cell Trafficking Studies**: Monitoring the movement and interactions of cells in real-time, crucial for understanding immune responses and tumor biology.\n- **Cell-Cell and Cell-Microenvironment Interactions**: Visualizing how cells interact with each other and their surrounding environment, providing insights into tissue dynamics and pathology.\n- **Physiological Response Monitoring**: Observing cellular responses to stimuli, such as drug treatments, in real-time, which is essential for drug development and testing.\n\n**Advantages** \nThe unique features of IVM-med offer several advantages over traditional imaging techniques:\n- **Real-Time Insights**: Provides immediate feedback on biological processes, allowing for rapid hypothesis testing and validation.\n- **Enhanced Resolution and Depth**: The combination of confocal and two-photon capabilities allows for high-resolution imaging at greater depths within tissues.\n- **Versatility**: The ability to adapt imaging modes and integrate various apparatuses makes IVM systems suitable for a wide range of research needs.\n- **Improved Drug Development**: By enabling detailed observation of drug interactions at the cellular level, IVM can significantly expedite the drug development process and improve clinical trial outcomes.\n\n## References\n\n1. https://www.ivimtech.com/intravital/product\n2. https://scintica.com/product/intravital-microscopy/\n3. https://oncomed-solutions.com/solutions/pre-clinical-imaging/intravital-microscopy/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "e532f9cb", "3850f7eb", "0c8677f6", "9beefd47", "64543c53", "706cb740" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "c3302077", "name": "live-cell Correlative Light and Electron Microscopy (live-cell CLEM)", "original_id": "3ca14139-5454-4d1c-9611-798c799fb4a5", "description": "Cells are imaged live by light microscopy (e.g. wide field, confocal or light sheet). Following the light microscopy image acquisition, specific CLEM protocols enable the scientist to retrace the position of the same cells in order to acquire high resolution EM images. This method allows one to image a labelled molecule of interest within the cell and combine it with the high-resolution information of the cellular landscape surrounding it. After live imaging, cells undergo chemical fixation or high pressure freezing and further processing for EM. The cells/regions of interest are retrieved by making use of a coordinate system present on the cell growing substrate, which is imprinted on the surface of the resulting resin block. \r\nAlternatively, methods such as infrared branding, fiducials and micro-CT can be used to find back the regions of interest in the resin block.\r\nSections (or serial sections) acquired through the cell of interest are inspected at the EM.\r\n\r\nA recently developed workflow allows one to link dynamic live imaging of subcellular compartments to 3D EM for providing ultrastructural context. Following this workflow, one can image live cells expressing fluorescent markers, then fix cells in-situ and process them for 3D EM imaging using FIB-SEM. This approach is very suitable to study live-cell organelle dynamics in relation to their high-resolution morphology in 3D.\r\n\r\nIntravital CLEM is one specific application of the above CLEM, where full organisms such as zebrafish or mouse embryos are imaged in vivo. By 3D targeting, the same region of interest is extracted and imaged by EM using any of the 3D EM techniques available.", "documentation": "## Live-cell Correlative Light and Electron Microscopy (live-cell CLEM)\n---\n**Cells are imaged live by light microscopy (e.g. wide field, confocal or light sheet). Following the light microscopy image acquisition, specific CLEM protocols enable the scientist to retrace the position of the same cells in order to acquire high resolution EM images. This method allows one to image a labelled molecule of interest within the cell and combine it with the high-resolution information of the cellular landscape surrounding it. After live imaging, cells undergo chemical fixation or high pressure freezing and further processing for EM. The cells/regions of interest are retrieved by making use of a coordinate system present on the cell growing substrate, which is imprinted on the surface of the resulting resin block.\nAlternatively, methods such as infrared branding, fiducials and micro-CT can be used to find back the regions of interest in the resin block.\nSections (or serial sections) acquired through the cell of interest are inspected at the EM.\nA recently developed workflow allows one to link dynamic live imaging of subcellular compartments to 3D EM for providing ultrastructural context. Following this workflow, one can image live cells expressing fluorescent markers, then fix cells in-situ and process them for 3D EM imaging using FIB-SEM. This approach is very suitable to study live-cell organelle dynamics in relation to their high-resolution morphology in 3D.\nIntravital CLEM is one specific application of the above CLEM, where full organisms such as zebrafish or mouse embryos are imaged in vivo. By 3D targeting, the same region of interest is extracted and imaged by EM using any of the 3D EM techniques available.**\n\n", "provider_node_ids": [ "90c8b0d6", "d039b533", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "d197dc73-bcb3-4583-bfc5-f416b3cdfc2a", "name": "Live-cell imaging and EM" } }, { "id": "b4a6f749", "name": "micro-CT", "original_id": "c5a618f7-232c-48d3-bfbf-dfcde1fd1564", "description": "High-resolution micro-CT: 100nm, 3D imaging, non-destructive, diverse applications.", "documentation": "## X-rays Computed Tomography (CT)\n---\n**X-rays Computed Tomography (CT) makes use of X-ray images (projections) taken from different angles and image reconstruction techniques to produce anatomic cross-sectional (tomographic) 3D  images. CT contrast agents (usually based on Iodine, Barium, Gold) can be used to enhance the contrast.**\nIn microCT, the instrumentation is implemented with accessories or with a technical set-up which provides optimum resolution and sensitivity for small animal studies.\nThe spatial resolution of microCT is higher with respect to clinical CT and typically the voxel size is lower than 100 mm for *in vivo* imaging and even smaller (less than 10 mm) for *ex-vivo* sample imaging. In order to achieve high spatial resolution a microfocus X-ray source is installed on microCT scanners.\nAnother difference with respect to clinical CT scanners is the use of flat panel detectors (FPD) with small pixel sizes (less than 100 mm) instead of curved detectors arrays. The use of a FPD results in a cone beam acquisition geometry. In this case, dedicated image reconstruction algorithms, such as the Feldkamp filtered back projection (FBP) algorithm, are needed.\nPreclinical microCT systems can be stand alone or integrated with other modalities like optical or nuclear medicine imaging in order to perform multimodal imaging.  microCT devices can be also found in small animal radiotherapy systems for animal positioning and treatment planning.\n**At Euro-BioImaging, preclinical and ex-vivo CT is provided by the following Nodes:**\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Hungary: Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n### Use cases\nClick here for\n[Use Cases](/content/use-cases/#CT) from our Nodes.\n## Dual energy CT\nDual energy CT (DECT) was firstly introduced in 1976 with the main\ngoal of obtaining the photoelectric and Compton components of the\nabsorption coefficients using a polychromatic x-ray beam with\ndifferent energies. These two components are respectively proportional\nto atomic number (Z) and density of the material (r) (R.E. Alvarez and\nE. Macovski, “Energy-selective reconstructions in X-ray computerized\ntomography”,\n).\nBy using DECT acquisitions it is thus possible to obtain rZ maps to\ngain material-specific information at each voxel as shown in the\nfigure below.\n![](upload/microCT.png)\nDECT imaging enables quantitative, 3D mapping of extrinsic contrast\nagents (iodine, red; gold, green) and soft tissues (gray) (from\n).\nA significant boost of DECT came in 2006 with the introduction of dual\nsource CT. In this case two x-ray tubes operating at different tension\nare orthogonally mounted in the gantry and both high and low tension\nimages are acquired (axial or spiral mode) at the same time, reducing\nartifacts induced by movement (T.G. Flohr et al. “First performance\nevaluation of a dual-source CT (DSCT) system”,\n).\n## Photon counting CT\nCurrent CT scanners are mostly based on scintillator energy\nintegrating detectors and it is thus not possible to gain information\nabout the energy of the detected x-ray photons. Photons counting\ndetectors (PCD) were firstly introduced for nuclear medicine imaging\nmodalities and their application for x-ray CT was limited by the low\ndetector rate PCD can handle.  However, considering also the\ndevelopments of DECT, there has been a significant research interest\nin improving their material composition and reading electronics.\nA PCD is made of a semiconductor (e.g. Cadmium Telluride) where the\ninteraction with the incoming x-ray generates positive and negative\ncharges proportional to the energy of the incoming photons. Different\nsignal thresholds corresponding to different energy values can be set\nin order to divide the detected transmitted x-ray spectrum into\ndifferent energy bins.\nThe use of PCD is particularly important for DECT as shown in the\nfigure below, where DECT imaging of a mouse using PCD is presented. In\nthis example, material decomposition into three basis materials was\nperformed.\n![](upload/microCT1.png)\nExample of photon-counting CT in a mouse. Material decomposition was\nperformed into iodine (red), photoelectric effect (PE, green), and\nCompton scattering (gray) (from\n)\n## K-Edge subtraction CT\nIn subtraction X-ray imaging, tissue structures or organs are\nvisualized using a contrast medium and measuring the changes in the\nattenuation between the contrasted structure and the surrounding\ntissue. In K-edge subtraction (KES) imaging, two X-ray images are\ntaken at different mean energies, slightly below and a bit above the\nK-edge of the contrast agent photoelectric absorption. Their\nsubtraction generates an image only displaying the contrasted\nstructure.\nSo far, this method mostly relies on monochromatic X-rays produced at\nlarge synchrotron facilities.\nKES allows to differentiate similarly absorbing substances in contrast\nenhanced CT, such as for example commonly used iodine contrast agents\nand calcium which is typically seen in calcifications, kidney stones\nand bones.\n## Phase contrast CT\nOne of the main limitations of CT is the poor contrast of low Z\nmaterials, e.g. soft tissues, because of similar X-ray absorption. In\norder to solve this problem the diffraction and refraction of the\nX-rays can be exploited to obtain more information about the structure\nof the object. This technique is called Phase Contrast Imaging. See\nPhase Contrast CT Imaging for more information\n[here](/service/phase-contrast-imaging-PCI).\n\n## AI Generated Documentation\n\n**Overview** \nMicro-computed tomography (micro-CT or μCT) is a cutting-edge imaging technology that provides high-resolution, three-dimensional (3D) visualization of small objects through X-ray imaging. Unlike conventional CT, micro-CT operates on a microscale, achieving resolutions down to 100 nanometers, making it an invaluable tool for detailed internal examinations of various specimens. \n\n**Key Capabilities** \nMicro-CT utilizes a rotating X-ray beam and a stationary detector to capture multiple 2D images from various angles, which are then reconstructed into a 3D model using advanced algorithms. This technique allows for the analysis of samples with diameters up to 200 millimeters while maintaining a non-destructive approach. The technology is capable of differentiating materials based on their X-ray attenuation properties, providing high contrast and detail in the resulting images. Micro-CT can also measure volumetric data, surface area, and other quantitative metrics, enhancing its utility in research. \n\n**Applications** \nMicro-CT has a broad range of applications across multiple fields: \n- **Biomedical Research**: It is extensively used for visualizing the anatomy of small animals, facilitating studies on disease progression, treatment effects, and congenital anomalies. \n- **Material Science**: Engineers and scientists utilize micro-CT to investigate the microstructure of materials, assessing porosity, cracks, and other flaws that may affect performance. \n- **Archaeology and Paleontology**: The technology allows for the non-destructive examination of artifacts and fossils, revealing intricate details that could be lost during traditional excavation methods. \n- **Pharmaceutical Development**: Micro-CT aids in studying drug formulations and their release mechanisms by providing critical information regarding the physical nature of compounds. \n\n**Advantages** \nMicro-CT offers several distinct advantages over traditional imaging techniques: \n- **High Resolution**: Its ability to achieve sub-micrometer resolutions enables the visualization of intricate structures that other imaging modalities cannot resolve. \n- **Non-destructive Analysis**: The preservation of specimen integrity is crucial for many scientific applications, making micro-CT an ideal choice for sensitive samples. \n- **3D Visualization**: The generation of detailed 3D models allows for comprehensive spatial analysis and a deeper understanding of complex structures. \n- **Quantitative Data Extraction**: The technology provides precise measurements of various parameters, enhancing the analytical capabilities in research settings. \n\nIn summary, micro-CT stands out as a versatile and powerful imaging tool that significantly contributes to advancements in scientific research and industrial applications.\n\n## References\n\n1. https://www.microphotonics.com/what-is-micro-ct-an-introduction/\n2. https://merkel.co.il/micro-ct-imaging/\n3. https://biologyinsights.com/what-is-x-ray-microtomography-and-how-does-it-work/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "23f7a2fd", "6319df36", "9c8d648e", "3850f7eb", "0c8677f6", "fc1893d4", "9beefd47", "cf8f008b", "d2be2f9c", "e5f30cac", "706cb740", "f1099f78" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "d74face8", "name": "micro-MRI/MRS (<7 T)ex-vivo", "original_id": "5bd81ae5-6ea0-4835-bf31-df8f37c1e814", "description": "High-resolution ex-vivo micro-MRI/MRS (<7 T) for detailed tissue analysis.", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n\n## AI Generated Documentation\n\n**Overview** \nMicro-MRI (Magnetic Resonance Imaging) and MRS (Magnetic Resonance Spectroscopy) technologies operating at field strengths below 7 Tesla (<7 T) are essential tools for ex-vivo studies in biomedical research. These systems provide high-resolution imaging and metabolic analysis of biological samples, enabling researchers to explore intricate anatomical and biochemical details that are critical for understanding various diseases and developing new therapies.\n\n**Key Capabilities** \nMicro-MRI/MRS systems, such as the Bruker Avance 7T and PharmaScan 7T, are equipped with advanced superconducting magnets and specialized imaging coils that facilitate high-resolution imaging. The Bruker Avance 7T features a wide-bore design with UltraShield™ technology, allowing for minimal interference and high-quality imaging of small samples. Typical imaging resolutions can reach sub-100 µm, enabling detailed visualization of microstructural features in tissues. The systems support a variety of imaging protocols, including T1, T2, DWI, CSI, and DCE-MRI, as well as single voxel spectroscopy, making them versatile for both anatomical and metabolic studies.\n\n**Applications** \nThese technologies are widely utilized in neuroscience, oncology, and pharmacology. For example, ex-vivo imaging of human brain specimens at 100 µm resolution has provided unprecedented insights into neuroanatomy, aiding in the understanding of neurological disorders. Additionally, micro-MRI/MRS is crucial for preclinical studies of drug efficacy and toxicity, allowing researchers to monitor metabolic changes in tissues and tumors. The ability to analyze fixed samples enhances the detail and accuracy of the findings compared to in-vivo imaging approaches.\n\n**Advantages** \nThe primary advantages of micro-MRI/MRS (<7 T) systems include their non-invasive nature, high spatial resolution, and the ability to provide comprehensive anatomical and functional information from ex-vivo samples. The cryogen-free designs, such as the MRS*DRYMAG 7.0T, eliminate the need for liquid helium, reducing operational costs and environmental impact. Furthermore, the combination of high-resolution imaging and spectroscopy capabilities allows for a more thorough understanding of biological processes, making these systems invaluable in advancing biomedical research and clinical applications.\n\n## References\n\n1. https://www.mrsolutions.com/mr-imaging/mr-imaging/mr-dry-magnet-cryogen-free/mr-7t/\n2. http://www.mmmi.unito.it/it/content/mrimrs-instruments\n3. https://www.nature.com/articles/s41597-019-0254-8\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "23f7a2fd", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "d2be2f9c", "64543c53", "6d068cfb", "2103118f" ], "abbr": "", "category": { "id": "3b54df7f-9def-4570-8dcf-fc2eeb4ad891", "name": "ex-vivo and materials imaging using biomedical technologies\r\n\r\n" } }, { "id": "4a91416e", "name": "micro-MRI/MRS (>= 7 T)ex-vivo", "original_id": "7f6c5c0f-653f-4713-be4a-4a01d59c3a7d", "description": "7T micro-MRI/MRS: 100µm resolution ex-vivo imaging for neuroanatomy and pathology.", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n\n## AI Generated Documentation\n\n**Overview** \nMicro-MRI/MRS (Magnetic Resonance Imaging/Spectroscopy) at ultra-high field strengths of 7 Tesla and above represents a cutting-edge approach in ex-vivo imaging, particularly for biological tissues such as the human brain. This technology leverages advanced imaging sequences and high-performance hardware to achieve unparalleled spatial resolution and sensitivity, making it a powerful tool for both research and clinical applications.\n\n**Key Capabilities** \nMicro-MRI/MRS systems operating at 7 T can achieve isotropic resolutions as fine as 100 µm, which is crucial for visualizing intricate anatomical structures. For example, a study utilized a custom-built 31-channel receive coil and a single-echo multi-flip Fast Low-Angle SHot (FLASH) sequence to produce high-fidelity images of an ex-vivo human brain specimen. The imaging process can be extensive, with some protocols requiring over 100 hours of scan time to ensure the highest quality data. The technology also supports multimodal imaging techniques, integrating structural MRI, diffusion MRI, and quantitative susceptibility mapping to provide a comprehensive view of brain microstructure and connectivity.\n\n**Applications** \nThe applications of micro-MRI/MRS are diverse and impactful. It is particularly valuable in neuroanatomical studies, allowing researchers to visualize small brain structures and tracts that are often difficult to assess in vivo due to motion artifacts and lower resolution. This capability is essential for understanding neurodegenerative diseases, brain injuries, and developmental disorders. Additionally, the integration of imaging data with histopathological findings enhances diagnostic accuracy and research outcomes, facilitating a deeper understanding of both normal and pathological brain conditions.\n\n**Advantages** \nThe advantages of micro-MRI/MRS (≥ 7 T) ex-vivo include: \n1. **High Resolution**: Achieving resolutions down to 100 µm allows for detailed anatomical delineation, surpassing traditional imaging methods. \n2. **Enhanced Contrast**: Improved signal-to-noise ratios and sensitivity to magnetic susceptibility provide clearer images of complex structures, aiding in accurate diagnosis. \n3. **Integration with Histopathology**: The ability to correlate imaging findings with histological data enhances the understanding of disease mechanisms and supports clinical decision-making. \n4. **Diverse Applications**: Useful in both basic research and clinical settings, this technology is instrumental in studies of neurodegenerative diseases, brain injuries, and developmental disorders, making it a versatile tool in modern biomedical research.\n\n## References\n\n1. https://arxiv.org/abs/2412.17816\n2. https://eurradiolexp.springeropen.com/articles/10.1186/s41747-023-00389-y\n3. https://www.nature.com/articles/s41597-019-0254-8\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "638ca876", "2b34e271", "6e382796", "e0395c6a", "23f7a2fd", "6319df36", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53", "706cb740", "2103118f", "f1099f78" ], "abbr": "", "category": { "id": "3b54df7f-9def-4570-8dcf-fc2eeb4ad891", "name": "ex-vivo and materials imaging using biomedical technologies\r\n\r\n" } }, { "id": "fc3c255a", "name": "micro-MRI/MRS (Field < 7 T)", "original_id": "0bc630de-4460-41f0-b8eb-94ca28a39e6c", "description": "Cryogen-free micro-MRI/MRS < 7 T: high-resolution, multi-nuclear imaging for small animals.", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n\n## AI Generated Documentation\n\n**Overview** \nMicro-MRI (Magnetic Resonance Imaging) and MRS (Magnetic Resonance Spectroscopy) systems operating at magnetic fields below 7 Tesla are pivotal in preclinical research, particularly for small animal models. The MRS*DRYMAG 7.0T exemplifies this technology, utilizing cryogen-free superconducting dry magnet technology, which eliminates the need for liquid helium cooling. This feature simplifies installation and reduces operational costs, making it highly accessible for research facilities.\n\n**Key Capabilities** \nMicro-MRI/MRS systems are designed to operate within a magnetic field range of 0.1 T to 7 T, providing high-resolution imaging and spectroscopic capabilities. The MRS*DRYMAG features bore sizes from 17 cm to 42 cm, accommodating various small animal sizes, including mice and rats, with a maximum weight capacity of 12 kg. The systems are equipped with advanced phased array multi-element coils that enhance signal detection and imaging quality. Gradient strengths can reach up to 2000 mT/m, facilitating rapid imaging sequences and improved spatial resolution. The technology supports multi-nuclear imaging, allowing researchers to analyze different elements within biological tissues, which is crucial for metabolic studies.\n\n**Applications** \nMicro-MRI/MRS is extensively used in preclinical research to investigate neurological disorders, cancer, and metabolic diseases. The high sensitivity of MRS at these field strengths enables the detection of subtle metabolic changes in tissues, providing critical insights into disease mechanisms and treatment responses. Institutions like the Mayo Clinic utilize 7-T MRI to enhance the diagnosis and management of conditions such as epilepsy and multiple sclerosis, showcasing the technology's clinical relevance.\n\n**Advantages** \nThe primary advantage of micro-MRI/MRS systems operating below 7 T is their operational simplicity and cost-effectiveness compared to higher-field systems. The absence of cryogens reduces logistical burdens and maintenance costs. Additionally, the integration with PET/MR and SPECT/MR imaging capabilities allows for comprehensive assessments of both anatomical and functional parameters in vivo. This versatility makes micro-MRI/MRS an invaluable tool for researchers aiming to explore complex biological processes and improve therapeutic strategies.\n\n## References\n\n1. https://www.mrsolutions.com/mr-imaging/mr-imaging/mr-dry-magnet-cryogen-free/mr-7t/\n2. https://www.mayoclinic.org/medical-professionals/neurology-neurosurgery/news/7-t-mri-providing-hope-by-seeing-the-previously-unseen/mac-20550624\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "23f7a2fd", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "d2be2f9c", "6d068cfb" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "9c64e406", "name": "micro-MRI/MRS (Field >= 7 T)", "original_id": "26c3dc40-5add-4b3b-9a3f-c41ee2f900e4", "description": "7 T micro-MRI/MRS: sub-millimeter resolution, multi-nuclear imaging, advanced neurological diagnostics.", "documentation": "## Magnetic Resonance Imaging (MRI)\n---\n**Magnetic resonance imaging (MRI) is a non invasive imaging technique used to obtain 2D/3D \"in vivo\" images representing anatomy and physiological processes (e.g. dynamic perfusion or dynamic changes in blood oxygenation for functional brain mapping, metabolism etc), with high spatial and temporal resolution. MRI scanners use strong magnetic fields, radiofrequency pulses, and field gradients to generate images of soft tissues throughout the body.**\nContrast agents based on paramagnetic compounds are commonly used to enhance the signal/noise ratio and assess vascularization or tissue permeability. More recently,  novel classes of contrast agents have been developed, such as hyperpolarized molecules for high sensitivity metabolic studies, or CEST agents for accurate pH parametric imaging.\nMagnetic Resonance Spectroscopy (MRS) can be used to complement MRI in the characterization of tissues. While MRI makes use of water proton signals to create images, MRS uses either proton or heteronuclei signals to determine the relative concentrations of metabolites within a specific organ/tissue.\nMRI scanners at high magnetic fields have the advantage to significantly increase the sensitivity and thus improve the image resolution and scan duration. MRS also benefits from high magnetic fields with an increased spectral resolution, which improves the separation between different chemical components. Nowadays, scanners at 3-7 Tesla are commonly used for both humans and animals, but for small-medium animal studies high field scanners operating at 7-9.4T are also quite common. Ultra-high field MR systems with fields of up to 17 T are also available mainly for preclinical studies.\nIn microMRI/MRS, the instruments are technically optimized for small animal studies, providing resolution in the mm to µm range.\nMRI, either as a single modality or paired to other imaging modalities, is largely used for *in vivo* (humans and animals) studies and also for ex-vivo analysis of specimens (organs or tissue samples).\nIn preclinical imaging, animal models of various pathologies, from tumors to cardiovascular, neurological or metabolic disorders, are commonly used to monitor disease development and to test the efficacy of therapeutic treatments, to develop novel diagnostic tools etc. Several quantitative imaging biomarkers can be used to monitor disease progression over time.\nAnimal imaging can also be used for veterinary studies.\nAt clinical level, MRI is generally a key tool for the diagnosis of various pathologies and for monitoring the efficacy of new therapies. It is also commonly used in studies involving healthy volunteers to evaluate metabolism or functions.\nMRI comprises a large number of techniques for various applications ranging from simple morphological measurements throughout all organs to the evaluation of complex systems, functions, and processes in living organisms.\n**Preclinical and ex-vivo MRI**is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n**Human MRI** is provided by the following Nodes:\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n### Use cases\nClick here for\n[Use Cases](https://www.eurobioimaging.eu/preclinical-and-medical-imaging-technologies-use-cases-from-our-nodes/) from our Nodes.\n## Anatomical, volumetric, morphometric MRI\nContrast in MRI images is generated by the differences in the nuclear relaxation times of water protons (T1 and T2) across tissues. The image contrast can be controlled by changing the values of specific acquisition parameters, generally the echo time (TE) and the repetition time (TR). Depending on their values, it is possible to obtain images where the contrast and brightness are predominantly determined by the T1 or T2 properties of water in tissues (T1-weighted and T2-weighted images respectively).\nContrast agents are frequently administered to enhance the contrast for assessment of organ functions (perfusion, vascularity, permeability) or better delineation of specific lesions or tissues. Mainly Gd based molecules are used with the acquisition of T1-weighted images and for specific cases iron Oxides could be used with T2-weighted images.\nThe acquisition of anatomical MR images is done with the scope of obtaining detailed morphological information ( shape, size, volume, texture…) of various body regions or lesions (e.g. tumors, ischemia, cysts etc) and to monitor disease progression or regression.\n* Kinnunen K. M., et al. \"Volumetric MRI-Based Biomarkers in Huntington's Disease: An Evidentiary Review\", \n* McCarthy J., et al. \"Morphometric MRI as a diagnostic biomarker of frontotemporal dementia: A systematic review to determine clinical applicability\", \nWhile MR images are typically assessed in a qualitative way, MRI can collect quantitative information about tissue properties. The range of properties includes the magnetic resonance (MR) relaxation times T1 and T2, T2\\*, diffusion, perfusion, fat and water fractions, iron fraction, elastic properties of tissue, temperature, chemical composition, and chemical exchange, just to mention some. Of note, new MRI methods are constantly being developed. By using the sensitivity of MRI to these tissue properties, it is possible to generate quantitative maps instead of qualitative anatomical images, where the intensity of each pixel corresponds to a measurement of one specific physical or physiological property. Quantitative measurements could help not only for identifying anatomical abnormalities but also for detecting initial loss of function or tissue alteration.\n[Use cases](https://www.eurobioimaging.eu/content/use-cases/#volumetric)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED](https://www.eurobioimaging.eu/nodes/digital-imaging-multimodal-platform-neuromed---dimp-neuromed)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n* [NORMOLIM, Norwegian Molecular Imaging Infrastructure](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Relaxation mapping - T1, T2, T2\\*, spin-lock MR techniques\nThe signal intensity in  MR images is  a function of water content, tissue properties and of MRI acquisition parameters.\nFor quantitative MR imaging, tissue relaxation times are measured by extracting the signal exponential decay (T2 or T2\\*) or recovery (T1) from multiple measurements.  T1, T2 and/or T1rho parametric images can be acquired.\nThe quantification of relaxation times provides more detailed information on the tissue characteristics (tumor cells invasion, ischemic lesions, vascular leakage, iron deposition, inflammation etc), thus supporting the clinicians in the diagnostic process. Furthermore, relaxation maps are used to quantitatively assess the presence of exogenous contrast agents.\nExample applications:\n* Evaluation of the structural integrity of the extracellular matrix in cartilage (T.J. Moshet et al., “Cartilage MRI T2 Relaxation Time Mapping: Overview and Applications” Seminars in Musculoskeletal Radiology, 2004, 8, 355) and of myocardial pathologies ().\n* Detection of initial nerve degeneration in ALS (N. Riva et al., “Defining peripheral nervous system dysfunction in the SOD-1G93A transgenic rat model of amyotrophic lateral sclerosis”, )\n* Detection of macrophage activities after a corneal lesion (G. Ferrari et al., “Ocular surface injury induces inflammation in the brain: in vivo and ex vivo evidence of a corneal-trigeminal axis”, )\n* R.P.M. Moonen et al., “Spin‐lock MR enhances the detection sensitivity of superparamagnetic iron oxide particles”, \n![](upload/hf.png)\nApplications of Noncontrast T1 Mapping. (A) Diffuse fibrosis: T1 maps from a normal control and diffuse changes in myocardial T1 in a patient with moderate aortic stenosis (AS) and severe AS. (B) Edema: A 46-year-old man with inferior wall acute myocardial infarction (MI). (C) Replacement fibrosis: LGE images and noncontrast T1 maps at 3-T from a patient with ST-segment elevation myocardial infarction. (D) Myocardial inflammation: A 51-year-old patient with myocarditis (on admission with elevated T1) and at 6-month follow-up (with T1 returned to normal values). (E) Myocardial iron overload: healthy (a); and mild, moderate, and severe (b-d) cases of iron overloading. From [https://doi.org/10.1016/j.jcmg...](https://doi.org/10.1016/j.jcmg.2015.11.005)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Microstructural/diffusion MRI\nWater molecules diffuse differently through tissues depending on their composition, integrity, architecture, and presence of barriers. Diffusion imaging is used to obtain important information about water movements within the architecture of tissues. This is achieved by using MRI sequences specifically designed to  measure the values of the water diffusion coefficient (Diffusion Weighted Imaging) and its components along the 3D space (Diffusion Tensor imaging).\nNeither contrast agents nor specific instrumentation are requested for this kind of experiments.\nDiffusion MRI is used to evaluate the molecular function and micro-architecture of tissues, and it acts as a tool for monitoring treatment response and disease progression for a variety of pathologies such as tumors, white matter diseases, inflammatory diseases and so on. See for example:\n* Baliyan V., et al. \"Diffusion weighted imaging: Technique and applications.\", \n* Qiu A., et al. \"Diffusion Tensor Imaging for Understanding Brain Development in Early Life\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Perfusion MRI with or without contrast agent - DSC, DCE and ASL-MRI\nThe decrease of the MRI signal in a given tissue after injection of a T1 or T2\\* contrast agent can be exploited to provide, after suitable post-processing which affords parametric maps of quantities such as blood volume, blood flow, mean transit time and others, a wealth of information about organ perfusion.\nPerfusion MRI can be performed either with or without the use of an exogenous contrast agent. In the first case, dynamic susceptibility contrast (DSC)-MRI, which measures the signal loss in T2- or T2\\*-weighted images, and dynamic contrast-enhanced (DCE)-MRI, which measures the signal loss in T1-weighted images, are used. In the latter case, arterial spin-labeling (ASL) is used.\nWhile ASL is mainly applied for the measurement of cerebral perfusion, DSC and DCE-MRI are used in a wider variety of clinical applications, including the classification of tumors, stroke regions, and characterization of other diseases, as well as for assessing response to antiangiogenic therapies.\n* Boxerman J.L., et al. \"Dynamic Susceptibility Contrast MR Imaging in Glioma: Review of Current Clinical Practice.\" \n* Sujlana, et al. \"Review of dynamic contrast-enhanced MRI: Technical aspects and applications in the musculoskeletal system\", \nIn neurology, brain perfusion parameters such as Normalized Cerebral Blood Flow (NCBF) and Cerebral Blood Volume (CBV) are relevant hemodynamic parameters, as their changes can precede abnormalities on conventional MR imaging. Thus, knowledge of whether a lesion identified in anatomic images is associated with increased or decreased CBF or CBV can frequently help narrow the differential diagnosis.\n![](upload/asl-mrileft.png)\n![](upload/asl-mriright.png)\nMR images (A) and parameter maps calculated from data of both dynamic susceptibility-contrast MRI (B), and dynamic contrast-enhanced MRI (C), obtained from a patient with anaplastic astrocytoma in the frontal lobe of the brain. From [https://doi.org/10.3348%2Fkjr....](https://doi.org/10.3348%2Fkjr.2014.15.5.554)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Functional MRI (fMRI)\nfMRI measures metabolic changes in the brain caused by neural activity. It is typically based on dynamic measurement of brain with BOLD (blood oxygenation level dependent) contrast which is achievable with T2\\* weighted images (e.g. GRE EPI). Other contrast principles can be used as well (e.g. blood perfusion). Typical spatial resolution ranges from 3 x 3 x 3 mm to 2 x 2 x 2 mm in whole brain coverage, or even up to 0.1 mm in limited field of view and at ultra-high fields (7T or more). Temporal resolution ranges from 3 s to 0.5 s with EPI sequence.\nfMRI can be used in medical research (and diagnostics) as well as psychology, neuroeconomy, and other disciplines related to understanding human brain and behavior. It is typically used to measure neural activity during tasks or following to stimuli (e.g. scenario with auditory, visual or tactile stimuli distributed during the acquisition time to induce required brain activity), but resting-state fMRI is possible too. It allows to obtain activation maps, evaluate the hemodynamic response in selected regions, estimate the functional connection among brain regions, and evaluate the relationship between activity/connectivity and external variables.\nfMRI can be combined with electrophysiological recordings or stimulation.\nA special case is fMRI hyperscanning (dual fMRI) with two participants measured simultaneously in two scanners.\nExample applications include:\n* localization of brain functions and networks\n* monitoring brain changes caused by stress\n* discovering brain changes in various diseases (e.g. Alzheimer disease, Schizophrenia etc)\n* understanding empathy, emotions and consciousness\n* understanding the learning process\n* observing brain plasticity, development, aging affects\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Chemical Exchange Saturation Transfer (CEST), Magnetization Transfer (MT) MRI\nIn CEST imaging, a radiofrequency pulse is applied at the resonant frequency(ies) of exchangeable protons in a given molecule or metabolite, in order to reach a saturation state. Chemical exchange of the protons with those of water molecules causes the transfer of magnetic saturation to water over time. The subsequent decrease in water signal is detected by standard MR imaging sequences and provides an indirect measure of the concentration of the species of interest.\nCEST MRI can detect a variety of endogenous small molecules (e.g. glucose, glycogen, lactate, creatine, glutamate), proteins and enzymes for molecular imaging. Development of exogenous CEST agents, including diamagnetic CEST (DIACEST), paramagnetic CEST (PARACEST) and liposome-based (LIPOCEST) agents, greatly enhanced the sensitivity and specificity of CEST imaging (Longo D.L. et al.; “A snapshot of the vast array of diamagnetic CEST MRI contrast agents” ; Ferrauto G. et al.; “LipoCEST and cellCEST imaging agents: opportunities and challenges” ).\nCEST imaging can provide information on tissue pH, temperature, oxygenation, metabolism, enzymatic reactions as well as for molecular imaging applications. Example applications include several disorders such as acute stroke, renal injury, tumors and multiple sclerosis.\n![](upload/chemicalmri.png)\nApplication of MRI-CEST tumor pH imaging for assessing response to novel anticancer therapies. Representative tumour extracellular pH (pHe, reflecting acidosis) maps for untreated (A) and treated mouse (B) superimposed on anatomical images at baseline (left), 3 days (middle) and 15 days (right) post-dichloroacetate treatment in a 4T1 triple negative breast tumor murine model. From [https://doi.org/10.3892/ijo.20...](https://doi.org/10.3892/ijo.2017.4029)\nMagnetization transfer (MT) is based on the observation of the immobile (restricted) hydrogen pool (protons bound to large macromolecular proteins and lipids, such as those found in such cellular membranes as myelin) throughout saturation of this restricted pool and detection on the mobile proton pool. The MT contrast is different from T1, T2, and PD, and it likely reflects the structural integrity of the tissue being imaged. Applications include tissue characterization, such as evaluation of multiple sclerosis and other white-matter lesions and in tumors.\nSee also: van Zijl PCM et al.; “Magnetization Transfer Contrast and Chemical Exchange Saturation Transfer MRI. Features and analysis of the field-dependent saturation spectrum” [https://doi.org/10.1016/j.neur...](https://doi.org/10.1016/j.neuroimage.2017.04.045)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n## Magnetic Resonance Spectroscopy Imaging (MRS/MRSI)\nMagnetic Resonance Spectroscopy Imaging is used to spatially map multiple tissue metabolites signals. Since the molecular concentrations of these metabolites are at least 10.000 times lower than water, they produce correspondingly much lower signal strengths. Thus, to detect enough signal above noise for quantification, 1H-MRSI must use much larger voxel sizes in comparison to MRI, leading to lower spatial resolution with respect to anatomical imaging. The use of high magnetic fields allows to overcome this issue.\nMRSI is used in the clinics for quantifying metabolic abnormalities in the human brain, prostate, breast and other organs.\nSee for example:\n* T.A.A. Boroeders et al., “Glutamate levels across deep brain structures in patients with a psychotic disorder and its relation with cognitive functioning”, [http://dx.doi.org/10.1101/2021...](http://dx.doi.org/10.1101/2021.02.01.21250977)\n* A.A. Bhogal et al., “Lipid-suppressed and tissue-fraction corrected metabolic distributions in human central brain structures using 2D 1H magnetic resonance spectroscopic imaging at 7 T”, [http://dx.doi.org/10.1002/brb3...](http://dx.doi.org/10.1002/brb3.1852)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Non-hydrogen MRI and MRS techniques (13C, 19F, 23Na, 31P)\nAmong all the nuclei found in the human body that have a non-zero nuclear spin (e.g., 1H, 13C, 17O, 19F, 23Na, 31P), hydrogen is by far the dominant nucleus of interest for clinical MRI. Nevertheless, technological progress, development of acquisition methods and the availability of equipment operating at high magnetic fields have made in vivo heteronuclear MRI/MRS possible in both humans and small animals despite sensitivity limitation, widening the number of applications and the range of metabolites that can be mapped by MRS.\nSodium (23Na) MRI has been applied in a large variety of biomedical/clinical research areas. Sodium ions (Na+) play an important role in many cellular physiological processes. An unbalanced concentration gradient across the cell membranes or an increase in the intracellular Na+ content is an early marker of cell viability in many disease processes. 23Na-MRI can be used for studying heart diseases, by exploiting the increase in the extracellular sodium signal in acute ischemia, for cancer investigations, by measuring the increase of sodium content in proliferating cells, and for testing therapies by evaluating the intracellular sodium accumulation due to cell death ).\n31P MRS can be used to study the energetic metabolism of a wide range of tissues such as muscle, heart, liver, and kidney in various pathological contexts. Using the endogenous 31P signal arising from the tissue, it is possible to obtain information about the energy status and also determine the intracellular pH (from the chemical shift of Pi). 31P signals from inorganic phosphate, adenosine triphosphate, adenosine diphosphate, creatine phosphate and sugar phosphates can be observed in whole-cell preparations, intact tissues or organs. Phosphate metabolites that are involved in ATP production and utilization can be quantified non-invasively by 31P-MRS/MRI, while 31P magnetization transfer (MT) techniques allow in vivo measurement of metabolic fluxes via creatine kinase (CK) and ATP synthase ().\nFor 13C-MRI, hyperpolarized probes are usually used in order to increase the sensitivity of the technique (see Hyperpolarized MRI).\n19F MRI is increasingly emerging as a multi-nuclear (1H/19F) technique that can be exploited for several purposes, e.g. cell tracking, detection of active inflammation, measuring tissue oxygenation and to study fluorinated pharmaceuticals. The lack of a 19F background signal in tissues affords an unequivocal detection suitable for quantification. Fluorine-based contrast agents can be engineered as nanoemulsions, nanocapsules, or nanoparticles to label cells in vitro or in vivo. Multispectral 19F-MRI using different fluorinated compounds could be also used to detect different labeled cells simultaneously. Specific fluorinated products can be used to map pO2 heterogeneity in tissues. (; )\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Israel BioImaging](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n## Hyperpolarized MRI (HP-MRI)\nIn respect to other imaging modalities, the major drawback of MRI is represented by the relatively low sensitivity of the technique. This is particularly true for nuclei other than protons. Hyperpolarized probes are molecules where the nuclei polarization has been artificially raised. Conversely to standard MRI contrast agents, which act on the relaxation of water protons, hyperpolarized molecules are themselves the source of the NMR signal, thus yielding to signal intensity and SNR that linearly depend upon their concentration and polarization level. Long relaxation times of the hyperpolarized nuclei are essential in order to preserve the polarization for as long as possible. For this reason HP-MRI relies on the detection of heteronuclei rather than protons. For most applications 13C-probes are used.\nThe use of hyperpolarized probes allows to obtain very strong signal enhancements, thus overcoming the MR sensitivity issue and making the detection of low concentration biological molecules possible. Hyperpolarized probes are usually employed for perfusion studies and for mapping metabolites and their transformations through MRS in the body. Hyperpolarized metabolic imaging is particularly useful for the early diagnosis of cancer and monitoring of treatments efficacy because it can reveal changes that happen well before the onset of macroscopic signs of the disease. A typical example is the monitoring of pyruvate and lactate levels after injection of hyperpolarized 13C-pyruvate.\nOther examples of applications in the preclinical and clinical fields can be found in the following reviews:\n* Z.J. Wang et al., Hyperpolarized 13C MRI: State of the Art and Future Directions, [https://doi.org/10.1148/radiol...](https://doi.org/10.1148/radiol.2019182391)\n* V.Z. Veloushei et al., Hyperpolarization MRI, [https://doi.org/10.1097%2FRMR....](https://doi.org/10.1097%2FRMR.0000000000000076)\n* R. Woitek et al., The use of hyperpolarised 13C-MRI in clinical body imaging to probe cancer metabolism, [https://doi.org/10.1038/s41416...](https://doi.org/10.1038/s41416-020-01224-6)\n**Available at:**\n* [Danish BioImaging](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n## Susceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)\nSusceptibility Weighted Imaging (SWI) and Quantitative Susceptibility Mapping (QSM)  are MRI techniques that measure and display differences in the magnetization that is induced in tissues, i.e. their magnetic susceptibility, when placed in the strong external magnetic field of an MRI system.\nSWI produces images in which the contrast is heavily weighted by the intrinsic tissue magnetic susceptibility.\nQSM is a further advancement of this technique that requires sophisticated post-processing in order to provide quantitative maps of tissue susceptibility.\nSWI and QSM  have been applied in a wide range of clinical applications in the neuroscience, cardiovascular and oncology fields.\nFor example, susceptibility-based techniques have a higher lesion contrast and sensitivity that leads to improved detection of cerebral haemorrhages when compared to conventional and magnitude-based techniques and/or CT; SWI is frequently used to image cerebral venous vascular networks, to better visualize and differentiate brain tumors from e.g. calcifications and to distinguish between types of tumors and metastasis.\nLiver pathologies can also be studied by these methods, based on the changes in iron concentrations in the diseased liver.\nRead more:\nRuetten P. P. R., et al. \"Introduction to Quantitative Susceptibility Mapping and Susceptibility Weighted Imaging\", \n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## Cardiovascular MRI (CMR)\nCardiovascular Magnetic Resonance (CMR) comprises a number of MRI techniques designed to assess various aspects of cardiac and vascular function, from cardiovascular morphology to ventricular function, myocardial perfusion, flow quantification and monitoring of coronary artery disease. A difference in respect to MRI of other body regions is that cardiac and respiratory motions cause artifacts. Thus, CMR requires synchronous cardiac and respiratory gating or breath-holding techniques. Cardiac synchronization with ECG is often used to “freeze” the hearth during MR acquisition.\nMRI can also be used to record movies of the cardiac cycle that permit the extraction of a good number of dynamic cardiac parameters (cine MRI).\nFor more details on CMR techniques and applications see:\n* W.-Y.I. Tseng et al., “Introduction to Cardiovascular Magnetic Resonance: Technical Principles and Clinical Applications”, \n* Saeed M., Van T. A., Krug R., Hetts S.W., Wilson M.W. \"Cardiac MR imaging: current status and future direction.\" \nCardiac MRI can also be successfully used to establish the eventual side effects of drugs on heart anatomy and physiology. For instance, it can be applied to assess the decrease of ejection fraction (EF%) in the heart upon multiple administrations of Doxorubicin for cancer treatment.\n![](upload/CMR.png)\nMRI of heart in diastole or systole for ctrl untreated mice and mice treated with doxorubicin. Adapted from [https://doi.org/10.1111%2Fbph....](https://doi.org/10.1111%2Fbph.15039)\n**Available at:**\n* [Advanced Light Microscopy and Medical Imaging Node Brno CZ](https://www.eurobioimaging.eu/nodes/advanced-light-microscopy-and-medical-imaging-node-brno-cz)\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Center for Advanced Preclinical Imaging (CAPI)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Brain Imaging Network (BIN)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Dutch High Field Imaging Hub](https://www.eurobioimaging.eu/nodes/dutch-high-field-imaging-hub)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Medical and Preclinicial Imaging Hungary](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n\n## AI Generated Documentation\n\n**Overview** \nMicro-MRI (Magnetic Resonance Imaging) and MRS (Magnetic Resonance Spectroscopy) operating at ultra-high field strengths of 7 Tesla (7 T) and above represent a cutting-edge advancement in biomedical imaging. This technology is distinguished by its ability to provide sub-millimeter spatial resolution and enhanced metabolic characterization of tissues, making it invaluable for both research and clinical applications. \n\n**Key Capabilities** \nThe 7 T micro-MRI/MRS systems utilize superconducting magnets to generate strong magnetic fields, significantly improving the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR). This results in high-resolution images that can reveal intricate anatomical details and subtle metabolic changes. The technology supports multi-nuclear imaging, allowing for the examination of various isotopes such as ^1H, ^13C, and ^31P, which is crucial for comprehensive tissue analysis. Advanced imaging sequences, such as the 3D edge-enhancing gradient-echo (EDGE), enhance the detection of specific pathologies, particularly in neurological applications. \n\n**Applications** \nMicro-MRI/MRS at 7 T is primarily utilized in clinical settings for neurological assessments, including the diagnosis and management of epilepsy, multiple sclerosis, and neurodegenerative disorders like Alzheimer's disease. The high-resolution imaging capabilities allow for precise localization of lesions and abnormalities, facilitating targeted treatment approaches. In musculoskeletal imaging, this technology provides detailed insights into cartilage and bone health, aiding in the diagnosis of conditions such as osteoarthritis. Additionally, in research, it enables the study of cerebral tissues, metabolic processes, and the effects of various diseases on brain structure and function. \n\n**Advantages** \nThe distinct advantages of 7 T micro-MRI/MRS include: \n- **Superior Resolution**: Achieving sub-millimeter resolution allows for detailed visualization of small anatomical structures. \n- **Enhanced Contrast**: Improved CNR facilitates better differentiation between various tissue types. \n- **Multi-Nuclear Capabilities**: The ability to analyze different isotopes enhances the understanding of tissue composition and metabolic activity. \n- **Clinical Relevance**: The technology's potential to significantly impact patient management and treatment outcomes through accurate diagnostics underscores its importance in modern medicine. \n\nIn summary, micro-MRI/MRS at 7 T is a transformative technology that bridges the gap between advanced research and clinical practice, providing profound insights into human health and disease.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC8189542/\n2. https://link.springer.com/chapter/10.1007/978-3-319-44174-0_23\n3. https://www.mayoclinic.org/medical-professionals/neurology-neurosurgery/news/7-t-mri-providing-hope-by-seeing-the-previously-unseen/mac-20550624\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "638ca876", "2b34e271", "6e382796", "e0395c6a", "23f7a2fd", "6319df36", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53", "706cb740", "f1099f78" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "4aa5d36d", "name": "micro-PET", "original_id": "64c3996e-d398-4658-a4fa-2075a529bb47", "description": "High-resolution small-animal imaging: 1-2 mm, oncology, neurology, non-invasive.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n**Overview** Micro-Positron Emission Tomography (micro-PET) is a cutting-edge imaging technology specifically designed for small animal research, enabling non-invasive visualization of biological processes at the molecular level. This technology is a miniaturized version of traditional PET, optimized for high-resolution imaging of small subjects such as mice and rats, thus facilitating advanced preclinical studies. **Key Capabilities** Micro-PET systems utilize advanced detector technologies, often incorporating scintillator materials like Lutetium Oxyorthosilicate (LSO) to achieve high spatial resolution, typically ranging from 1 to 2 mm. The imaging process involves the injection of radiolabeled biomolecules into the subject. As these isotopes decay, they emit positrons that interact with electrons, resulting in the emission of high-energy gamma rays. These gamma rays are captured by the micro-PET detectors, which reconstruct the data into detailed three-dimensional images. The high sensitivity and quantitative accuracy of micro-PET allow researchers to monitor dynamic biological processes in real-time. **Applications** Micro-PET is extensively used in various fields, including oncology, neurology, and cardiology. It facilitates the study of enzyme activity, receptor-ligand interactions, and cellular metabolism. Notably, micro-PET has been instrumental in advancing research on diseases such as Alzheimer's, where it aids in understanding pathophysiological changes and evaluating therapeutic interventions. The ability to perform longitudinal studies on the same subject enhances the relevance and applicability of findings to clinical settings. **Advantages** The primary advantages of micro-PET include its capacity for quantitative and qualitative data acquisition on molecular processes in live animals, which is crucial for preclinical studies. Its high spatial resolution enables the detection of subtle changes in biological systems that may not be visible with other imaging modalities. Additionally, the non-invasive nature of micro-PET allows for repeated imaging over time, providing insights into disease progression and treatment efficacy without the need for invasive procedures. Overall, micro-PET represents a significant advancement in preclinical imaging, bridging the gap between basic research and clinical applications, making it an invaluable tool in modern biomedical research.\n\n## References\n\n1. https://www.news-medical.net/life-sciences/Micro-PET-Principles-Strengths-and-Weaknesses.aspx\n2. https://www.sciencedirect.com/science/article/pii/S0002944012008206\n3. https://pmc.ncbi.nlm.nih.gov/articles/PMC2713341/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "6e382796", "e0395c6a", "23f7a2fd", "9c8d648e", "3850f7eb", "0c8677f6", "cf8f008b", "d2be2f9c", "64543c53" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "c41fb0d1", "name": "micro-PET/CT", "original_id": "41e8ecfc-8c3b-4e65-9135-bdab0fdd9bd6", "description": "High-resolution micro-PET/CT: 1.4mm resolution, multimodal imaging for small animals.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n### Overview\nMicro-PET/CT (Micro-Positron Emission Tomography/Computed Tomography) is a cutting-edge imaging technology designed for preclinical research, particularly in small animal models. This integrated system combines the functional imaging capabilities of PET with the anatomical detail provided by CT, enabling comprehensive insights into biological processes and disease mechanisms at a high resolution.\n\n### Key Capabilities\nThe Siemens Inveon micro-PET/CT scanner exemplifies this technology, featuring a 64-block PET detector interfaced with 64 channels, which allows for high quantitative accuracy and efficient operation. The system has a bore size of 12 cm, with a detector diameter of 16.1 cm, and a transaxial active field of view (FOV) of 10 cm, extending to an axial FOV of 12.7 cm. It achieves a spatial resolution of approximately 1.4 mm at the center of the FOV, making it suitable for detailed imaging of small animals such as mice and rats. The axial range can be extended up to 50 cm through continuous bed motion.\n\nThe integrated CT module utilizes an 80-W tungsten-anode X-ray source with a focal spot smaller than 50 mm, achieving a CT resolution of 20 µm with variable focus and 40 µm with a standard source. This combination allows for seamless acquisition and processing of multimodal data, facilitating post-processing, image review, and analysis.\n\n### Applications\nMicro-PET/CT is particularly valuable in fields such as oncology, cardiology, and neuroscience research. It enables the assessment of cellular microenvironments, metabolic changes, and the biodistribution of drugs, making it instrumental in characterizing disease progression and evaluating therapeutic efficacy. The technology supports the use of radiolabeled tracers, which can be tailored to target specific biological pathways, thus allowing for quantitative measurements of tissue perfusion and metabolic activity. The ability to combine functional imaging from PET with anatomical data from CT enhances the precision of identifying sites of radiotracer uptake, improving the understanding of disease mechanisms and treatment responses.\n\n### Advantages\nThe micro-PET/CT system offers several advantages, including high spatial resolution, the ability to perform multimodal imaging in a single session, and the capability to analyze dynamic biological processes in vivo. This technology is essential for translational research, bridging the gap between preclinical studies and clinical applications, and providing insights that can lead to the development of novel therapeutic strategies. In summary, micro-PET/CT stands out as a powerful tool in preclinical imaging, offering detailed insights into the biological processes underlying diseases while facilitating the evaluation of new treatments in small animal models.\n\n## References\n\n1. https://med.nyu.edu/research/scientific-cores-shared-resources/preclinical-imaging-laboratory/instruments/micro-pet/ct\n2. https://cmgi.ucdavis.edu/services/positron-emission-tomography-pet/\n3. https://fei-lab.org/high-resolution-small-animal-petct-micropetct/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "90c8b0d6", "2b34e271", "e0395c6a", "6319df36", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53", "6d068cfb", "706cb740", "f1099f78" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "15ef9b0e", "name": "micro-PET/MRI", "original_id": "1712b3ed-be0a-4cb5-9839-7db6e33668fc", "description": "Hybrid imaging: simultaneous micro-PET/MRI, high-resolution, in vivo molecular imaging.", "documentation": "## Positron Emission Tomography–Magnetic Resonance Imaging (PET-MRI)\n---\n**Positron Emission Tomography–Magnetic Resonance Imaging (PET-MRI) is a hybrid imaging technology that incorporates Magnetic Resonance Imaging ([MRI](/service/Magnetic-Resonance-Imaging-MRI)****) soft tissue morphological imaging, and Positron Emission Tomography ([PET](/service/Nuclear-Medicine))****molecular imaging. The technology combines the exquisite structural and functional characterization of tissue provided by MRI with the extreme sensitivity of PET imaging for the determination of receptor density/biological reaction rates/detection of radiolabelled drugs or vectors.**\nMR and PET acquisition can be made either separately or inline on individual MR and PET scanners, or simultaneously on bimodal machines. MR and PET images are then superimposed to provide single images with the characteristics of both technologies.\nRead more on applications and used PET tracers [here](/service/Nuclear-Medicine)\n### Preclinical PET-MRI is provided by the following nodes:\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM (NO)](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n### Human PET-MRI is provided by the following nodes:\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Medical and Preclinical Imaging Hungary (HU)](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [Population Imaging Node Valencia (ES)](https://www.eurobioimaging-access.eu/nodes/population-imaging-valencia)\n**Use cases**\n| Use cases | Preclinical or human | Node | DOI |\n| --- | --- | --- | --- |\n| [11C]-tracers, investigation of the potential link between availability of specific neuroreceptors and transporters and gray matter density | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [11C]-carfentanil, association of endogenous μ-opioid receptor (MOR) and neuronal rewards response to food picture | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [11C](R)-PK11195, Evaluation of widespread Multiple Sclerosis | Human | [Finnish Biomedical Imaging Node](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node) | |\n| [18F]FDG, Monitoring the side effects of radiation therapy in mice | Animal | [HU Med & Preclinical Node](https://www.eurobioimaging.eu/nodes/medical-and-preclinical-imaging-hungary) | |\n| [18F]FDG, spinal cord | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n| [18F]FDG, cancer | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n| [18F]FDG, injured brain imaging | Human | [Molecular Imaging Italian Node](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node) | |\n\n## AI Generated Documentation\n\n**Overview** \nMicro-PET/MRI is an advanced hybrid imaging technology that integrates Positron Emission Tomography (PET) with Magnetic Resonance Imaging (MRI), providing a powerful tool for in vivo molecular imaging. This combination allows for the simultaneous acquisition of metabolic and anatomical data, enhancing the understanding of biological processes and disease mechanisms. The technology is particularly beneficial in preclinical research and clinical applications, where precise imaging is crucial.\n\n**Key Capabilities** \nThe micro-PET component features high-resolution imaging capabilities, utilizing silicon photomultipliers (SiPM) for superior sensitivity and count rate performance. Systems like the Mediso nanoScan® PET/MRI are equipped with a dual PET configuration that allows for simultaneous or sequential imaging, ensuring optimal performance across various studies. The PET subsystem is designed for real dynamic scanning, providing quantitative imaging of small animals, such as mice and rats. The MRI subsystem typically employs robust, cryogen-free superconducting magnets, available in strengths of 3T and 7T, which deliver exceptional soft-tissue contrast and spatial resolution. This integration minimizes motion artifacts and enhances the accuracy of spatial localization of radiotracers.\n\n**Applications** \nMicro-PET/MRI is widely used in oncology, neurology, and cardiology, allowing researchers to observe metabolic processes and anatomical structures concurrently. It is instrumental in tumor characterization, monitoring therapeutic efficacy, and studying neurodegenerative diseases. In preclinical studies, micro-PET/MRI facilitates drug development by enabling the evaluation of pharmacokinetics and biodistribution of new compounds in live animal models. The technology supports longitudinal studies, allowing for repeated imaging of the same subjects, which reduces variability and improves data quality.\n\n**Advantages** \nThe primary advantages of micro-PET/MRI include reduced radiation exposure compared to PET/CT, enhanced soft-tissue contrast from MRI, and the ability to acquire functional and anatomical data in a single session. This hybrid approach streamlines the imaging process and provides a more comprehensive view of biological processes, making it an invaluable tool in both preclinical and clinical research. Micro-PET/MRI's unique capabilities significantly differentiate it from traditional imaging modalities, offering enhanced insights into complex biological systems and improving patient outcomes.\n\n## References\n\n1. https://pmc.ncbi.nlm.nih.gov/articles/PMC4451572/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC4463332/\n3. https://mediso.com/global/en/product/pre-clinical-products/nanoscanr-petmri-3t-and-7t\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "6e382796", "e0395c6a", "23f7a2fd", "9c8d648e", "3850f7eb", "0c8677f6", "cf8f008b", "d2be2f9c", "3e52fd14", "64543c53" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "36d4a2a7", "name": "micro-SPECT", "original_id": "4dcb4a01-d464-4411-a143-69d5443f50cd", "description": "Ultra-high-resolution micro-SPECT: 0.13 mm, dynamic imaging, multi-isotope capability.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n### Overview\nMicro-SPECT (Micro Single Photon Emission Computed Tomography) is a cutting-edge imaging technology designed for high-resolution, functional imaging in preclinical research. This advanced modality allows for the visualization of biological processes at the molecular level, making it essential in various fields, including oncology, cardiology, and neurology. Micro-SPECT systems, such as the U-SPECT from MILabs, are distinguished by their ability to provide rapid, high-resolution imaging of small animal models, enabling researchers to gather critical data on disease mechanisms and treatment efficacy.\n\n### Key Capabilities\nMicro-SPECT systems achieve remarkable spatial resolutions of up to 0.13 mm ex vivo and 0.25 mm in vivo, which is significantly higher than traditional SPECT systems. The technology employs stationary gamma-ray detectors that facilitate fast imaging without the need for geometrical recalibrations, allowing for focused imaging in as little as 1 second and whole-body scans in 8 seconds. The systems can reach a sensitivity of 150,000 counts per second per MBq, making them suitable for a wide range of isotopes, including high-energy and theranostic isotopes like 131I, 188Re, and 213Bi. Additionally, the U-SPECT system can be upgraded to include PET capabilities, enabling simultaneous PET/SPECT imaging with unprecedented spatial resolution.\n\n### Applications\nMicro-SPECT is widely used in preclinical studies to assess the biodistribution of radiolabeled compounds, monitor disease progression, and evaluate therapeutic responses. Its ability to perform dynamic imaging and quantitative 3D autoradiography allows researchers to visualize the distribution of multiple isotopes simultaneously, enhancing the understanding of complex biological interactions. This capability is particularly valuable in drug development and cancer research, where precise imaging of tumor responses to therapies is critical.\n\n### Advantages\nThe primary advantage of micro-SPECT lies in its high sensitivity and resolution, which enables the detection of low concentrations of radiotracers in small animal models. This is crucial for studies where the amount of tracer is limited, allowing for more accurate assessments of biological processes. Furthermore, the flexibility of micro-SPECT systems, which can be upgraded to include additional functionalities like PET imaging, makes them versatile tools in research settings. Overall, micro-SPECT represents a significant advancement in molecular imaging, providing researchers with the necessary tools to explore intricate biological processes and advance biomedical research.\n\n## References\n\n1. https://www.milabs.com/u-spect/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC11241697/\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "23f7a2fd", "9c8d648e", "0c8677f6", "cf8f008b", "64543c53" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "8fa56005", "name": "micro-SPECT-CT", "original_id": "67ebbaed-164c-4aa7-bbf3-cae42343ea42", "description": "High-res micro-SPECT-CT: 0.3mm, dynamic imaging, preclinical applications.", "documentation": "## Nuclear medicine: PET, PET/CT, SPECT, SPECT/CT\n---\n**Nuclear Medicine is the field dedicated to the imaging of short-lived radiolabelled compounds injected into the body, and is thus true ‘molecular imaging’. Due to its exquisite sensitivity, very low amounts of compounds that bind to cellular targets (radioligands) or are substrates for biological processes (radiotracers) can be detected, providing quantitative information about the rate of biological processes or number of receptors within organs and tissues without altering the underlying biology (the ‘tracer’ principle). Nuclear medicine makes use of two major modalities depending on the type of radioisotope used for radiolabelling, namely PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computed Tomography).**\nPET and SPECT imaging can be performed as single modality acquisition but are more often used in combination with CT (PET-CT, SPECT-CT) or [MRI (PET-MRI)](https://www.eurobioimaging.eu/service/MRI-PET), which allow for precise spatial localization of the PET/SPECT signals within the body.\n\n## AI Generated Documentation\n\n**Overview** \nMicro-SPECT-CT (Single Photon Emission Computed Tomography-Computed Tomography) is a cutting-edge imaging technology that merges the functional imaging capabilities of SPECT with the anatomical detail provided by CT. This hybrid modality is particularly suited for preclinical research, enabling in vivo visualization of biological processes in small animal models with high precision and sensitivity. \n\n**Key Capabilities** \nMicro-SPECT-CT systems, such as the Mediso nanoScan® SPECT/CT, achieve spatial resolutions down to 0.3 mm, making them capable of detecting minute biological changes. The technology employs advanced multi-pinhole collimators that optimize imaging performance for various applications, ranging from whole-body scans to focused imaging of small animals like mice and rats. The systems utilize thick sodium iodide (NaI:Tl) crystals (9.5 mm) for enhanced sensitivity, particularly for high-energy isotopes. Additionally, the Tera-Tomo™ 3D SPECT reconstruction algorithm provides absolute quantitative imaging through real-time Monte Carlo simulations, allowing for precise assessment of radiotracer distribution. \n\n**Applications** \nMicro-SPECT-CT is extensively utilized in biomedical research, particularly in the following areas: \n- **Oncology**: Imaging metabolic processes and receptor binding in tumors, facilitating the assessment of tumor biology and treatment responses. \n- **Pharmacokinetics**: Evaluating drug distribution and efficacy in preclinical trials, essential for drug development. \n- **Cardiovascular and Neurological Studies**: Monitoring disease progression and therapeutic interventions in heart and brain disorders. \n- **Gene Expression Studies**: Investigating cellular processes and gene therapy effects in live subjects. \n\n**Advantages** \nThe integration of SPECT and CT in a single platform offers several distinct advantages: \n- **Enhanced Diagnostic Accuracy**: The combination of functional and anatomical data improves localization and characterization of lesions. \n- **High Sensitivity and Resolution**: The ability to detect small lesions and subtle biological changes is critical for early diagnosis and treatment monitoring. \n- **Dynamic Imaging Capability**: The system allows for rapid acquisition of data without gantry or table motion, which is essential for time-sensitive studies. \n\nIn summary, micro-SPECT-CT stands out in the field of preclinical imaging by providing a powerful tool for researchers to explore complex biological systems and improve therapeutic strategies through its high-resolution, quantitative imaging capabilities.\n\n## References\n\n1. https://mediso.com/global/en/product/pre-clinical-products/nanoscanr-spectct\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC11241697/\n3. https://link.springer.com/book/10.1007/978-3-030-65850-2\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "e0395c6a", "3850f7eb", "0c8677f6", "cf8f008b", "d2be2f9c", "64543c53", "706cb740", "f1099f78" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "2ce231cc", "name": "micro-US", "original_id": "0d82e46a-ca31-428b-99ee-ad61d2c373dc", "description": "29 MHz resolution, real-time imaging, prostate cancer diagnosis, biopsy guidance.", "documentation": "## Ultrasound Imaging (US)\n---\nUltraSound Imaging (US) relies on the use of Ultrasound. Ultrasonic images are created by sending pulses of ultrasound into tissues and recording echoes, which are reflected to a different extent by different tissues.\nIn microUS, the instrumentation is implemented with accessories or with a technical set-up which provide optimum resolution and sensitivity for small animal studies.\nThe resolution range of US depends on which transducer is used. The higher transducer resolution, the higher the frequency, but the smaller the FOV. By choosing the right transducer it is thus possible to optimize US resolution and sensitivity for a specific organ or other tissue.\nUS imaging is particularly suitable to visualize soft tissues such as muscles, tendons, organs etc and for cardiovascular studies.\nSpecific US techniques and example applications of US imaging can be found  in the following articles:\n* C.M. Moran & A.J.W. Thomson, “Preclinical Ultrasound Imaging - A Review of Techniques and Imaging Applications”, \n* A. Coppola  et al., “Imaging in experimental models of diabetes” \n**Within Euro-BioImaging, preclinical US Imaging is provided by the following Nodes:**\n* [Austrian BioImaging / CMI (AT)](https://www.eurobioimaging.eu/nodes/austrian-bioimagingcmi)\n* [Brain Imaging Network (PT)](https://www.eurobioimaging.eu/nodes/brain-imaging-network-bin)\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish BioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)\n* [Facility of Multimodal Imaging - AMMI Maastricht (NL)](https://www.eurobioimaging.eu/nodes/facility-of-excellence-in-imaging---alm-and-molecular-imaging-node-maastricht)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Flanders BioImaging Node (BE)](https://www.eurobioimaging-access.eu/nodes/flanders-bioimaging-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM (NO)](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n* [Preclinical Imaging Centre (PRIME)](https://www.eurobioimaging.eu/nodes/preclinical-imaging-centre-(prime)---molecular-imaging-dutch-node)\n### Use cases\nClick here for\n[Use Cases](/content/use-cases/#US) from our Nodes.\n## B-Mode (2D, 3D, 4D) US\nB-mode (or brightness-mode) imaging is the most commonly used mode in\nultrasound imaging. In 2D B-Mode US images the organs and tissues of\ninterest are depicted as dots of variable brightness, depending on the\namplitude of the returned echo signal.\n3D preclinical ultrasound images are generated by the acquisition of\nconsecutive B-mode ultrasound images acquired at discrete step sizes\nalong a predetermined path. Commercial software then reconstructs the\n3D volume.\nUsing High Frequency UltraSound (HFUS, frequency higher than 10MHz)\nallows to obtain very high resolution images (e.g. up to the\nmicroscopic scale in preclinical imaging).\nB-mode US imaging is widely used for visualizing and quantifying\nanatomical structures, such as for example organs, lesions, cysts or\ntumors as well as for the visualization of cardiac and vascular\nmovement across the cardiac cycle. Complete 3D acquisitions are\npossible over a cardiac cycle (4D) enabling the dynamic movement of\nthe heart to be viewed from any orientation.\n![](upload/Bmode.png)\n2D B-mode image of a rat heart in diastole, from [https://doi.org/10.3389/fphy.2...](https://doi.org/10.3389/fphy.2020.00124)\nB-Mode US imaging is also used for needle placement during injection or aspiration\nprocedures.\n![](upload/needle.png)\nNeedle localization by HFUS. From the Molecular Imaging Italian Node, Naples [(https://doi.org/10.1089/thy.2015.0511)](https://doi.org/10.1089/thy.2015.0511)\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Finnish Biomedical Imaging Node (FI)](https://www.eurobioimaging.eu/nodes/finnish-biomedical-imaging-node)\n* [Israel BioImaging (IL)](https://www.eurobioimaging.eu/nodes/israel-bioimaging)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## M-Mode US\nM-mode imaging or motion-imaging is used principally to study fast moving structures such\nas heart-wall or valvular movement. A single line is selected in the B-mode image\nintersecting the chamber walls or valves of interest and ultrasound data is acquired only\nalong the pre-selected M-mode line. Consequently data is acquired with high temporal\nresolution, as only one line of data is acquired rather than 128 lines of data in a full\nB-mode image. The M-mode data is displayed as a continuous function of time scrolling across\nthe screen with depth on the y-axis and time on the x-axis.\nSee for example: Zhou YQ et al. “Comprehensive transthoracic cardiac imaging in mice using\nultrasound biomicroscopy with anatomical confirmation by magnetic resonance imaging”.\n![](upload/mmode.png)\nM-Mode US imaging of the right ventricle with wall thickness measurements.\nCourtesy from Visualsonics\n**Available at:**\n* ****[Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)****\n* ****[NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)****\n****## Color Doppler, Power Doppler (2D, 3D) US\nDoppler techniques are used to measure blood flow based on the Doppler principle: the\nfrequencies of transmitted and received US beams are different and the difference depends\non the velocity of the scattering red blood cells along the blood flow direction, on the\nUS beam frequency and on the angle between the US beam and the flow direction.\nUsing Color Doppler Mode, flow velocities within vessels are color-coded and the color\nintensity is a function of velocity. Blood moving away from the transducer (larger\nwavelength, i.e. red-shift) is usually encoded in shades of blue while blood moving toward\nthe transducer (shorter wavelength, i.e. blue-shift)  is encoded in shades of\nred.\nColor Doppler provides a visual overview of the flow within the vessels or in the heart,\nprovides an assessment of the flow direction and velocity and, when combined with 3D mode,\nallows to quantify the volume and percent of vascularity.\nIn Power Doppler mode the Doppler signal is displayed as a function of time within a\npre-selected region of interest. In this case, no directional information on blood flow is\nobtained but power Doppler is useful in the detection of small vessels containing slower\nblood flow and it allows to evaluate the percent vascularity.  Changes in vascularity\ncan be informative on the progression and regression of pathologies or on the response to\ntherapy.\n![](upload/colorus.png)\nPower Doppler image of mouse testes, from [https://doi.org/10.3389/fphy.2...](https://doi.org/10.3389/fphy.2020.00124)\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n* [NORMOLIM](https://www.eurobioimaging.eu/nodes/normolim,-norwegian-molecular-imaging-infrastructure)\n## Pulsed Wave Doppler US\nIn Pulsed Wave (PW) Doppler US, short and quick pulses of sound are sent and reflected\nsound waves between the pulses are analyzed. In respect to continuous Doppler techniques,\nPW Doppler US has the advantage of providing an accurate measure  of the blood\nvelocity in a precise location and in real time.\nPW Doppler can measure velocity of diastolic function, right ventricular function, renal\nartery resistive index and pulsatility index or abdominal aortic velocities.\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n## Non-Linear Contrast Mode US\nNonlinear Contrast Imaging is performed by intravenously injecting microbubbles, which on\nthe opposite of tissues which typically react linearly to ultrasound energy, react in a\nnon-linear way to the same energy (S. Unnikrishnan et al. “Microbubbles as Ultrasound\nContrast Agents for Molecular Imaging: Preparation and Application”, ).\nThus, after removing or canceling the linear component of the backscattered signal, the\nincrease in non-linear signal as a function of time allows the evaluation of the kinetics\nand dynamic enhancement of organs. Non-targeted microbubbles allow to visualize and\nquantify blood perfusion within an organ or tissue of interest in 2D or 3D. Targeting\nmicrobubbles can also be used to visualize specific biomarkers e.g. in tumors.\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Molecular Imaging Italian Node (IT)](https://www.eurobioimaging.eu/nodes/molecular-imaging-italian-node)\n## US - Volumetric analysis\nVolumetric analysis is used to quantify the amount of the drug or contrast agent in the\nspecific organ volume. A 3D scan is used for this purpose.\n**Available at:**\n* [Center for Advanced Preclinical Imaging (CAPI) (CZ)](https://www.eurobioimaging.eu/nodes/center-for-advanced-preclinical-imaging-capi)\n* [Danish\nBioImaging (DK)](https://www.eurobioimaging.eu/nodes/danish-bioimaging)****\n\n## AI Generated Documentation\n\n**Overview** \nMicro-ultrasound (micro-US) is a cutting-edge imaging technology that employs high-frequency ultrasound waves, typically operating at 29 MHz, to provide exceptional resolution in tissue imaging. This technology is particularly significant in the field of urology, specifically for the diagnosis and management of prostate cancer (PCa). Micro-US distinguishes itself from traditional ultrasound and other imaging modalities through its ability to detect tissue alterations as small as 100 microns, enabling precise visualization of pathological changes. \n\n**Key Capabilities** \nMicro-US systems are designed to integrate seamlessly with multiparametric MRI (mpMRI) data, enhancing the diagnostic workflow and improving the targeting accuracy for biopsy procedures. The imaging process is facilitated by a standardized risk assessment scale known as PRI-MUS, which categorizes findings based on their likelihood of malignancy. This integration allows clinicians to make informed decisions based on comprehensive imaging data. The technology supports both transrectal and transperineal biopsy techniques, making it versatile for various clinical applications. \n\n**Applications** \nThe primary application of micro-US is in the diagnosis and characterization of clinically significant prostate cancer (csPCa). Research has shown that micro-US offers detection rates comparable to mpMRI, making it a valuable tool for both initial diagnosis and active surveillance protocols. It is particularly useful in guiding reclassification biopsies, optimizing treatment decisions, and staging prostate cancer by identifying extraprostatic extension. The technology's real-time imaging capability allows for immediate assessment during procedures, enhancing clinical outcomes. \n\n**Advantages** \nMicro-US offers several advantages over traditional imaging modalities. Its high sensitivity and negative predictive value are critical for effective patient management. The non-invasive nature of the technology, combined with its cost-effectiveness compared to other imaging techniques, makes it accessible for widespread clinical use. Furthermore, ongoing advancements, including potential integration with artificial intelligence, promise to enhance the diagnostic accuracy and overall utility of micro-US in clinical practice. In summary, micro-ultrasound represents a significant advancement in biomedical imaging, particularly for prostate cancer management, offering high-resolution imaging, integration with existing diagnostic modalities, and a robust framework for clinical decision-making.\n\n## References\n\n1. https://www.marsbioimaging.com/\n2. https://pmc.ncbi.nlm.nih.gov/articles/PMC9691355/\n3. https://link.springer.com/chapter/10.1007/978-3-031-78135-3_61\n\n**AI Enhancement Confidence Score:** 0.95\n", "provider_node_ids": [ "2b34e271", "6e382796", "9c8d648e", "3850f7eb", "0c8677f6", "9beefd47", "d2be2f9c", "3e52fd14", "64543c53", "e5f30cac", "706cb740" ], "abbr": "", "category": { "id": "d8cc9cda-6406-4a71-bc44-553cca9ae938", "name": "Animal and plant Imaging\t\t\t\t\t\t\t\t\t\t\t\t" } }, { "id": "0abb2c96", "name": "post-embed Correlative Light and Electron Microscopy (on-section CLEM)", "original_id": "95f3c035-6373-4bbd-bc40-89009fd2fb59", "description": "Correlative Light and Electron Microscopy (CLEM) combines the advantages of both techniques, allowing scientists to spot cellular structures and processes of interest in whole cell images with LM and then zoom in for a closer look with EM. \r\nIn post-embedding CLEM, fluorescently-tagged molecules within the sample are preserved during the sample preparation for EM. To maintain the fluorescence, either specialised fixation methods or specialised fluorescent proteins are commonly used, to allow the fluorescence to survive the fixation. \r\nPlastic sections are collected and screened with a fluorescence microscope. Thanks to fiducial markers which are fluorescent and electron dense, the precise location of the fluorescent spots is retrieved in the EM enabling the ultrastructural assignment to the fluorescent marker. The precision of such CLEM is in the range of 50 to 100 nm. Very often, TEM tomography is performed on such samples.\r\n\r\nCLEM on Tokuyasu sections belongs to the “on-section” CLEM techniques. The difference is on the sample preparation. Here, specimens are chemically fixed, cryo-protected and frozen. The sample is then hard enough to be sectioned by cryo-ultramicrotomy. Next, the cryo-sections are thawed and exposed to probes or antibodies. If fluorescent probes are used, their signal can be correlated to the ultrastructure by CLEM.\r\n\r\nAn alternative method to post-embedding CLEM is pre-embedding CLEM, which has a different trade-off of challenges and advantages in performing the light microscopy at a different stage of the sample preparation process. \r\n\r\nThe Euro-BioImaging Nodes offering these techniques will support users in selecting the best method for their particular sample and scientific question.\r\n", "documentation": "", "provider_node_ids": [ "90c8b0d6", "d039b533", "b19711d3", "fc1893d4", "9beefd47", "64543c53", "f1099f78" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "90e98166", "name": "post-embedding CLEM (post-emb CLEM)", "original_id": "2b64a79b-c487-4597-a827-6310aa10bf9f", "description": "Correlative Light and Electron Microscopy (CLEM) combines the advantages of both techniques, allowing scientists to spot cellular structures and processes of interest in whole cell images with LM and then zoom in for a closer look with EM. \r\nIn post-embedding CLEM, fluorescently-tagged molecules within the sample are preserved during the sample preparation for EM. To maintain the fluorescence, either specialised fixation methods or specialised fluorescent proteins are commonly used, to allow the fluorescence to survive the fixation. \r\nPlastic sections are collected and screened with a fluorescence microscope. Thanks to fiducial markers which are fluorescent and electron dense, the precise location of the fluorescent spots is retrieved in the EM enabling the ultrastructural assignment to the fluorescent marker. The precision of such CLEM is in the range of 50 to 100 nm. Very often, TEM tomography is performed on such samples.\r\n\r\nCLEM on Tokuyasu sections belongs to the “on-section” CLEM techniques. The difference is on the sample preparation. Here, specimens are chemically fixed, cryo-protected and frozen. The sample is then hard enough to be sectioned by cryo-ultramicrotomy. Next, the cryo-sections are thawed and exposed to probes or antibodies. If fluorescent probes are used, their signal can be correlated to the ultrastructure by CLEM.\r\n\r\nAn alternative method to post-embedding CLEM is pre-embedding CLEM, which has a different trade-off of challenges and advantages in performing the light microscopy at a different stage of the sample preparation process. \r\n\r\nThe Euro-BioImaging Nodes offering these techniques will support users in selecting the best method for their particular sample and scientific question.\r\n", "documentation": "", "provider_node_ids": [ "d039b533", "b19711d3", "0c8677f6", "fc1893d4", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "0dee2953", "name": "pre-embed Correlative Light and Electron Microscopy (pre-embed CLEM)", "original_id": "30d6596b-4cb0-49b3-83dc-20d9f0f0b2c6", "description": "Correlative Light and Electron Microscopy (CLEM) combines the advantages of both techniques, allowing scientists to spot cellular structures and processes of interest in whole cell images with LM and then zoom in for a closer look with EM. \r\nPre-embedding CLEM obtains the fluorescent images before the sample is processed for EM. This provides the advantage that the fluorescence signal can be collected under optimal conditions. Most fluorescence probes do not survive the EM sample preparation process without total or significant loss of signal. However, due to changes in sample morphology during the fixation and post-processing for EM, correlation of pre-embedding fluorescence images with post-embedding EM images can present a challenge. \r\n\r\nAn alternative method to pre-embedding CLEM is post-embedding CLEM, which has a different trade-off of challenges and advantages in performing the light microscopy at a different stage of the sample preparation process. \r\n\r\nThe Euro-BioImaging Nodes offering these techniques will support users in selecting the best method for their particular sample and scientific question.\r\n", "documentation": "## pre-embed Correlative Light and Electron Microscopy (pre-embed CLEM)\n---\n**Correlative Light and Electron Microscopy (CLEM) combines the advantages of both techniques, allowing scientists to spot cellular structures and processes of interest in whole cell images with LM and then zoom in for a closer look with EM.\nIn post-embedding CLEM, fluorescently-tagged molecules within the sample are preserved during the sample preparation for EM. To maintain the fluorescence, either specialised fixation methods or specialised fluorescent proteins are commonly used, to allow the fluorescence to survive the fixation.\nPlastic sections are collected and screened with a fluorescence microscope. Thanks to fiducial markers which are fluorescent and electron dense, the precise location of the fluorescent spots is retrieved in the EM enabling the ultrastructural assignment to the fluorescent marker. The precision of such CLEM is in the range of 50 to 100 nm. Very often, TEM tomography is performed on such samples.\nCLEM on Tokuyasu sections belongs to the “on-section” CLEM techniques. The difference is on the sample preparation. Here, specimens are chemically fixed, cryo-protected and frozen. The sample is then hard enough to be sectioned by cryo-ultramicrotomy. Next, the cryo-sections are thawed and exposed to probes or antibodies. If fluorescent probes are used, their signal can be correlated to the ultrastructure by CLEM.\nAn alternative method to post-embedding CLEM is pre-embedding CLEM, which has a different trade-off of challenges and advantages in performing the light microscopy at a different stage of the sample preparation process.\nThe Euro-BioImaging Nodes offering these techniques will support users in selecting the best method for their particular sample and scientific question.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "d039b533", "b19711d3", "46ccfb38", "fc1893d4", "9beefd47", "64543c53", "09122290" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "13e1b5d4", "name": "pre-embedding CLEM (pre-emb CLEM)", "original_id": "078f977d-64d2-4e82-a68f-e998c5f771b9", "description": "Correlative Light and Electron Microscopy (CLEM) combines the advantages of both techniques, allowing scientists to spot cellular structures and processes of interest in whole cell images with LM and then zoom in for a closer look with EM. \r\nPre-embedding CLEM obtains the fluorescent images before the sample is processed for EM. This provides the advantage that the fluorescence signal can be collected under optimal conditions. Most fluorescence probes do not survive the EM sample preparation process without total or significant loss of signal. However, due to changes in sample morphology during the fixation and post-processing for EM, correlation of pre-embedding fluorescence images with post-embedding EM images can present a challenge. \r\n\r\nAn alternative method to pre-embedding CLEM is post-embedding CLEM, which has a different trade-off of challenges and advantages in performing the light microscopy at a different stage of the sample preparation process. \r\n\r\nThe Euro-BioImaging Nodes offering these techniques will support users in selecting the best method for their particular sample and scientific question\r\n", "documentation": "", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "d039b533", "b19711d3", "46ccfb38", "0c8677f6", "fc1893d4", "64543c53", "a44edc42", "f1099f78" ], "abbr": "", "category": { "id": "a25c8e07-7a33-45df-8b4a-85872af50d67", "name": "Correlative Light Microscopy and Electron Microscopy" } }, { "id": "143e2504", "name": "pre-embedding immunolabelling (pre-embed IL)", "original_id": "97bd2bd4-17de-42c9-9bbd-ab8243676827", "description": "In contrast to immuno-gold EM on sections, in pre-embedding immunolabeling, the sample is immunolabeled before the standard processing for EM takes place. This can offer the advantage of improved antibody recognition of the targets, as it is not hampered by the fixation process. \r\n\r\nThe Euro-BioImaging Nodes offering these services will advise you whether pre-embedding immunolabeling or immuno-gold EM on sections is best suited for your particular sample and scientific question.\r\n", "documentation": "## Pre-embedding Immunolabelling (pre-embed IL)\n---\n**In contrast to immuno-gold EM on sections, in pre-embedding immunolabeling, the sample is immunolabeled before the standard processing for EM takes place. This can offer the advantage of improved antibody recognition of the targets, as it is not hampered by the fixation process.\nThe Euro-BioImaging Nodes offering these services will advise you whether pre-embedding immunolabeling or immuno-gold EM on sections is best suited for your particular sample and scientific question.**\n\n", "provider_node_ids": [ "522e8aaa", "fcf6bac6", "90c8b0d6", "2b34e271", "ca2e3748", "d039b533", "46ccfb38", "fc1893d4", "64543c53", "a44edc42", "e5f30cac", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "0322ced1-416a-4e40-badc-fcb5e1fc57d5", "name": "Ultrastructural localization of molecules" } }, { "id": "d169e03b", "name": "serial section TEM (ssTEM)", "original_id": "bfb36ae0-c46d-455e-9f8d-a4616164985f", "description": "ssTEM is performed on series of thin sections that are acquired by conventional ultramicrotomy, compared to the ribbons of sections in Array Tomography. The sections are collected on EM grids and imaged sequentially by transmission electron microscopy (TEM). Specific methods exists to allow the post-hoc reconstruction of the spatial relationship of the imaged sections, allowing the 3D reconstruction of the sample volume.", "documentation": "## Serial Section TEM (ssTEM)\n---\n**ssTEM is performed on series of thin sections that are acquired by conventional ultramicrotomy, compared to the ribbons of sections in Array Tomography. The sections are collected on EM grids and imaged sequentially by transmission electron microscopy (TEM). Specific methods exists to allow the post-hoc reconstruction of the spatial relationship of the imaged sections, allowing the 3D reconstruction of the sample volume.**\n\n", "provider_node_ids": [ "522e8aaa", "90c8b0d6", "ca2e3748", "d039b533", "b19711d3", "fc1893d4", "9beefd47", "64543c53", "f1099f78", "09122290" ], "abbr": "", "category": { "id": "a21b9e32-1f69-4a4e-b657-2f5ad081273b", "name": "Ultrastructural analysis in 3D (volume EM)" } } ], "nodes": [ { "id": "522e8aaa", "name": "Advanced Light Microscopy Italian Node", "original_id": "7409a98f-1bdb-47d2-80e7-c89db73efedd", "description": "Italy's multi-modal node: 5 sites, advanced imaging, diverse applications.", "documentation": "## ITALY\n## Advanced Light Microscopy Italian Node\n---\n**The Italian ALM Node is a large multi-modal and multi-sited Node that comprises five imaging facilities located in Naples, Genoa, Padua, Florence and Milan.**\nThe Italian ALM Node is a large multi-modal and multi-sited Node that comprises five imaging facilities located in:\n**Naples:** Institute of Biochemistry and Cell Biology ()\n**Genoa:** Italian Institute of Technology ([https://www.iit.it/research/lines/nanoscopy-nic-iit](https://www.iit.it/it/web/nanoscopy-and-nikon-centre-iit))\n**Padua:** Laboratory of CA2+ and cAMP signaling in physiology and pathology ([https://www.biomed.unipd.it/ricerca/aree-tematiche/cell-signaling/ca2-and-camp-signalling-physiology-and-pathology](https://www.biomed.unipd.it/ricerca/aree-tematiche/cell-signaling/ca2-and-camp-signalling-physiology-and-pathology#))\n**Florence:** European Laboratory for Non-linear Spectroscopy, LENS ()\n**Milan:** Advanced Light and Electron Microscopy Bio-Imaging Centre (Alembic) ()\nThese facilities have a long experience of mutual interaction and collaboration. The Node is coordinated by the Institute of Biochemistry and Cell Biology, Naples, an institute belonging to the National Research Council of Italy. The Node provides open-access imaging services to both academia and industry and serves about 1000 users annually. While each location provides access to a wide range of technologies, they also specialize in one or two specific technologies as listed below. The Node offers a complete service package starting from sample preparation and imaging to final image analysis, quantitation and visualization.\n### Specialties and expertise of the Node\nThe facilities of this Node offer a broad range of services but they specialize in particular in the following technologies and research areas:\n#### Technologies\n* Naples: Correlative light electron microscopy with 3D imaging, correlative microscopy with FRET imaging\n* Genoa: Super-resolution, multiphoton and fast volumetric imaging\n* Padua: Functional imaging, FRET-based imaging, FRAP, Two-photon microscopy in living cells, tissues and animals\n* Florence: Non-linear microscopy, functional imaging in animals and structural imaging of cleared and expanded samples (human and animal), 2D - 3D single molecule localization and tracking\n* Milan: Correlative microscopy with 3D tomography, large sample imaging, high-throughput microscopy and in-flow microscopy\n#### Research applications\n* Naples: Cell biology, membrane trafficking, signaling, cancer biology\n* Genoa: Development of novel technologies and instruments for advanced diagnostics from the nano- to the macro-scale\n* Padua: Signaling, neurobiology, intracellular signaling molecules real time imaging, two-color microscopy, biosensors generation and characterization\n* Florence: Human and mouse brain connectome reconstruction, Neurodegenerative diseases, Remapping of lost functions after stroke, Clearing specimens, Multimodal fiber-probe spectroscopy for tissue diagnostics, Bacterial biofilm\n* Milano: Cell biology, Neuroscience, Oncology, Immunology, Gene and Cell Therapy\nThe member groups also have experience with a wide spectrum of model systems including mammalian cell culture systems, insect cell culture systems, and model organisms like Drosophila, Zebrafish and mouse and also with handling human tissue samples.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| 4PI | ✓ | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| Raman Spectroscopy (RS) | ✓ | ✓ |\n| Second/Third Harmonics Generation (SHG/THG) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Voltage/pH/Ion Imaging \\* | ✓ | – |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Expansion Microscopy \\* | ✓ | ✓ |\n| Tissue Clearing (TC)\\* | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| EM tomography | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| FIB-SEM | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| Pre-embed CLEM | ✓ | ✓ |\n| Pre-embeded CLEM | ✓ | ✓ |\n| Atomic Force Microscopy (AFM)\\* | ✓ | – |\n| Mass spectrometry-based imaging\\* (MSI) | ✓ | – |\n### Additional services offered by the Node\n* Support in experimental design\n* Technical assistance to use the microscopes\n* Practical training courses\n* Cell culture facilities\n* Wet lab space\n* Animal facilities\n* Data processing and analysis\n* Biosensors generation and characterization\n### Instrument highlights\nThe members of the Italian ALM Node are also involved in the development of novel imaging methods, instrumentation and reagents. These include:\n* Naples: FRET-based methods to detect large multi-molecular complexes, Raman microscopy, image analysis methods and microfluidics\n* Genoa: Super-resolution microscopy, fast volumetric light sheet, Expansion Microscopy, correlative light - atomic force microscopy (AFM-STED)\n* Padua: functional imaging, genetically encoded and chemical probes for functional imaging of intracellular signaling molecules and metabolites, whole brain and tissue two-photon microscopy\n* Florence: functional imaging, Raman imaging, whole brain and tissue expansion imaging\n* Milan: Correlative light Microscopy methods, High-throughput microscopy approaches and image analysis\n### Contact details\n**Alberto Luini**\nCoordinator of the Italian ALM Node\n[alberto.luini@ibbc.cnr.it](mailto:alberto.luini@ibbc.cnr.it)\n+39 081 6132 535\n**Seetharaman Parashuraman**\nHead, Bioimaging facility, IBBC-CNR\n[raman@ibbc.cnr.it](mailto:raman@ibbc.cnr.it)\n+39 081 6132 283", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "d3d66a1d", "f1f735b6", "f68070c5", "e7adfd19", "dcb85d5e", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "3a4d793f", "f05d797c", "a2a0f4a8", "af33ff84", "df1896a3", "d169e03b", "eebba7a7", "e32e05f1", "143e2504", "0dee2953", "13e1b5d4", "a9f0fcad", "4b561f4f", "a6cee2e2", "4e5bcb9e" ], "country": { "id": "0af8a17e-b371-4f0b-a408-9ee57dc20943", "name": "Italy", "iso_a2": "IT" } }, { "id": "fcf6bac6", "name": "Advanced Light Microscopy Node Poland", "original_id": "099e48ff-7204-46ea-8828-10025e945081", "description": "Multi-modal imaging: super-resolution, CLEM, high-throughput, training.", "documentation": "## POLAND\n## Advanced Light Microscopy Node Poland\n---\n**The Polish Advanced Light Microscopy (ALM) Node is a multi-sited, multimodal EuroBioimaging Node offering open access to instrumentation in biological imaging including multi-modal ALM, CLEM, EM, functional imaging, high-throughput microscopy and super-resolution microscopy. The ALM Polish Node provides full hands-on and theoretical training in all of the imaging techniques available at the Node facilities. We support in-house scientists and visitors in using microscopy methods, project planning, sample preparation, microscope selection and use, image processing and visualization. Our Node comprises two imaging facilities located in Warsaw at the Nencki Institute of Experimental Biology PAS and the Mossakowski Medical Research Centre PAS and one imaging facility in Cracow at the Faculty of Biochemistry, Biophysics and Biotechnology, Jegiellonian University.**\n### Specialties and expertise of the Node\nExpertise in the study of life at all major levels of organization, beginning at the molecular and elemental levels, through subcellular organelle dynamics, cellular and tissue-level processes, as well as the whole organism. The main fields of expertise: molecular interactions, protein dynamics, single molecule methods, intracellular processes in neuronal cells, energy metabolism (in cancer, cardiovascular, neurodegeneration), cell biology (nucleus, mitochondria, cytoskeleton, Golgi complex), physiology of the cell (intracellular membrane transport, membrane channels, apoptosis, regeneration stem cells, lymphoma cells, pharmacology).\n![](upload/poland_collage.png)\n*The collage of images acquired by our users*\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ |\n| Quantitative Phase Imaging\\* (QPI) | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n| Microdissection \\*\\* | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ |\n| EM tomography | ✓ |\n| serial section TEM | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ |\n| pre-embeded CLEM | ✓ |\n### Additional Services offered by the Node\n* Instruments\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Technical assistance to run instrument\n* Wet lab space and cell culture room\n* Data processing and analysis\n### Instrument highlights\nSpecial features of instruments at the Polish ALM Node:\n* Availability of array of different imaging modalities, including: spectral, two-photon, time-resolved and super-resolution fluorescence microscopy\n* The use of 3D high-resolution imaging with block-face Scanning electron microscopy (SEM)\n![](upload/animated_microscope.png)*Our new friend: CD7 LSM900 automated microscope (upper left corner) and the rest of the equipment*\n### Contact details\n**Olga Sumara**, [o.sumara@nencki.edu.pl](mailto:o.sumara@nencki.edu.pl)\nOffice of International Relations and Project Management at the Nencki Institute of Experimental Biology PAS\n**Joanna Szczepanowska**, [j.szczepanowska@nencki.edu.pl](mailto:j.szczepanowska@nencki.edu.pl)\nProfessor at Nencki Institute of Experimental Biology Polish Academy of Sciences\n**Jędrzej Szymański**, [j.szymanski@nencki.edu.pl](mailto:j.szymanski@nencki.edu.pl)\nHead of the Laboratory of Imaging Tissue Structure and Function at the Nencki Institute of Experimental Biology PAS\n+4822 5892508", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "d3d66a1d", "f1f735b6", "f6b01df1", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "b5ef918c", "af33ff84", "df1896a3", "c9ddc22b", "3f84bc36", "143e2504", "0dee2953", "c60b4a73", "13e1b5d4", "4e5bcb9e" ], "country": { "id": "2d6e489f-0893-4e1f-83cc-6cc729e28a3d", "name": "Poland", "iso_a2": "PL" } }, { "id": "638ca876", "name": "Advanced Light Microscopy and Medical Imaging Node Brno CZ", "original_id": "510ac696-5bb2-40ad-8ed7-611db9a0b7aa", "description": "Brno CZ: 9.4T ultra-high field MR, multi-modal imaging, training programs.", "documentation": "## CZECH REPUBLIC\n## Advanced Light Microscopy and Medical Imaging Node Brno CZ\n---\n**The Czech Advanced Light Microscopy and Medical Imaging Multi Modal Node in Brno provides open access to a wide range of imaging technologies and expertise to all scientists through a unified and coordinated logistics approach. The light microscopy and medical imaging units organize special programs for training scientists in biological and medical imaging techniques and data analysis.**\n### Specialties and expertise of the Node\nThe Euro-BioImaging Node in Brno consists of two parts. The **Medical Imaging** part is formed by two closely collaborating facilities. One is focused on animal ultra-high field MR imaging and spectroscopy (9.4T), the other on human MR imaging (3T) accompanied with electrophysiological techniques. Together, these facilities enable translational research and offer a complex portfolio of MRI techniques including multimodal approaches (e.g. simultaneous EEG-fMRI) and human hyper-scanning (fMRI with two participants measured simultaneously in two scanners). The **Advanced Light Microscopy** part is organized as a central core facility Cellular Imaging (CELLIM) and several closely cooperating laboratories offering together access to equipment, training and image analysis tools. The light microscopy is further specialized in imaging of plant systems, mammalian germs cells, stem cells and embryos, and development of image analysis tools.\nThe Experimental Biophotonics Facility of this Node offers user access to their Q-Phase Multimodal Holographic Microscope developed in-house and commercialized by Tescan / Telight. The microscope provides highly quantitative and rapid measurements of cell behavior, mainly growth and motility, with unprecedented accuracy where the distribution of dry mass inside cells is determined with standard deviation of 0.4 pg/µm2. The microscopy is an implementation of Quantitative Phase Imaging where the dynamic morphometry with live cells in tissue culture is a label free technique and the accuracy is achieved by using an incoherent light source, which also uniquely allows quantitative imaging of cells in 3D environments such as collagen matrix. Integrated fluorescence imaging is available for automated time-lapse with alternating phase imaging and overlaid images are available for examination.\n###\n###\n![](/upload/CELLIM_2.png)\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Image Scanning microscopy (ISM) | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ |\n| Quantitative Phase Imaging\\* (QPI) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Expansion Microscopy \\* | ✓ |\n| Tissue Clearing \\* | ✓ |\n| micro-MRI/MRS (>= 7T) | ✓ |\n| micro-MRI/MRS (>=7T) - ex-vivo | ✓ |\n| Human MRI/MRS (< 7T) | ✓ |\n| Image Analysis-bio \\* | ✓ |\n| Image Analysis-med \\* | ✓ |\n###\n![](/upload/CELLIM_4.jpg)\n###\n### Instrument highlights\nThe Brno Node is equipped with two 3T Siemens Prisma scanners for human medical imaging. These scanners are designed specifically for high quality research data based on features like strong gradient fields, excellent homogeneity of mg. field and excitation, high sensitivity with 64 channel head/neck coils. Simultaneous use of two scanners enables a relatively unique feature of hyper-scanning (dual fMRI). The human MR scanners are accompanied with several MR compatible electrophysiological devices for recording of high-density EEG, ECG, breathing, skin conductance, etc.\nThe Node also offers extensive image analysis services including tailor-made software development.\nBesides providing access to a wide selection of equipment and analysis tools, the light microscopy unit specializes in plant in vivo imaging and techniques useful for research on live mammalian cells, mammalian germ cells, stem cells and embryos. The light microscopy unit CELLIM recently expanded to include a new SIM/SMLM system from Carl Zeiss, the Elyra 7 – Lattice SIM. This instrument provides several imaging modalities, like structural illumination microscopy (SIM), total internal reflection microscopy (TIRF) and single molecule localization microscopy (SMLM), which allows for a wide range of applications.\n###\n![](/upload/MAFIL_MR_scanner.jpg)\n###\n### Contact details\n**Michal Mikl**\nHead of the Node\nRepresentative of medical imaging within node\n[michal.mikl@ceitec.muni.cz](mailto:michal.mikl@ceitec.muni.cz)\n+00420549496099\n**Milan Esner**\nDeputy head of the Node\nRepresentative of microscopic imaging within node\n[milan.esner@ceitec.muni.cz](mailto:milan.esner@ceitec.muni.cz)\n3D view of Multimodal and Functional Imaging Laboratory:\n", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "ff8ab803", "8399c5a7", "31d30c68", "d3d66a1d", "e7adfd19", "f6b01df1", "e9910d1c", "018d2770", "3a4d793f", "f05d797c", "9c64e406", "4a91416e", "639a72d3", "22875d0d", "4707da44", "4e5bcb9e" ], "country": { "id": "86dfebd7-34b9-4794-9440-be27c69f14c4", "name": "Czech Republic", "iso_a2": "CZ" } }, { "id": "90c8b0d6", "name": "Advanced Light and Electron Microscopy Node Prague CZ", "original_id": "456c134f-3603-4fbf-87e7-a70b681a6e4c", "description": "Prague Node: Multi-modal, super-resolution, live imaging, training courses.", "documentation": "## CZECH REPUBLIC\n## Advanced Light And Electron Microscopy Node Prague CZ\n---\n**The Czech Advanced Light and Electron Microscopy Multi Modal Multi Sited Node located in Prague and in České Budějovice offers a wide range of state-of-the-art light and electron microscopy equipment and techniques, offered by seven closely collaborating core facilities. The Node is also active in organizing training and courses focused on theoretical and practical aspects of basic and advanced microscopy techniques. Light microscopy instrumentation includes microscopy systems that range from multi-functional point and spinning disc confocal microscopes, light-sheet and intravital systems, up to high-end multi-photon and super-resolution microscopy systems. In the area of electron microscopy, the Node provides expertise and cutting-edge equipment for a broad range of biological sample preparation and ultrastructural imaging techniques, including some cryo techniques, a complete set of volume EM methods (electron tomography, FIB-SEM, SBF-SEM, AT), EDS elemental analysis and CLEM. Broad expertise in experiment design and data acquisition is also complemented by extensive data analysis services.**\n### Specialties and expertise of the Node\nThe main strength is the wide and deep expertise covering most of light and electron microscopy biological applications, allowed by the complementary nature of collaborating core facilities and more than 25 FTE of expert staff operating more than 50 advanced microscopy systems. In super-resolution imaging all main approaches are covered, including STED, SIM and SMLM, by multiple commercial systems from different manufacturers. Information about molecular dynamics and interactions can be obtained by functional imaging, particularly from spatial-temporal correlation analysis (point, line and image F(C)CS), FRAP, photoactivation, FRET, FLIM or PLIM. Label-free imaging profits from non-linear processes induced by femtosecond NIR lasers and offers methods like SHG, THG, autofluorescence FLIM including metabolic imaging and CARS not only for lipid droplets visualization. Innovative low-toxicity label-free imaging is offered by quantitative phase imaging (QPI). Plants growing in their natural gravity conditions can be directly visualized on the vertical microscope stage of CZ LSM880 with Airyscan. Fast 3D acquisitions are covered by spinning disc and light-sheet systems. In the light intravital microscopy (IVM), the node offers a complete package of services: advanced 2-photon imaging systems, infrastructure for the care and management of small rodents and assistance with surgeries. In electron microscopy the Node offers complete workflow from sample preparation (room temperature or cryo- methods, immunolocalization) through various imaging modalities (TEM, SEM, SBF-SEM, FIB-SEM, array tomography, STEM-EDS elemental analysis) to data analysis (clustering and colocalization in immunolabeling, 3D visualizations). Targeted CLEM workflows allow 3D ultrastructural imaging of rare structures. Data analysis ranges from commercial software packages (Imaris, Huygens, Amira, NIS-Elements and many more) via custom modified routines for image processing and analysis (for example image reconstruction, registration and semi-automatic and AI assisted segmentations, volume reconstruction and 3D visualization, tracking, colocalization analysis, mathematical modeling and analysis of photokinetic experiments, and more) to new software and modules development in the field of stereology and spatial statistics, FLIM and FCS methods.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| cryoFM \\* | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Single Particle Tracking (SPT) | ✓ | - |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| Optical projection tomography (OPT) | ✓ | ✓ |\n| Coherent Raman Anti-stokes Scattering Microscopy (CARS)\\* | ✓ | ✓ |\n| Quantitative Phase Imaging (QPI)\\* | ✓ | ✓ |\n| Polarisation microscopy (PM) | ✓ | ✓ |\n| Second/Third Harmonics Generation (SHG/THG) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Voltage/pH/Ion Imaging \\*\\* | ✓ | - |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Intravital Microscopy (IVM) | ✓ | ✓ |\n| High-speed Imaging \\* | ✓ | ✓ |\n| Imaging at Biosaftey Level>1 | ✓ | - |\n| Photomanipulation | ✓ | ✓ |\n| Phosphorescence Lifetime imaging (PLIM) \\* | ✓ | ✓ |\n| Expansion Microscopy \\* | ✓ | - |\n| Anisotropy/Polarisation Microscopy | ✓ | ✓ |\n| Tissue Clearing (TC)\\* | ✓ | ✓ |\n| Multiplexing imaging (Codex, Opal, Celldive)\\*\\* | ✓ | - |\n| Single molecule FRET \\* | ✓ | - |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| EM tomography (ET) | ✓ | ✓ |\n| Serial Blockface SEM | ✓ | ✓ |\n| Focussed Ion beam SEM (FIB-SEM) | ✓ | ✓ |\n|\n| Array tomography | ✓ | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| Genetic encoded EM probes (e.g. APEX) | ✓ | - |\n| Pre-embed CLEM | ✓ | ✓ |\n| immunolabeling on immobilized particles | ✓ | - |\n| Post-embed CLEM | ✓ | ✓ |\n| Cryo Electron Tomography (Cryo-ET)\\* | ✓ | ✓ |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ | ✓ |\n| Cryo Scanning Electron Microscopy (Cryo-SEM)\\* | ✓ | ✓ |\n| Cryo Focussed Ion beam (Cryo-FIB)\\* | ✓ | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ | ✓ |\n| Elemental analysis including EDS in TEM (STEM)\\* | ✓ | ✓ |\n| Cryo-CLEM\\* | ✓ | ✓ |\n| 3D-CLEM\\* | ✓ | - |\n| live-cell CLEM | ✓ | ✓ |\n| in vivo optical imaging (OI) | ✓ | ✓ |\n| micro-PET/CT | ✓ | – |\n| Long-term vertical-stage confocal/Airyscan microscopy | ✓ | – |\n| Intravital Microscopy | ✓ | – |\n| Atomic Force Microscopy (AFM)\\* | ✓ | – |\n| Image Analysis-bio \\* | ✓ | ✓ |\n### Additional services offered by the Node\n* Instruments\n* Technical assistance to run instrument\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Training in infarstructure use\n* Probe preparation\n* Animal facilities\n* Surgery room\n* Wet lab space\n* Server Space\n* Data processing and analysis\n* Training workstations\n* Training seminar room\n* Housing facilities\n* Biobanking, biological material storage and processing\n### Instrument highlights\nLeica TCS SP8 STED 3X and Abberior Instruments Easy 3D STED, DeltaVision OMX™ V4, Zeiss Elyra 7, Leica STELLARIS 8 FALCON, Leica SP8 AOBS WLL MP, Bruker Ultima IntraVital, Femtonics FEMTO3D Atlas, Carl Zeiss LSM 880 NLO, Nikon CSU-W1 with FRAP, Andor Dragonfly 503, Olympus SpinSR10, Nikon iLas 2 ring-TIRF with FRAP, Carl Zeiss Lightsheet Z.1, vertical-stage plant-optimized Carl Zeiss LSM880 with Airyscan, Akoya PhenoCycler-Fusion, TESCAN Q-PHASE, Jeol JEM-F200 “F2” with STEM and EDS, Thermo-Fisher Helios NanoLab 660 G3, Thermo Fisher UC Apreo VolumeScope SEM, JEOL JEM-2100F with GATAN K2 Summit direct detector), TESCAN Amber Cryo with nanomanipulator, Leica THUNDER Imager EM and SP8 Cryo CLEM\n![](upload/CZ_Prague.jpg)\n### Contact details\nThe Prague Node is managed by the Institute of Molecular genetics CAS. Please see the respective contacts below:\n**Administration contact person**\nDaniela Klimesova: [info.praguenode@czech-bioimaging.cz](mailto:info.praguenode@czech-bioimaging.cz)\n**Strategic representative (representation in the Panel of the Euro-BioImaging Nodes)**\nAleš Benda: [ales.benda@natur.cuni.cz](mailto:ales.benda@natur.cuni.cz)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "60f50c0f", "d3d66a1d", "f1f735b6", "e7adfd19", "17dd34eb", "53fc2771", "f6b01df1", "4ba07d0c", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "d6cec7b4", "f65a70b8", "b5333ef4", "b015d920", "47c84335", "3a4d793f", "f05d797c", "3ba9fb09", "931ee18e", "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0dee2953", "0abb2c96", "a7128dd1", "cb003121", "904149e2", "4b452472", "c60b4a73", "3965a906", "593e3440", "73094724", "c3302077", "a9f0fcad", "59a33aed", "c41fb0d1", "3744dad8", "22875d0d", "a6cee2e2", "4e5bcb9e", "7add3aac", "4e2f1176", "b773e740" ], "country": { "id": "86dfebd7-34b9-4794-9440-be27c69f14c4", "name": "Czech Republic", "iso_a2": "CZ" } }, { "id": "2b34e271", "name": "Austrian BioImaging Node/CMI", "original_id": "53c1631e-2874-4b67-987f-33227d7e6c66", "description": "Austria 8-site: cryo-EM, microCT, microPET, multimodal workflows, data analysis", "documentation": "## AUSTRIA\n## Austrian BioImaging Node/CMI\n---\n**The Austrian BioImaging Node CMI (Correlated Multimodality Imaging Node) is a multi-sited, multimodality Node covering biological and biomedical imaging from cryo-electron and advanced light microscopy up to the preclinical level (including microCT, microMRI, microPET). It is hosted by 8 leading institutions across Austria with a broad service offer for organic materials, biomedical model organisms and humans, numerous multimodality imaging pipelines, and various support services, such as data and image analysis. Imaging technologies at Austrian BioImaging/CMI can be combined or used as stand-alone technologies depending on the specific biomedical research question of the user. Imaging techniques span the entire resolution range of interest for (pre)clinical and biological studies, and provide complementary sample information about structure, function, dynamics and chemical composition. More than 30 imaging techniques allow both in- and ex-vivo imaging and molecular analysis. The Node offers unique imaging techniques and expertise, such as in Optical Coherence Tomography, X-Ray Fluorescence and Mass Spectroscopy Imaging or High-Resolution Episcopic Microscopy. We are specialized in the development of advanced multimodality workflows at the forefront of correlated imaging, which can involve more than two imaging modalities.**\n### Specialties and expertise of the Node\nAustrian BioImaging/CMI has unique expertise in combining and correlating imaging technologies within multimodality pipelines to allow holistic and multiscale characterization of exactly the same sample, establishing an unprecedented and highly beneficial concept for potential customers which is solely guided by the research question at hand rather than by a fixation on a specific imaging technique. This enables Austrian BioImaging/CMI to offer individually customized imaging solutions with a variety of state-of-the-art and unique imaging technologies and support services.\n### Offered Technologies\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n**Offered Technologies:**\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | – |\n| Spinning disk confocal microscopy (SDCM) | ✓ | – |\n| Structured illumination microscopy (SIM)\\* | ✓ | – |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | – |\n| Two-photon microscopy (2P) | ✓ | – |\n| Single Molecula localisation microscopy (SMLM) | ✓ | – |\n| Stimulated emission depletion microscopy (STED) | ✓ | – |\n| Photoacoustic imaging (PAI) - bio\\* | ✓ | – |\n| Coherent Raman Anti-stokes Scattering Microscopy (CARS)\\* | ✓ | – |\n| Raman Spectroscopy (RS) | ✓ | – |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | – |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | – |\n| Brillouin Scattering Microscopy (BSM) \\* | ✓ | – |\n| TEM of chemical fixed samples (TEM) | ✓ | – |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ | – |\n| EM tomography (ET) | ✓ | – |\n| Focussed Ion beam SEM (FIB-SEM) | ✓ | – |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ | – |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | – |\n| Rre-embedding immunolabelling (pre-embed IL) | ✓ | – |\n| Cryo Electron Tomography (Cryo-ET)\\* | ✓ | – |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ | – |\n| Cryo Scanning Electron Microscopy (Cryo-SEM)\\* | ✓ | – |\n| Cryo Focussed Ion beam (Cryo-FIB)\\* | ✓ | – |\n| Scanning Electron Microscopy (SEM) | ✓ | – |\n| micro-MRI/MRS (Field >= 7 T) (HF) | ✓ | – |\n| micro-MRI/MRS (Field < 7 T)(LF) | ✓ | – |\n| micro-PET | ✓ | – |\n| micro-SPECT | ✓ | – |\n| in-vivo micro-CT | ✓ | – |\n| micro-US | ✓ | – |\n| in vivo optical imaging (OI) | ✓ | – |\n| PhotoAcoustic Imaging (PAI) - med | ✓ | – |\n| micro-PET/MRI | ✓ | – |\n| micro-PET/CT | ✓ | – |\n| micro-SPECT/CT | ✓ | – |\n| Correlated Optical Coherence Tomography/PhotoAcoustic Tomography (OCT/PAT) | ✓ | – |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ | – |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ | – |\n| micro-CT - ex-vivo | ✓ | ✓ |\n| Mass spectrometry-based imaging (MSI) - med\\* | ✓ | – |\n| Atomic Force Microscopy (AFM)\\* | ✓ | – |\n| Micro X-ray Fluorescence Spectrometry (XRF)\\* | ✓ | – |\n| Macro Serial Blockface Fluorescence Imaging (S-BFI)\\* | ✓ | ✓ |\n| Image Analysis-bio \\* | ✓ | ✓ |\n| Image Analysis-med \\* | ✓ | ✓ |\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Wet labs\n* Histology labs\n* Cell culture facilities\n* Animal housing\n* Imaging probes\n* Tracer development and radiopharmacy facility with cyclotron\n* Data processing and analysis\n* Data storage\n### Testimonials\n‘Austrian BioImaging/CMI combines tremendous expertise, imaging modalities, and data management services in one organizational structure. It is managed professionally and with a lot of enthusiasm, which makes it a pleasure to work with them. I am particularly pleased with the high quality of services provided for our multimodality imaging project of mouse vasculature, the quick turnover, and also the training opportunities provided.’\nDr. Anna Obenauf, Group Leader, Research Institute of Molecular Pathology (IMP), Vienna BioCenter.\n‘We were very pleased and impressed by the services provided by Austrian BioImaging/CMI for a high-quality (multimodality) analysis of our experimental samples from a a jawbone osteonecrosis project (including AFM, SEM, microCT and XRF). Many thanks for the commitment and the great work of Austrian BioImaging/CMI!’\nAndrea Szabó MD, PhD, University of Szeged, Hungary.\n‘Imaging support for the simulation of surgery and development of implant material at the body donor imaging unit of Austrian BioImaging/CMI was professionally supported by helpful and competent personnel. My stay was very well coordinated and I was able to produce excellent results.’ Dr. med. univ. Guan-Min Ho, Aprevent Medical Ltd.\n![](upload/skeleton_of_ruthenium.png)\nMicroCT-based volume rendering, showing the developing skeleton of a ruthenium red-stained E16.5 mouse fetus.\n![](upload/subungual_vascularisation.jpg)\nHigh Resolution Episcopic Microscopy (HREM) -Subungual Vascularisation.\n![](upload/confocal_laser_scanning.png)\nConfocal laser scanning microscope image of a COS-7 cell, showing the nucleus (DAPI), mitochondria (anti-TOM20, AF488), actin(SiR), and microtubules (anti-tubulin, TRITC).\n### Contact details\nBaubak Bajoghli [baubak.bajoghli@vbcf.ac.at](mailto:baubak.bajoghli@vbcf.ac.at)\n", "offer_technology_ids": [ "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "d3d66a1d", "f1f735b6", "f4eef350", "83b4baea", "53fc2771", "dcb85d5e", "e9910d1c", "018d2770", "af33ff84", "4ae7143c", "df1896a3", "eebba7a7", "e32e05f1", "3f84bc36", "143e2504", "a7128dd1", "cb003121", "904149e2", "4b452472", "c60b4a73", "a9f0fcad", "4b561f4f", "afeaed8d", "9c64e406", "fc3c255a", "4aa5d36d", "36d4a2a7", "b4a6f749", "2ce231cc", "59a33aed", "d54d34a2", "15ef9b0e", "c41fb0d1", "8fa56005", "6709f67e", "4a91416e", "d74face8", "c83c6c2b", "9c814a85", "639a72d3", "22875d0d", "4e5bcb9e", "eeee8c89", "a97f4fa4", "3ef7ea02" ], "country": { "id": "34800c7e-2b30-446b-9701-1b0d934b7754", "name": "Austria", "iso_a2": "AT" } }, { "id": "e532f9cb", "name": "Barcelona Live and Intravital Node", "original_id": "31d6f7d0-adcc-4829-af95-c0e9e67e9dfd", "description": "Live-cell and in vivo imaging, multi-modal techniques, advanced fluorescence.", "documentation": "## SPAIN\n## Barcelona Live and Intravital Node\n---\n**The Barcelona Live and Intravital - Advanced Light Microscopy Node (BLivIN) provides expert support for biomedical projects requiring functional live-cell and in vivo imaging. BLivIN offers expertise in a wide range of advanced and innovative technologies, including widefield fluorescence and transmitted optical microscopy, laser scanning and spinning disk confocal microscopy, two-photon excitation (2PE), second harmonic generation (SHG), Total Internal Reflection Fluorescence (TIRF) and image scanning microscopy (ISM), time-correlated single photon counting, lifetime imaging (or FLIM) and laser photomanipulation. Additionally, the Node supports functional imaging technologies with robust capabilities in image processing, analysis, and custom-developed solutions.**\nTo enhance the success of visitor projects, BLivIN provides tailored planning and comprehensive support throughout all project stages, from experimental design and sample preparation to acquisition, image processing and analysis. Visitors also gain access to complementary resources such as animal facilities, wet labs, cell culture capabilities, and non-invasive bioluminescence imaging.\n### Specialties and expertise of the Node\nOur node provides scientific and technological expertise to extract functional, dynamic, and high-content information from living biological systems through advanced bioimaging applications. Our areas of expertise include:\n* Functional imaging: Techniques based on photobleaching and photoactivation, Fluorescent Resonance Energy Transfer, FRET ratio imaging, Lifetime imaging (FLIM) based on Time-Correlated Single Photon Counting and FLIM/FRET imaging.\n* High-content and high throughput automated live-cell imaging: Long-time lapse, multi-position imaging (mosaics, multi-well plates), live-cell high-content screening, smart screening and rare event detection. Applications include cell tracking, wound healing, autophagy, cell viability, mitochondrial health, protein synthesis, transcription factor activation, cell cycle, mitotic index, cytoskeletal rearrangement, apoptosis (TUNEL), cell proliferation, endocytosis and oxidative stress.\n* Two-Photon in vivo imaging: Deep tissue imaging of organs (brain, skin, liver, kidney, muscle, lymph nodes, eye) in rodents and small animals (Xenopus, Drosophila, zebrafish). Imaging at molecular, subcellular, and cellular levels using transgenic fluorescent animals or intravenous vital fluorescent contrast agents.\n* Non-linear applications: Functional live-cell imaging, photo-stimulation assays (optogenetics, uncaging, photothermal and photochemical studies), SHG for collagen, myosin and starch imaging and third harmonic generation (THG) for lipids studies. Imaging of UV fluorochromes such as Laurdan and Filipin.\n* Fast optical sectioning: Techniques for living samples including image-scanning microscopy and spinning-disk microscopy.\n* Laser nanosurgery: Ablation in living cells and tissues using pulsed laser irradiation, combined with spinning disk or widefield microscopy. Applications include DNA damage kinetics, wound healing, subcellular damage and intra- and inter-cellular (mechanical) tension release, …\n* Bioimage analysis: Our team of four BioImage analysts develops advanced workflows to integrate the processing, analysis, quantification and visualisation and interpretation of Bioimage data. We offer training in commercial and open-source software tools. When these tools are insufficient to extract results, we develop custom workflows that combine various packages and algorithms. Special tools for in vivo imaging tracking and custom deconvolution are also available.\n* Complementary imaging techniques and services: Multimodal or correlative imaging capabilities combined with live/ in vivo imaging applications, such as correlative light and electron microscopy (CLEM), super resolution imaging , light sheet- based imaging and histological sectioning.\n### Offered Technologies\n* Deconvolution widefield microscopy (DWM)\n* Laser scanning confocal microscopy (LSCM/CLSM)\n* Spinning disk confocal microscopy (SDCM)\n* Total internal reflection fluorescence microscopy (TIRF)\n* Two-photon microscopy (2P)\n* Image Scanning Microscopy (ISM)\n* Second/Third Harmonic Generation\n* High throughput microscopy/high content screening (HTM/HCS)\n* Fluorescence Resonance Energy Transfer (FRET)\n* Fluorescence Recovery after Photobleaching (FRAP)\n* Fluorescence Lifetime Imaging (FLIM)\n* Fluorescence (cross)-correlation spectroscopy (FCS/FCCS)\n* Intravital Microscopy (IVM)\n* Microdissection \\*\n* Photomanipulation (Pmnip)\n* Intravital microscopy (IVM) - Med\n* Image Analysis-bio \\*\n### Additional Services offered by the Node\n* Instruments\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Technical assistance to run instrument\n* Training in infrastructure use\n* Training in techniques for optical clearing of biological samples\n* Probe preparation\n* Biological material storage and processing\n* Animal facilities (Rodents, Zebrafish, *Xenopus laevis*, *Xenopus tropicalis, Drosophila melanogaster)*\n* Wet lab space\n* Data processing and analysis\n* Server space\n* Training workstations\n* Training seminar rooms\n* Housing facilities\n* Regulatory affairs management service\n### Instrument highlights\n* Laser nanosurgery (custom system) based on subnanosecond pulsed laser yielding submicron damage control.\n* Lifetime imaging through visible pulsed lasers (including white laser), FLIM analysis in the time domain and phasor plot analysis.\n* Image scanning microscopy (e.g. Airyscan) provides super resolution and/or fast imaging capabilities for live samples.\n* Fast spinning disk with parallel cameras for synchronous multichannel imaging\n* High-content imaging and analysis of multiwell plates includes plates robot-loading and in situ incubation for long term (days, weeks) time lapse imaging. Primary and secondary screenings.\n* Multiphoton microscope with motorized bridge-type upright configuration, translation over sample, high-speed resonant and conventional scanners, three high-sensitivity GaAsP detectors, lenses with high working distance and numerical aperture, corrected for infrared imaging, dual tunable pulsed laser (100fs, 80MHz) with a wavelength range of 660-1320nm and a fixed line at 1040nm.\n### Contact details\nMaria Calvo- University of Barcelona\n[mariacalvo@ub.edu](mailto:mariacalvo@ub.edu )\nJulien Colombelli- Institute for Research in Biomedicine- IRB Barcelona\n[julien.colombelli@irbbarcelona.org](mailto:julien.colombelli@irbbarcelona.org)\nNadia Halidi- CRG - Centre for Genomic Regulation\n[nadia.halidi@crg.eu](mailto:nadia.halidi@crg.eu)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "31d30c68", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "b5333ef4", "3744dad8", "22875d0d", "4e5bcb9e" ], "country": { "id": "88bb821e-347c-42b2-b756-1b689acf531e", "name": "Spain", "iso_a2": "ES" } }, { "id": "1fa342de", "name": "Barcelona Mesoscopic Imaging Node", "original_id": "cfecb32d-9ebc-4049-a64a-c52c461c7ad0", "description": "Barcelona Node: LSFM, 50µm-5cm, live imaging, multiview, organ resolution.", "documentation": "## SPAIN\n## Barcelona Mesoscopic Imaging Node (BMIN)\n---\n**BMIN is a multi-sited, single-technology Flagship EuroBioimaging Node, with two access sites located in the area of Barcelona, at IRB Barcelona (Institute for Research in Biomedicine) and ICFO (Institute of Photonics Science). It offers open access to a wide range of mesoscopic imaging modalities, mostly based on ***Lightsheet Fluorescence Microscopy (LSFM)*** customized and unique instrumentation, for multiscale optical imaging spanning from 50µm to over 5 cm samples size. BMIN applications include the observation of living organisms, at fast imaging pace, great depth and “all around” (e.g. multiview), or imaging whole organs and organisms in toto with cellular resolution.**\n### Specialties and expertise of the Node\nThe imaging modalities are centrally devoted to multimodal **lightsheet imaging** (e.g. SPIM, DSLM, ASLM, iSPIM, OPM, “scattered” sLS, and more), which can be also combined with other complementary technologies for correlative workflows. BMIN aims to provide life scientists in the public and private sectors with full imaging workflows, including project’s definition and supervision, sample preparation, image data acquisition, bioimage analysis and visualization, and temporary data storage.\nLSFM enables either fast, gentle and/or large volume imaging with samples ranging from mid-sized organoids/spheroids up to embryos or entire organisms. Both living samples and fixed tissues can be imaged under LSFM with great benefits compared to conventional point-scanning 3D imaging techniques (e.g. confocal). At BMIN, seven custom instruments are designed to enhance specific imaging features or performance tailored to either the samples’ size or its longevity. Our strength stands in our ability to pick, or develop/adapt, the optical configuration that best suits the biological question, and in cases to tackle multiscale imaging with the combined use of several instruments.\nHere below, we review the features and advantages of the Lightsheet variants implemented at the Node’s instruments.\n![](upload/Lightsheet_imaging_Live_in_Zebrafish.png)\n**Lightsheet imaging, Live in Zebrafish**. Top Left: larva, head and trunk imaged at 2 angles. Macrophages movements in tail fin (Top Right) and head (Center): color scale shows time projection tracks. Bottom: Zebrafish embryo at different time points across epiboly.\nLightsheet (LS) variants and features available for multimodal live imaging.\n“**SPIM**”: Selective Plane Illumination Microscopy. With a static LS illumination, SPIM enables deep, fast and gentle imaging. Commonly set with a horizontal detection arm and vertical ligthsheet illumination, it offers the simplest and most flexible readout for samples hanging from the top or disposed in a cuvette or chamber.\n**Multiview SPIM**: Most instruments enable sample rotation, hence enabling one to access the sample from the best angle, or to generate a more homogeneous and more isotropic 3D volume in large samples after multiview reconstruction.\n**Double-sided illumination:**\nFor large samples, two lightsheets are used, e.g. from “right” and from “left”, and can be combined to improve the image quality over large fields of view\n**Double-sided detection:** Imaging large samples from both sides simultaneously enables sharper images with large samples. With live samples it results in faster imaging (no rotation), with cleared samples it extends the size of the sample that can be imaged.\n**DSLM:** *Digitally Scanned Lightsheet Microscopy.* The lightsheet is produced by a rapidly scanned beam (in one direction only) to form a LS that yields improved image contrast, quality and resolution. Especially suited to work in the two-photon regime.\n**ASLM**: *Axially Swept Lightsheet Microscopy.* While in SPIM, adjusting the LS focus to the field of view brings a known resolution trade-off, ASLM enables one tosweep the LS waist laterally to achieve the best possible axial resolution across the entire (or larger) field of view.\n**iSPIM**: An inverted SPIM. The illumination and detection objective lenses reach the sample from the top (e.g. by dipping). This inverted geometry allows for easy sample mounting in dish-like or chamber-slide sample carriers.\n**Refocused imaging**: This is either a SPIM or DSLM add-on based on active optics that adjusts the image plane across large volume without moving any part. By moving both the lightsheet and the focus optically, rather than the sample mechanically, one achieves fast volumetric imaging of living samples, reaching up to several tens of volumes per second.\n**OPM,** *Oblique Plane Microscopy*: the lightsheet is formed through the same detection lens and the image is reconstituted through an optical assembly downstream of the primary objective lens. Mounted on an inverted microscope, OPM enables to combine the lightsheet benefits with the use of conventional sample carriers (e.g. multiwell plates), hence true high-throughput and long-term live imaging.\n**MacroSPIM with optical clearing:** For large samples in the order of 5-30mm, imaging with cellular resolution in entire organs at variable magnifications (i.e. continuous zoom) ranging from 0.3x to 24x. Illumination and detection from both sides ease the capture of high contrast images in very large volumes. 3D Tiling enables good resolution over large volumes.\n**Diverging LS**: A diverging lightsheet fills a very extended field of view and offers to image exceptionally large sample (5-7cm or beyond) in a single scan. Typically suited to late development (e.g. late chicken embryo) or full organisms.\n**sLS:  Scattered ligthsheet***.*\nA label free modality that captures the elastic scattering of the laser through the sample to reveal specific scatterers, e.g. nanoparticles, different tissues composition or fibers in tissues\n**Sample mounting expertise:** Depending on the instrument and application, we can employ several strategies to mount and image the sample:\n* Embedding in agarose: top-mounted for live imaging or cleared inside the agarose block.\n* In conventional sample carriers: slide, chamber-slide, petri-dish, multiwell-plates.\n* Resting in a custom cuvette\n* Fluidic approach: imaging samples flowing through a tube enables high-throughput imaging, turning a SPIM into a 3D image-based flow cytometer.\n**Optical Clearing expertise****:** a wide range of clearing protocols have been integrated and tested, including solvent-based for efficient clearing (“Murray’s clear” BABB, DISCO family e.g. iDISCO+, including whole-mount immunofluorescence, DeepCLEAR, PEGASOS, FocusClear, ECI, ECI2, etc..) and water-based clearing for the preservation of endogeneously expressed fluorescent proteins (CUBIC, CLARITY, etc..). We have tested a large variety of clearing protocols since 2010 and we are able to define a strategy to find in reasonable time which technique is best suited to the target sample/tissue.\n![](upload/Cleared_organs.png)\n**Cleared organs imaged with lightsheet microscopes:** Top Left: GFP-expressing metastases in Liver (1mm chunk), Top Right: Whole Bladder (7mm diameter) with tumour (blue tumour, grey Autofluorescence) and nanoparticles (scattered lightsheet, orange), Bottom Left: Whole mouse Brain (1.5cm) with Alzheimer plaques (thioflavin staining), Bottom Right: Chicken embryo stage HH39 (5cm beak-to-toe, Autofluorescence surface render).\n**Label free capabilities**: Through cleared tissues, autofluorescence and scattered lightsheet imaging can provide additional and complementary channels for tissue imaging. Using non-fluorescent elastic scattering of the lightsheet illumination, macroscopic structures or exogenous targets (e.g. nanoparticles) can be revealed at very low laser power levels.\n***Large data image analysis****:*The Node develops tools to enable large image data (>TBs) processing of lightsheet data, including tiled images stitching, multiview fusions, live data analysis, cell tracking.\n***Complementary imaging modalities:***\nWhether to check the sample at higher resolution or to perform correlative imaging workflows, the Node offers alternative modalities to be used in combination with lightsheet imaging, including confocal microscopy, non linear microscopy, super resolution microscopy, Raman microscopy histological sectioning and imaging, etc.\n### Offered Technologies\n* Lightsheet Mesoscopic Imaging (SPIM /sDSLM)\n* Tissue Clearing\\*\n* Expansion Microscopy\\*\n* High-Speed Imaging\\*\n* Feedback Microscopy\\*\n* Laser scanning confocal microscopy (LSCM/CSLM)\n* High Throughput Microscopy / High-Content Screening (HTM/HCS)\n* Fluorescence Lifetime Imaging (FLIM)\n* Two-Photon microscopy (2P)\n* Second/Third Harmonic Generation\n* Raman Spectroscopy\n* Image analysis -bio (IA-bio)\\*\n### Additional Services offered by the Node\n* Project planning and methodological setup (e.g. design of study protocol and standard operation procedures)\n* Instruments\n* Training in sample preparation and mounting\n* Customization of sample mounting\n* Technical assistance to run instrument\n* Probe preparation\n* Animal facilities (Drosophila)\n* Wet lab space\n* Bioimage Data processing, analysis and visualization facilities\n* Bioimage Data storage\n* Meeting and training seminar rooms\n* Administrative support for housing\n* Training in infrastructure use\n* Training workstations\n* Biological material storage and processing\n* Training in techniques for optical clearing of biological samples\n* Workshop services for mechanical prototyping (metal, 3D printed), electronics\n* Histology services (separate service) for correlative imaging after lightsheet imaging\n### Instrument highlights\n* DSLM with Two-photon (2P) excitation,\n* Multiview SPIM imaging,\n* DSLM with dual sided illumination, ASLM for high resolution across large field of view, and all optical refocusing for fast volumetric imaging,\n* Macro DSLM: DSLM at low magnification for 0.5-1cm cleared tissues,\n* MacroSPIM: SPIM with ASLM at low magnification for 0.5-3cm cleared tissues, dual side illumination dual side collection,\n* LEMOLISH: SPIM at very low magnification for 1-5cm cleared tissues, single-side illumination, dual side collection,\n* SPIM with fluidics sample mounting for High-throughput Imaging\n* SPIM for in vivo imaging and/or with fluidic sample mounting dual side illumination, dual side collection,\n* SPIM for fast volumetric imaging, incorporating electrically tunable lenses or adaptive optics,\n* Scattered Lightsheet label-free imaging available for cleared and living samples,\n* Oblique Plane Microscopy (dOPM): lightsheet *on an inverted microscope* for High-Throughput Live Imaging, dual view.\n![](upload/Classical_SPIM_with_DSLM.png)\nTop, from Left to right: Classical SPIM with DSLM for high resolution imaging, SPIM for multimodal imaging (with double-sided illumination and multiple detection) with fluidics for sample mounting, iSPIM for fast refocused imaging at high resolution, dOPM for high-throughput imaging in multiwell plates (figure adapted from Maioli et al Sci. Rep. 2016). Bottom, Left to Right for cleared organs: DSLM at low magnification, MacroSPIM with double detection sides, LEMOLISH for very large samples.\n### Contact details\nJulien Colombelli: **Head of Advanced Digital Microscopy Core Facility**\nInstitute for Research in Biomedicine - IRB Barcelona\n[julien.colombelli@irbbarcelona.org](mailto:julien.colombelli@irbbarcelona.org)\nPablo Loza-Alvarez: **Head of Super-resolution Light Microscopy and Nanoscopy Laboratory (SLN)**\nInstitute of Photonic Sciences – ICFO\n[pablo.loza-alvarez@icfo.eu](mailto:pablo.loza-alvarez@icfo.eu)", "offer_technology_ids": [ "019f553c", "2fa1c4a2", "e7adfd19", "dcb85d5e", "d52b6d15", "722bb380", "0de0802c", "d6cec7b4", "1f3001ca", "3a4d793f", "f05d797c", "22875d0d", "4e5bcb9e" ], "country": { "id": "88bb821e-347c-42b2-b756-1b689acf531e", "name": "Spain", "iso_a2": "ES" } }, { "id": "161021f6", "name": "Barcelona Super-resolution Light and Nanoscopy Node", "original_id": "d952eba9-7d9b-470b-be47-da84a55d006f", "description": "Multi-site: super-resolution, bioimage analysis, custom training, complex datasets.", "documentation": "## SPAIN\n## Barcelona Super-resolution Light and Nanoscopy Node\n---\n**The Barcelona Super-resolution Light and Nanoscopy Node (SLN@BCN) is a multi-site bioimaging Node that brings together two core facilities in Barcelona, Spain. The Node offers a collection of state-of-the-art super-resolution imaging techniques, along with a wide range of complementary and advanced imaging technologies. SLN@BCN has the expertise and infrastructure for experimental design, sample preparation, acquisition, as well as the processing and analysis of the complex datasets generated by the acquired images. The Node also has the capacity to provide customized bioimage analysis based on project requirements. Each unit within the SLN@BCN Node is actively involved in organizing training courses focused on both theoretical and practical aspects of basic and advanced microscopy techniques and bioimage analysis.**\n### Specialties and expertise of the Node\nAt SLN@BCN, we perform research and development at the cutting-edge of several microscopy and super-resolution imaging techniques to continually improve the specifications of our microscopes, aiming to provide unique features that adapt to project needs. We collaborate with industry, hospitals and research centres. Our research covers a wide range of applications, including the visualization of single molecules, subcellular components, and cells. The SLN@BCN Node provides the required infrastructure for storing generated data and tailored data analysis pipelines, as well as secure data transfers between organizations.\n![](upload/SLN1.png)\nSTED image of nuclear pore complexes in a HeLa cell’s nucleus.\n![](upload/SLN2.png)\nCytoskeletal compartments in Bovine Pulmonary Arteries (airyscan)\n![](upload/SLN3.jpg)\nSTORM reveals Encephalopathy proteins organized as nano-sized objects.\n![](upload/SLN4.png)\nData analysis: HiDen Maps is used for exploration of the interaction of proteins.\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Single Molecule localisation microscopy (SMLM) | ✓ |\n| Reversible saturable optical fluorescence transitions (RESOLFT) | ✓ |\n| Laser scanning confocal microscopy (LSCM / CLSM) | ✓ |\n| Spinning disc confocal microscopy systems (SDCM) | ✓ |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Second/Third Harmonic Generation | ✓ |\n| Image Scanning Microscopy (ISM) | ✓ |\n| Fluorescence-lifetime imaging microscopy (FLIM) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Raman spectroscopy (RS) | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ |\n| Image Analysis-bio | ✓ |\n### Additional Services offered by the Node\n* Instruments\n* Technical assistance to run instrument\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Training in infrastructure use\n* Probe preparation\n* Wet lab space\n* Server Space\n* Data processing and analysis\n* Training workstations\n* Training seminar room\n* Logistics support for housing facilities\n* Cell culture facilities - Safety level 1\n* Cell culture facilities - Safety level 2\n* Mechanical and electronic workshop\n* Micro- and macro-fabricated parts through rapid prototyping\n### Instrument highlights\nSTORM: The Nikon N-STORM system is equipped with 4 laser lines (405, 488, 561, 647nm), a cage stage incubator for live-cell experiments (facilitating PALM experiments) and an EMCCD. The system includes an additional CMOS (Hamamatsu Orca Flash V3), NIS-Elements AR v5 software upgrade and enhanced performances of the current system. We can perform N-STORM, dSTORM, PALM, and DNA PAINT. The system is also equipped with environmental control for temperature, humidity and CO2 for live-cell imaging.\nSTED: The Leica TCS SP8 FALCON STED 3X is based on the TCS SP8 confocal microscope equipped with temperature control. The STED 3X module allows 3D super-resolution capabilities in 3 optical bands due to its 3 depletion lasers (592 & 660 nm CW, and 775 nm pulsed laser). The FALCON (FAst Lifetime CONtrast) is a fluorescence lifetime imaging microscopy (FLIM) platform fully integrated in the confocal microscope that can deliver video-rate FLIM with pixel-by-pixel quantification. The single molecule detector (SMD HyD) provides a high detection efficiency. Resonant scanners provide fast scanning capabilities up to video-rate at 512×512 pixels. The system includes a white light laser source as well as a 405 nm semiconductor laser. Live-cell imaging is possible due to controlled environmental conditions. We also provide STED image processing with the Huygens software.\nSTED: The Abberior STED microscope is based on the INFINITY platform, which is built around an Olympus IX83 microscope. The system is equipped with four pulsed lasers (485, 518, 561, 640nm) as well as a CW 405nm laser. Moreover, the STED module has two STED depletion lasers (595, 775nm). The detection units are based on avalanche photodiodes (APDs) and we have the MATRIX detector upgrade, which consists on a hexagonal arrangement of avalanche photodiodes (APDs) enabling a higher signal-to-background. Moreover, we have an additional spectral detection unit including ultra-high sensitivity FLIM optimized APD.\nAiryscan: The LSM980 airyscan 2 and definite focus 2 microscope is equipped with temperature, humidity and CO2 control for live-cell imaging. The system is equipped with several objectives including silicon, water, glycerol and oil to accommodate various sample refractive indices and multiple laser lines (405, 488, 561 and 639 nm). The airyscan’s multiplex mode allows to choose from or find a compromise between super-resolution, fast or better contrast imaging.\n### Contact details\n**Dr. Pablo Loza-Alvarez**\nICFO- The Institute of Photonic Sciences\nSuper Resolution Light Microscopy and Nanoscopy (SLN) Lab\nMediterranean Technology Park\nAv. Carl Friedrich Gauss, 3\n08860 Castelldefels (Barcelona), Spain\nTel: +34 93 55 34 075\ne-mail: [PabloLoza@icfo.eu](mailto:PabloLoza@icfo.eu)\n[http://www.icfo.es](mailto:http://www.icfo.es)\n\n**Dr. Nadia Halidi**\nAdvanced Light Microscopy Unit (ALMU)\nCentre for Genomic Regulation (CRG)\nDoctor Aiguader, 88,\n08003 Barcelona, Spain\nTel: +34 93 316 03 72\ne-mail: [nadia.halidi@crg.eu](mailto:nadia.halidi@crg.eu)\n\n", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "31d30c68", "d3d66a1d", "f1f735b6", "a42333c3", "dcb85d5e", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "22875d0d" ], "country": { "id": "88bb821e-347c-42b2-b756-1b689acf531e", "name": "Spain", "iso_a2": "ES" } }, { "id": "6e382796", "name": "Brain Imaging Network (BIN)", "original_id": "ded5d6d6-dc90-48c1-bd64-b713988405fd", "description": "Portugal Node: PET/MR, neuroimaging focus, multimodal expertise, radiotracer development.", "documentation": "## PORTUGAL\n## Brain Imaging Network (BIN)\n---\n**The Brain Imaging network (BIN) – Portugal is a single modality Node, offering open access to PET and MR technologies for human and preclinical imaging, with particular focus on neuroimaging. The Node provides expertise in the multimodal MR/PET imaging, machine learning approaches and development of new radiolabeled molecules that can be used as tracers for processes that cannot currently be studied with PET, in clinical neuroscience, oncology and cardiology. Work is complemented by studies on developing new nuclides on the cyclotron to respond to new clinical and research needs and also services to the local pharmaceutical companies regarding pre-clinical testing of new, candidate drugs currently under development.**\n### Specialties and expertise of the Node\nThe BIN Node offers an innovative technology at European leading level, because it combines PET and MR studies of the same subject in the same day (often two PET in the same visit, because of the possibilities of using short lived Carbon 11 tracers and one or more MR scans). The feasibility of MR-PET projects is ensured by the availability of a local Radiopharmacy-CYCLOTRON Facility which helps to provide PET- radiotracers adequate for specific research questions. A number of radiotracers (focus on F18, C11, GA68, CU64 and N13), allow for flexible exploitation of multiple applications. A local clinical trial Unit is also present at the Node, to provide researchers support in their interaction with regulatory authorities. Machine learning approaches are also a strong asset.\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| micro-MRI/MRS (Field >= 7 T) (HF) | ✓ |\n| micro-PET | ✓ |\n| micro-US | ✓ |\n| in vivo optical imaging (OI) | ✓ |\n| PhotoAcoustic Imaging (PAI) - med | ✓ |\n| micro-PET/MRI | ✓ |\n| MRI/MRS (< 7T) | ✓ |\n| MRI-PET | ✓ |\n| PET | ✓ |\n| Population Imaging (PI-med) | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| Population Imaging (PI-data) | ✓ |\n### Additional services offered by the Node\n* Project planning and methodological setup, including clinical trials\n* Data processing and analysis\n* Data storage\n* Patient / Subject recruitment\n* Animal housing\n* Radiopharmacy\n### Instrument highlights\nOur PET – Cyclotron facilities allow for flexible use of different types of radiotracers, short and long lived, the former even allowing for multiple scans in the same day.\nOur MR facility has a research agreement with the Industrial provider which permits the implementation of high-end research protocols (WIPs, including multinuclear approaches).\nAn important feature is the ability to perform simultaneous EEG/fMRI and Transcraneal Magnetic Stimulation within the MR bore.\n### Contact details\n**Current URLs**\n (Organic Unit)\n (Research Support)\n (Focus on Neuroimaging Support)\n**Contacts**\nMiguel Castelo-Branco, [mcbranco@fmed.uc.pt](mailto:mcbranco@fmed.uc.pt) (Coordinator)\nSonia Pires, [soniapires@uc.pt](mailto:soniapires@uc.pt) (Administrative Office)\nSara Ribeiro, [sararibeiro@uc.pt](mailto:sararibeiro@uc.pt) (Administrative Office)\nJoao Castelhano, [joaocastelhano@uc.pt](mailto:joaocastelhano@uc.pt) (Imaging and Technical Support)\nCatarina Duarte, [CatarinaDuarte@uc.pt](mailto:CatarinaDuarte@uc.pt) (Imaging and Technical Support)\nPedro Almeida, [palmeida@securenetworks.pt](mailto:palmeida@securenetworks.pt) (IT Technical Support)\nAntero Abrunhosa, [antero@pet.uc.pt](mailto:antero@pet.uc.pt) (Head of University Organic Unit)", "offer_technology_ids": [ "9c64e406", "4aa5d36d", "2ce231cc", "59a33aed", "d54d34a2", "15ef9b0e", "a9c43bba", "3a2f2c38", "0f1e5f18", "1fe88685", "4a91416e", "fd0e8053", "4707da44", "4e5bcb9e" ], "country": { "id": "7a4f7490-b813-4d9d-8c9b-21220f5f3b70", "name": "Portugal", "iso_a2": "PT" } }, { "id": "ca2e3748", "name": "Cellular Imaging Hungary", "original_id": "e964170c-c051-4814-bb49-c1b12ccdb649", "description": "Multi-modal node: LSCM, ISIDORe, infectious disease focus, pandemic readiness.", "documentation": "## HUNGARY\n## Cellular Imaging Hungary\n---\n**The Cellular Imaging Hungary Node is a multi modal, multi sited Node.**\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Anisotropy/Polarization Microscopy | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| Serial Blockface SEM | ✓ | ✓ |\n| Array tomography | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| in vivo optical imaging | ✓ | ✓ |\n| Atomic Force Microscopy (AFM)\\* | ✓ | ✓ |\n### Contact details\n**György Vámosi**\n[vamosig@med.unideb.hu](mailto:vamosig@med.unideb.hu)\n+36204532400", "offer_technology_ids": [ "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "31d30c68", "d3d66a1d", "f1f735b6", "e7adfd19", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "b015d920", "af33ff84", "d169e03b", "c9ddc22b", "63775639", "3f84bc36", "143e2504", "a9f0fcad", "59a33aed", "4e5bcb9e" ], "country": { "id": "ad818e51-e4da-40fd-9ced-4e0f8fb3a5b2", "name": "Hungary", "iso_a2": "HU" } }, { "id": "e0395c6a", "name": "Center for Advanced Preclinical Imaging (CAPI)", "original_id": "74467d20-a18b-4850-b6ff-15bbc95bccb5", "description": "CAPI: Multimodal preclinical imaging, in vivo research, contrast media expertise.", "documentation": "## CZECH REPUBLIC\n## Center for Advanced Preclinical Imaging (CAPI)\n---\n**The Center for Advanced Preclinical Imaging (CAPI) at the First Faculty of Medicine, Charles University is a single-sited, multimodal Czech-BioImaging and Euro-BioImaging Node covering a wide range of biomedical imaging modalities at the preclinical level. CAPI offers its expertise in in vivo preclinical research, multimodal image co-registration, and contrast media characterization.**\n![](upload/CAPI12.png)\nWhole body images of a mouse at 1T MRI and of a rat on CT-SPECT\n### Specialties and expertise of the Node\nCAPI is the only multimodal imaging center in the Czech Republic, being part of Czech-BioImaging Node since 2016 and since 2021 it offers its services to the Euro-BioImaging users as well.\nCAPI is oriented primarily on *in vivo* preclinical imaging of small laboratory animals (mice and rats). Range of methods together with laboratory background enables to work on projects focused on various fields of biomedical research, development of new diagnostic/theranostic procedures, tracer development and testing, and also material research.\nExamples of research application areas cover cancer research studies on immunocompetent, immunodeficient, and PDX mice, neurology studies including neurodegenerative diseases, functional cardiology studies, vascularization, and also development and characterization of new contrast agents. We are approved for radiation work (open and closed sources of ionizing radiation), and GMO (including GMO-2 cell lines). Our SPF animal facility enables to breed and maintain various transgenic mouse and rat models. We are equipped and skilled for microsurgery, whole-body irradiation (60Co irradiator), stem cell transplantation and tracking, and hematology/immunology characterization.\nOur team collaborates with customers on experimental setup, obtaining approvals on experimental animal research, data evaluation and interpretation, and also on publication of results for the given problem in the area of preclinical research.\n![](upload/CAPI11.png)\nCT/PET/SPECT preclinical scanner, Magnetic Particle Imager and 7T Magnetic Resonance in dedicated labs\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| micro-MRI/MRS (>= 7T) | ✓ |\n| micro-MRI/MRS (< 7T) | ✓ |\n| micro-CT | ✓ |\n| micro-PET | ✓ |\n| micro-SPECT | ✓ |\n| micro-US | ✓ |\n| in vivo Optical Imaging | ✓ |\n| Photoacoustic Imaging (PAI) - med | ✓ |\n| micro-PET/MRI | ✓ |\n| micro-PET/CT | ✓ |\n| micro-SPECT/CT | ✓ |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Wet labs\n* Cell culture facilities\n* Animal breeding and housing (IVCs for mice and rats)\n* Development and test/validation of novel imaging probes\n* Chemistry/radiochemistry labs for analytical/physico-chemical characterization of imaging probes\n* Separate radiochemistry and dissection lab – cryotome, autoradiography, auto gamma-counter, radio-HPLC\n* Evaluation of material magnetic properties – relaxometer 0.5T\n* Data processing and analysis\n* Data storage\n* 3D print (FDM and SLA printers)\n* Flow cytometry lab – imaging flow cytometer, multicolor analysis and sorting\n* Molecular biology lab - rtPCR\n### Instrument highlights\n**1T MRI** high throughput machine for basic anatomical screening of mice and rats, possibility of colocalization with PET/SPECT/CT, MPI, OI\n**7T MRI** precise anatomical imaging, MR spectroscopy, diffusion weighted imaging, time-resolved imaging (heart imaging with both prospective and retrospective gating), quantitative imaging (diffusion tensor imaging, relaxometry), X-nuclei imaging and spectroscopy\n**MPI**3D in vivo imaging (i.e., imaging of distribution of the injected magnetic tracer) with 20-ms temporal resolution, possibility to quantify the tracer amount. Suitable for tumor imaging and in situ, hyperthermia therapy (MFH), acute stroke detection, molecular imaging, stem cell tracking, characterization of magnetic nanoparticles, targeted tissue imaging.\n**US & PA**or multimodal imaging in oncology (tumor detection & sizing in 2D + 3D, vascularization, hypoxia), molecular biology (characterization of nanoparticles, dyes and contrast agents; drug delivery and pharmacokinetic, cell tracking), neurobiology (oxygen saturation, total hemoglobin and blood flow velocity), cardiology (cardiac function in 2D, 3D and 4D, ischemia & hypoxia). Available transducers are\n·      MX201 (10-22MHz, Centre Transmit: 15 MHz) - mouse whole body imaging, brain (mouse, rat), cardiovascular and abdominal                 imaging, tumor imaging, neurobiology\n·      MX400 (20-46 MHz, Centre Transmit: 30 MHz) - mouse abdominal imaging, vascular imaging, embryology, lymph nodes, tumor           imaging\n·      MX550D (25-55 MHz, Centre Transmit: 40 MHz) - mouse & Rat eye imaging, skin, abdominal & microvasculature imaging,                     lymphatics & reproductive imaging\nMX700 (29-71 MHz, Centre Transmit: 50 MHz) - vascular, embryology, superficial tissue,                   ophthalmology imaging\n### Contact details\nLudek Sefc, Head of Department \nPavla Francova, Project Coordinator \nCAPI website \n### Additional sections and material\n![](upload/CAPI_miceheart.png)Native imaging of mice heart at 7T MRI\n![](upload/mouse_whole_body.png)X-ray / PET colocalized whole-body images of mouse (tracer – 99m Tc)\n![](upload/CAPI_sub_cutanous.png)Co-registered fluorescence / reflectance image of sub-cutaneous tumors on set of three mice (tracer – RFP)\n![](upload/CAPI_last.png)\nUS visualization of venal blood flow in rat", "offer_technology_ids": [ "9c64e406", "fc3c255a", "4aa5d36d", "36d4a2a7", "b4a6f749", "59a33aed", "d54d34a2", "15ef9b0e", "c41fb0d1", "8fa56005", "4a91416e", "d74face8", "c83c6c2b", "4e5bcb9e", "0d8de032" ], "country": { "id": "86dfebd7-34b9-4794-9440-be27c69f14c4", "name": "Czech Republic", "iso_a2": "CZ" } }, { "id": "f68673b1", "name": "Challenges Framework Flagship Node", "original_id": "c1fcefb6-7dce-42c7-b187-b1f48930bdfe", "description": "Open-source platform: algorithm evaluation, cloud collaboration, data repository", "documentation": "## NETHERLANDS\n## Challenges Framework Flagship Node\n---\n**The Challenges Framework flagship Node organizes a series of Grand Challenges in Medical Image Analysis ([www.grand-challenge.org](http://www.grand-challenge.org)), focused at standardized evaluation of different image analysis algorithms in the field. The goal of this Node is to go much further and create a generic open-source platform that allows MIC researchers to make their data and evaluated software available for on-line collaboration and cloud computing. The Node physically consists of storage, computational resources, and web access. It includes a repository with relevant data for challenges, software for download of training data, upload of results and display of results.**\n**### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Challenges Framework | ✓ | ✓ |\n* Image Analysis algorithms\n* AI and machine learning approaches\n![](upload/challenges.jpg)\n### Contact details\n**Prof. Dr. W. J. Niessen**\nErasmus MC & TU Delft\n[w.niessen@erasmusmc.nl](mailto:w.niessen@erasmusmc.nl)\n[www.grand-challenge.org](http://www.grand-challenge.org)**", "offer_technology_ids": [ "89bab6f3", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "d039b533", "name": "Correlative Light Microscopy Dutch Flagship Node", "original_id": "0628db19-ec24-4d7f-bdd0-0155a621bcfe", "description": "Dutch CLEM consortium: live-cell correlation, open access, multi-lab expertise.", "documentation": "##\n## NETHERLANDS\n## Correlative Light Microscopy Dutch Flagship Node\n---\n**The Dutch Correlative Light Electron Microscopy flagship Node is a consortium of the 4 most prominent correlative LM-EM (CLEM) labs in the Netherlands, headed by Klumperman (Utrecht), Gerritsen (Utrecht), Koster (Leiden) and Giepmans (Groningen). All labs have an international track record in microscopy technique development, application, training and open access and are at the forefront of CLEM.**\n### Specialties and expertise of the Node\nMaking use of the complementary specialties of the participating labs, collectively the Node provides a unique package of CLEM methods for open access. These include state-of-the-art techniques to correlate live-cell imaging and a variety of room temperature and cryo-fluorescence microscopy techniques with immuno-EM of ultrathin cryosections, cryo-EM, 3D electron tomography and FIB-SEM. Also we can prepare samples imaged by LM in the home lab for subsequent EM analyses in our Node.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| TEM of chemical fixed samples | ✓ | ✓ |\n| TEM of cryo-immobilized samples \\* | ✓ | ✓ |\n| Large scale EM | ✓ | ✓ |\n| EM tomography | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| Serial Blockface SEM | ✓ | ✓ |\n| FIB-SEM | ✓ | ✓ |\n| STEM tomography | ✓ | ✓ |\n| Array tomography | ✓ | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu Method) | ✓ | ✓ |\n| Immuno-gold EM on resin sections | ✓ | ✓ |\n| pre-embedding immunolabelling | ✓ | ✓ |\n| Genetic encoded EM probes | ✓ | ✓ |\n| pre-embed CLEM | ✓ | ✓ |\n| Large scale EM | ✓ | ✓ |\n| on-section CLEM | ✓ | ✓ |\n| CryoET \\* | ✓ | ✓ |\n| Cryo TEM \\* | ✓ | ✓ |\n| SEM (topography) | ✓ | ✓ |\n| Elemental analysis \\* | ✓ | ✓ |\n| pre-embeded CLEM | ✓ | ✓ |\n| in-section CLEM | ✓ | ✓ |\n| Cryo-CLEM \\* | ✓ | ✓ |\n| live-cell CLEM | ✓ | ✓ |\n| EDX-CLEM (Correlative EDX and SEM) \\* | ✓ | ✓ |\n### Additional services offered by the Node\n* Execution of pilot studies by node staff\n* Assistance with experimental design (e.g. experimental set up, choice of technique)\n* Training in sample preparation\n* Training in use of light and electron microscopes\n* Assistance of users in the execution of experiments\n* Wet lab space\n* Data processing and analysis software\n* Desk space and training seminar room\n* Cell culture facilities\n* Biological sample preparation for EM\n* EM automation software\n### Instrument highlights\nThe Dutch CLEM Node contains the full set of equipment to allow CLEM experiments from light or live cell imaging to biological sample preparation to EM analysis. Specialized equipment includes cryomicrotomes, cryo-EM, iCLEM and FIB-SEM. Specific CLEM techniques include correlative light - immuno-electron microscopy on ultrathin cryosections (Tokuyasu technique), correlative live cell – 3D electron microscopy, cryo-CLEM and large volume CLEM.\n![](upload/225991_orig.png)\n### Contact details\n**Judith Klumperman**\nChair Department of Cell Biology, Head Cell Microscopy Center UMC Utrecht\n[j.klumperman@umcutrecht.nl](mailto:j.klumperman@umcutrecht.nl)\n+31887556550\n### Additional services offered by the Node\n* Execution of pilot studies by node staff\n* Assistance with experimental design (e.g. experimental set up, choice of technique)\n* Training in sample preparation\n* Training in use of light and electron microscopes\n* Assistance of users in the execution of experiments\n* Wet lab space\n* Data processing and analysis software\n* Desk space and training seminar room\n* Cell culture facilities\n* Biological sample preparation for EM\n* EM automation software\n### Instrument highlights\nThe Dutch CLEM Node contains the full set of equipment to allow CLEM experiments from light or live cell imaging to biological sample preparation to EM analysis. Specialized equipment includes cryomicrotomes, cryo-EM, iCLEM and FIB-SEM. Specific CLEM techniques include correlative light - immuno-electron microscopy on ultrathin cryosections (Tokuyasu technique), correlative live cell – 3D electron microscopy, cryo-CLEM and large volume CLEM.\n![](upload/225991_orig.png)\n### Contact details\n**Judith Klumperman**\nChair Department of Cell Biology, Head Cell Microscopy Center UMC Utrecht\n[j.klumperman@umcutrecht.nl](mailto:j.klumperman@umcutrecht.nl)\n+31887556550", "offer_technology_ids": [ "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "995a6055", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0dee2953", "0abb2c96", "a7128dd1", "cb003121", "c60b4a73", "3965a906", "13e1b5d4", "90e98166", "593e3440", "60335007", "c3302077", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "23f7a2fd", "name": "Danish BioImaging", "original_id": "17530c7c-d86b-481c-8695-112a5a2f6b84", "description": "Multi-site Danish Node: pre-clinical to cryo-EM, diverse applications, data analysis focus.", "documentation": "## DENMARK\n## Danish BioImaging\n---\n**Danish BioImaging (DBI) is a multi-sited, multimodal Node bringing together five facilities across the country, representing the joined national imaging infrastructure of Denmark. The Node provides a broad service offer covering a wide range of advanced and state-of-the-art bioimaging technologies - from pre-clinical imaging of big animals and humans to cryo-electron microscopy for single particle analysis- and fields of expertise – covering plant biology, HCS of yeast libraries, zoology, pathology, neurosciences and metabolism. The increase in size and complexity of image-based data sets produced by single and multimodal bioimaging technologies makes image analysis a key part of the DBI consortium. To support data storage, management and image analysis needs, DBI includes a national Image analysis service.**\n### Specialties and expertise of the Node\n* Dedicated MRI, CT, ultrasound and PET systems at the world’s largest\nexperimental pig surgery facility\n* Exotic animal models in vivo and ex vivo pre-clinical imaging\n* A unique animal imaging data repository, covering preclinical imaging data\nfrom more than 5000 species.\n* Metabolism imaging in whole animals using hyperpolarized MRI and PET\n(Incl. specialized radiochemistry and novel PET tracers laboratory)\n* Imaging cardiac and renal oxygen metabolism\n* Cardiovascular live imaging (4D MRI and 4D ultrasound imaging of flow\npatterns, CT imaging of cardiac electric conduction networks and imaging\nmyocardial blood perfusion with PET)\n* Bioimaging models and applications in Neuroscience\n* 3D printing of organs, animals and personalized human skin (Incl. skin\ncancer models)\n* Blood barrier models based on primary porcine cells and/or human stem\ncells\n* Plant live imaging (including plant growth visualization) and hystology\n* Light Microscopy super resolution expertise and dedicated microscopes to\nperform MP- STED, FCS-STED, FLIM-STED and stimulated Raman scattering\nmicroscopy\n* Molecule dynamics analysis with CARS and spatial transcriptomics using\nMERFISH to simultaneously measure the amount and spatial distribution of\nhundreds to thousands of RNA species in single cells\n* Screening of large genome-wide yeast libraries\n* Deep imaging of organs and organisms with SPIM\n* Correlative Light and Electron Microscope pipelines\n* Image-based Computer science expertise and computing infrastuctures\n![](upload/Picture1.png)\n*Green mitochondria on fat: The inside of a brown fat cell with multilocular lipid droplets (white and brown) surrounded by mitochondria and other smaller organelles (green). Dual beam SEM with FEI Quanta FEG 3D and 3D rendering with Amira. Elahu Gosney Sustarsic\nAssistant Professor, Novo Nordisk Foundation Center for Basic Metabolic Research,\nUniversity of Copenhagen*\n### Offered Technologies\n![](upload/Picture2.png)\n*Streptococcus imaged with SEM FEI XL30 and pseudocolored with photoshop by Professor Mattias Mörgelin, University of Lund*\n![](upload/Picture3.png)\n*Human intestine section stained with Hematoxylin-Eosin and imaged with a Zeiss Axioscan Z1. Histology Laboratory at the Core Facility for Integrated Microscopy*\n##### List of offered technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Image Scanning microscopy (ISM) | ✓ |\n| cryoFM \\* | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ |\n| Coherent Anti-Stokes Raman Scattering microscopy\\* (CARS) | ✓ |\n| Raman Spectroscopy (RS) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ |\n| EM tomography (ET) | ✓ |\n| FIB-SEM | ✓ |\n| Serial Blockface SEM | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ |\n| micro-MRI/MRS (>= 7T) | ✓ |\n| micro-MRI/MRS (< 7T) | ✓ |\n| micro-CT | ✓ |\n| micro-PET | ✓ |\n| micro-SPECT | ✓ |\n| micro-US | ✓ |\n| in vivo Optical Imaging | ✓ |\n| micro-PET/MRI | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n| Image Analysis-bio \\* | ✓ |\n| Image Analysis-med \\* | ✓ |\n![](upload/Picture4.png)\n*Human vastus lateralis single muscle fiber stained against mitochondrial networks (Green) and myonuclei (blue). Images acquired with a Zeiss LSM700 by Associate Professor Clara Prats, University of Copenhagen*\n![](upload/Picture5.png)\n*Bacteria imaged in a FEI Quanta 3D FEG and pseudocolored with Amira software*\n![](upload/Picture6.png)\n*MRI of pig kidneys, visualization of tubule structures. Method: MRI clinical system and diffusion tensor sequence, Aarhus University Hospital*\n![](upload/Picture7.png)\n*CT of giraffe heart, visualization of blood vessels. Method: CT clinical system and iodine filling, Aarhus University Hospital*\n![](upload/Picture8.png)\n*OCT of mouse brain cortex, visualization of cerebral vessels. Method: Preclinical Fourier-domain OCT imaging with en face maximum intensity projection, Aarhus University Hospital.*\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Wet labs\n* Cell culture facilities\n* Animal housing\n* Imaging probes\n* Data processing and analysis\n* Data storage\n### Contact details\n**Clara Prats** [cprats@sund.ku.dk](mailto:cprats@sund.ku.dk)\n**Sonia Diaz Garcia** [sonia.garcia@sund.ku.dk](mailto:sonia.garcia@sund.ku.dk)\n[www.danishbioimaging.dk](https://www.danishbioimaging.dk/)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "60f50c0f", "d3d66a1d", "f1f735b6", "e7adfd19", "53fc2771", "dcb85d5e", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "af33ff84", "4ae7143c", "df1896a3", "c9ddc22b", "eebba7a7", "e32e05f1", "3f84bc36", "cb003121", "c60b4a73", "9c64e406", "fc3c255a", "4aa5d36d", "36d4a2a7", "b4a6f749", "59a33aed", "15ef9b0e", "4a91416e", "d74face8", "c83c6c2b", "639a72d3", "22875d0d", "4e5bcb9e" ], "country": { "id": "a92ed4cb-105f-4d82-85c6-653797539878", "name": "Denmark", "iso_a2": "DK" } }, { "id": "6319df36", "name": "Digital Imaging Multimodal Platform Neuromed – DIMP NEUROMED", "original_id": "c5daad4a-f503-4c11-ac83-e37f72a03024", "description": "Integrated multimodal platform for neuroscience, preclinical to clinical imaging.", "documentation": "## ITALY\n## Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED\n---\n**The Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED is a single- sited, multimodal Node aiming to provide access to an integrated digital analysis support for preclinical and clinical studies in the field of neuroscience, extending from the study and evaluation of animal models to their translation into clinical practice. It is composed of a preclinical (Multimodal Molecular Imaging) and clinical (Population Imaging) access to imaging technologies and molecular probes, producing digital images which are elaborated in a dedicated High Performance Computing System (Population Imaging). Data are collected with multimodal imaging instrumentation and analyzed to extrapolate imaging features to quantitative parameters of clinical interest. These parameters are exported to the classification of the clinical case.**\nA similar approach is used for the study of cancer therapies response, which are first done with mice models and xenografted cancers.\n![](upload/banner_neuromed.jpg)\n*A view of the NEUROMED campus*\nUsers can either perform their preclinical and population imaging studies using the measurement and analysis infrastructure, or profit of the large database of preclinical and clinical digital images in order to test their hypothesis with artificial intelligence tools developed by Neuromed (based on Convolutional Neural Networks and local TensorFlow applications).\n### Specialties and expertise of the Node\nBeyond the conventional functional imaging equipment (including among others a micro PET/CT and a 7T MRI system), the available instrumentation includes a Digital microPET/CT (RAYCAN E180) scanner, which, unique in Europe, allows to obtain high resolution functional images in dynamic mode, with time slices as short as 30 seconds thanks to its extremely high sensitivity.NEUROMED develops its own dedicated image reconstruction algorithms, image visualization and analysis techniques. Brain segmentation, textural characterization and statistical analysis algorithms developed by the center are available for precise quantitative analysis.\nThe equipment has been recently completed by one of the most modern high performance computing systems based on the Memory Driven Computing architecture by Hewlett Packard Enterprise (HPE), which has been developed specifically for “-omics” studies and population imaging studies. Access to the digital imaging platform iPLAT, with customized artificial intelligence and convolutional neural network-based image analysis software developed by the Neuromed scientists for the classification of neurological and oncological diseases based on medical images, is provided.\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| micro-MRI/MRS (>= 7T) | ✓ |\n| micro-CT | ✓ |\n| in vivo Optical Imaging | ✓ |\n| micro-PET/CT | ✓ |\n| population imaging (PI) | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n| Image Analysis-med \\* | ✓ |\n![](upload/nueromed_2.jpeg)\n*Micro PET/CT for small animal and plant models*\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Wet labs\n* Cell culture facilities\n* Animal housing\n* Chemistry and radiochemistry labs\n* Biobanking\n* Data processing and analysis\n* Data storage\n![](upload/banner_neuromed3.jpg)\n*A view of the Bio Bank for Population Imaging studies*\n### Contact details\nAdministrative coordinator:\nDr. Emilia Belfiore\n[dimp@neuromed.it](mailto:dimp@neuromed.it)\nScientific coordinator (representation in the Panel of the\nEuro-BioImaging Nodes)\nProf. Dr. Nicola D’Ascenzo\n[nicola.dascenzo@neuromed.it](mailto:nicola.dascenzo@neuromed.it)", "offer_technology_ids": [ "9c64e406", "b4a6f749", "59a33aed", "c41fb0d1", "1fe88685", "4a91416e", "c83c6c2b", "639a72d3", "fd0e8053", "4e5bcb9e" ], "country": { "id": "0af8a17e-b371-4f0b-a408-9ee57dc20943", "name": "Italy", "iso_a2": "IT" } }, { "id": "4278635d", "name": "Dutch High Field Imaging Hub", "original_id": "18ab4dc8-094e-436d-b8bd-9743955adcd1", "description": "Ultra-high field MRI, 7T+, precision neuroimaging, multi-site collaboration.", "documentation": "## NETHERLANDS\n## Dutch High Field Imaging Hub\n---\n**The Dutch High Field Imaging Hub is a a multi-sited, single modality Node, offering high field MRI infrastructure for human imaging. It is front runner in precision MRI focusing on medical and neuro science using advanced MRI methodologies.The five imaging centers are equipped with ultra-high Field MR instruments that can be used to obtain ultra-high resolution images of the brain, spine, breast, heart, abdomen and extremities, and benefit from increased signal to noise and new contrast associated with higher magnetic field strengths. They work closely in exchanging imaging protocols, data processing technology and RF coil technology to expedite the further development of high precision imaging in close contact with the imaging industry and national and international academic colleagues that would like to make use of the open access provided by this hub to external users.**\n### Specialties and expertise of the Node\nWhereas some of the sites excel in technical developments and translational studies in a variety of medical applications (LUMC, UMCU), other sites are more focused on more basic neurosciences oriented studies (Maastricht, Spinoza Amsterdam) with ample overlap between the sites to create a strong network that supports the knowledge base required to provide the expertise needed to support academic and non-academic user requests for ultra high field studies. This also implies that applications can be supported not only for neuro/brain studies, but for head&neck, heart, breast, pelvic and abdominal area and extremities as well.\n### Offered Technologies:\n* Human MRI/MRS (>=7T)\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Data processing and analysis\n* Data storage\n* Patient / Subject recruitment\n* Coil lab\n### Instrument highlights\nBeyond the typical 7T MRI equipment, one site of the node provides access to a 9.4T MRI scanner for human brain studies. Another site provides the capability for metabolic MRI using quintuple tuned head coil or multi tuned body coils. All sites have setups in place not only for brain studies but also for body studies.\n![](upload/Dutch_Hub.png)\nFig 1: Example of metabolic body MRI using 31P MRSI with an embedded body transmitter and an array of 31P receivers merged to a multi-transceiver 1H array.\n![](upload/dutch_page2.jpeg)\nFig2: Example of 1H, 31P, 23Na, 13C and 19F scans, potentially all in one scan session from the human brain.\n### Contact details\n[d.w.j.klomp-2@umcutrecht.nl](mailto:mailto:d.w.j.klomp-2@umcutrecht.nl)", "offer_technology_ids": [ "6324bef6", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "4f1ca4db", "name": "Erasmus MC OIC - Advanced Light Microscopy Rotterdam Node", "original_id": "e64b2b7d-a019-4e96-8b09-9d4918a16f8f", "description": "Quantitative live cell imaging, FRAP, FRET, FCS, high resolution.", "documentation": "## NETHERLANDS\n## Erasmus MC OIC - Advanced Light Microscopy Rotterdam Node\n---\n**The Erasmus Optical Imaging Centre (OIC) – Multimodal Imaging Node in Rotterdam is dedicated to the innovation, application and maintenance of a wide variety of optical imaging modalities [(https://erasmusoic.nl/).](https://erasmusoic.nl/) An important focus of the OIC is to develop and implement innovative technology, mainly quantitative methods (largely, but not exclusively based on FRAP, FRET, FCS and time lapse imaging) to study living cells. This Node also has experience with molecular biology, tissue culture and cell biology, animal experimentation and drug delivery. The OIC provides high resolution (intracellular) imaging, stringent control over animal and tissue condition (for instance tight control of tissue temperature for hyperthermia studies), and expertise in intratumoral processes during drug delivery and tumor manipulation.**\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Structured illumination microscopy\\* (SIM) | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| 4PI | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n### Instrument highlights\nThe OIC offers the capability to do combined STORM/PALM super-resolution imaging. This can also be combined with laser scanning confocal microscopy. This system is also equipped with an incubator for live cell super-resolution imaging. Two confocals are equipped with a 355nm and/or 266nm deep-UV laser for localized subcellular manipulation for studying DNA repair and organelle healing. Spinning disc confocal system and TIRF microscope are equipped with ultra-fast FRAP unit for localized subcellular manipulation.\n### Contact details\n**Prof. Dr. A. B. Houtsmuller**\nScientific director of Erasmus Optical Imaging Centre / Professor of Functional Cell Anatomy\n[a.houtsmuller@erasmusmc.nl](mailto:a.houtsmuller@erasmusmc.nl)+31646154564", "offer_technology_ids": [ "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "d3d66a1d", "f68070c5", "e9910d1c", "018d2770", "5a688552", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "b19711d3", "name": "Euro-BioImaging EMBL-Node", "original_id": "4fc7db24-3a88-4976-8a21-2675203ba358", "description": "EMBL Node: state-of-the-art imaging, project planning, training, advanced methods.", "documentation": "## European Molecular Biology Laboratory (EMBL)\n## Euro-BioImaging EMBL-Node\n---\n**The Euro-BioImaging EMBL-Node offers a collection of state-of-the-art microscopy equipment and image processing tools. The facility was set up as a cooperation between EMBL and industry to improve communication between users and producers of high-end microscopy technology. This Node supports in-house scientists and visitors in using microscopy methods for their research and regularly organizes in-house and international courses to teach basic and advanced microscopy methods. The services provided include project planning, sample preparation, microscope selection and use, image processing and visualization. The Euro-BioImaging EMBL-Node supports advanced microscopy techniques such as FRAP, FRET, FCS, high-throughput microscopy, laser nanosurgery, CLEM, mesoscopy and super-resolution microscopy.**\n### Specialties and expertise of the Node\nThe Euro-BioImaging EMBL-Node offers its expertise in the development of user defined comprehensive workflows in automated high throughput microscopy, including automated sample preparation, image acquisition, image analysis and data mining. This technology is most typically applied by users to large-scale projects, e.g. genome-scale siRNA screening. Based on its experience in high throughput microscopy and image analysis the Euro-BioImaging EMBL-Node *is* able to offer approaches, that allow scanning of the sample for objects of interest by fast image acquisition and online image analysis followed by more detailed automated imaging such as multi-color 3D time-lapse microscopy, FRAP or FC(C)S.\n###\n![](/upload/embl1.jpg)\n*Light Microscopy*\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| cryoFM \\* | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Reversible optical fluorescence transitions (RESOLFT) | ✓ | ✓ |\n| Minimal Photon Fluxes Microscopy (MINFLUX)\\* | ✓ | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| Optical projection tomography (OPT) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Intravital Microscopy (IVM) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Microdissection \\* | ✓ | ✓ |\n| Imaging at Biosafety Level >1 | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ | ✓ |\n| Large scale EM | ✓ | ✓ |\n| EM tomography (ET) | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| Serial Blockface SEM | ✓ | ✓ |\n| Focussed Ion beam SEM (FIB-SEM) | ✓ | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| pre-embed CLEM | ✓ | ✓ |\n| pre-embeded CLEM | ✓ | ✓ |\n| on-section CLEM | ✓ | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ | ✓ |\n| live-cell CLEM | ✓ | ✓ |\n###\n![](/upload/embl2.jpg)\n*Single plane illumination microscopy image of a portion of a chemically cleared adult mouse lung. Structures are shown with colour encoding depth. Montse Coll/EMBL; Jim Swoger/EMBL; Greetje Vande Velde/KU Leuven*\n###\n### Additional services offered by the Node\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Technical assistance to run instrument\n* Training in infrastructure use\n* Probe preparation\n* Animal preparation\n* Animal facilities\n* Wet lab space\n* Server space\n* Data processing and analysis\n* Training workstations\n* Training seminar rooms\n* Housing facilities\n* Biological material storage and processing\n* Training in techniques for optical clearing of biological samples\nPlease note that not all technologies & services are available at all node sites.\n![](/upload/embl3.jpg)\n*JEOL JEM 2100 Plus - On-section CLEM adapted from Avinoam et. al., 2015*\n### Contact details\n**Dr. Rainer Pepperkok**\nHead of Advanced Light Microscopy Facility\n+4962213878332\n[EuBI-EMBL-Node@embl.org](mailto:EuBI-EMBL-Node@embl.org)\n", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "60f50c0f", "d3d66a1d", "f1f735b6", "a42333c3", "fc6e9ebb", "e7adfd19", "17dd34eb", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "f65a70b8", "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "e32e05f1", "3f84bc36", "0dee2953", "0abb2c96", "a7128dd1", "cb003121", "904149e2", "4b452472", "c60b4a73", "13e1b5d4", "90e98166", "c3302077", "4e5bcb9e" ], "country": { "id": "2fd76a48-eea1-4445-bd4c-a69ec0ba916d", "name": "EMBL", "iso_a2": "EM" } }, { "id": "9c8d648e", "name": "Facility of Multimodal Imaging - AMMI Maastricht", "original_id": "71c09435-a9ba-4eb1-a1be-9b72d672876d", "description": "Multimodal imaging: light/electron microscopy, mass spectrometry, non-invasive bioimaging.", "documentation": "## Facility of Multimodal Imaging - AMMI Maastricht, The Netherlands\n---\n**The Advanced Microscopy and Molecular Imaging (AMMI) Node connects state-of-the-art (light and electron) microscopy and mass spectroscopy-based innovative molecular imaging with high-end, non-invasive (bio)medical imaging technologies. It aims to assist academic and industrial users performing fundamental and applied studies in biological and biomedical (molecular) imaging. The AMMI infrastructure contains both basic and high-end/one-of-a-kind imaging techniques on microscopic and macroscopic level combined with an extensive palette of non-invasive imaging techniques.**\n### Specialties and expertise of the Maastricht Node\nThe Advanced Microscopy and Molecular Imaging (AMMI) facility offers state-of-the-art (light and electron) microscopy, mass spectrometry-based molecular imaging, and non-invasive pre-clinical and clinical imaging technologies. AMMI aims to provide diagnostic and prognostic imaging technologies for personalized medicine. As such, AMMI offers access to a translational, interdisciplinary research program in leading international expertise centers, combining research and education.\nVia our world-leading local Research Schools, our imaging platform covers a broad palette of research topics as resulting from collaborations on cardiovascular, oncological, orthopedics, metabolic, neurological, and regenerative medicine research. For more information, see [link](https://www.maastrichtuniversity.nl/research/institutes/organisation/3566).\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ |\n| Second/Third Harmonic Generation | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ |\n| Intravital Microscopy (IVM) | ✓ |\n| Tissue Clearing \\* | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n| micro-MRI/MRS (>= 7T) | ✓ |\n| micro-MRI/MRS (< 7T) | ✓ |\n| micro-CT | ✓ |\n| micro-PET | ✓ |\n| micro-SPECT | ✓ |\n| micro-US | ✓ |\n| micro-PET/MRI | ✓ |\n| micro-PET/CT | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n| Mass spectrometry-based imaging (MSI) - med\\* | ✓ |\n![two_photon_microscopy](upload/AMMI_figure_combined.png \"two_photon_microscopy\")\n*Example of Two-photon microscopy: Imaging of the attachment of anti-ICAM-1 bimodal (US-TPLSM) bubbles to damaged carotid artery ex vivo (top) and in vivo (bottom) For more information see: Noninvasive molecular ultrasound monitoring of vessel healing after intravascular surgical procedures in preclinical setup. A. Baleanu-Curaj, Z. Wu, T. Lammers, C. Weber, M.A.M.J. van Zandvoort, and F. Kiessling Arterioscler Thromb Vasc Biol 2015, 35(6): 1366-1373. DOI: 10.1161/ATVBAHA.114.304857*\n![](upload/PET_MRI_AMMI.png)\n*Example of PET/MRI imaging: 18F-FDG PET image of the neck (left arrow) of a patient with a carotid plaque; (B) a color overlay of the PET image as displayed in (A) on the corresponding MR image in (B) For more information see: PET/MRI of atherosclerosis. M. Aizaz, R. Moonen, J. van der Pol, C. Prieto, R. Botnar and M. Kooi Cardiovasc Diagn Ther 2020;10(4):1120-1139. DOI: cdt.2020.02.09*\n![](upload/Tumor_AMMI.png)\n*Example of microPET/CT fusion imaging in a tumour-bearing mouse For more information see: Synthesis and in Vivo Biological Evaluation of (68)Ga-Labeled Carbonic Anhydrase IX Targeting Small Molecules for Positron Emission Tomography. D. Sneddon, R. Niemans, M. Bauwens, A. Yaromina, S. van Kuijk, N. Lieuwes, R. Biemans, I. Pooters, P. Pellegrini, N. Lengkeek, I. Greguric, K. Tonissen, C. Supuran, P. Lambin, L. Dubois and S. Poulsen Journal of Medicinal Chemistry, 29 Jun 2016, 59(13):6431-6443. DOI: 10.1021/acs.jmedchem.6b00623 [https://radiomicsimagingarchiv...](https://radiomicsimagingarchive.org)*\n### Additional services offered by the Node\n* Technical assistance (running instruments, probe preparation, sample preparation)\n* Methodological setup (design of study protocol and standard operation procedures)\n* Training in infrastructure use\n* Wet lab space including biological material storage and processing possibilities\n* Animal breeding, ethical licenses, experiment protocols\n* Animal holders for clinical devices\n* Server space, data processing and analysis (AI, deep learning and radiomics)\n* Training workstations and seminar rooms\n* Cryo-sectioning\n* Image (CT and BLI)-guided small animal irradiator\nThrough collaboration we also offer the possibility to use various other advanced microscopy techniques at different close-by labs (e.g. Uniklinik Aachen), such as animal whole-body fluorescence imaging, Lightsheet, Rescan Confocal, and Two-photon intravital and lifetime microscopy.\n### Instrument highlights\nWith this broad range of techniques, we have created an imaging platform, ranging from EM, via super-resolution STED (592-depletion, resonant scanning), confocal (resonant scanning, white-light laser, in vivo cell system), and multi-photon (intravital and lifetime included) microscopy, towards whole body imaging. This platform connects a broad range of microscopic and macroscopic imaging techniques. Some of the EM and LM techniques are located in the Microscopy Core Lab (MCL) run by Dr. C. Lopez-Iglesias.\nFurthermore, the Node provides access to the Mass Spectrometry Imaging CORE laboratory, as run by Dr. B. Cillero Pastor. Technical features include:\n* High throughput, high spatial resolution, and high mass resolution MALDI imaging\n* MALDI 2-postionization technology\n* Isomeric resolution by ozone‐induced dissociation\n* Nano-ToF-SIMS for biomolecular imaging at single cell level\n* i-Knife technology for real time tissue classification\n* Laser microdissection capabilities\n* Label free proteomics\n* Native MS\n![](upload/MALDI_AMMI.png)\n*Example of MALDI imaging: Molecular visualization of intratumor heterogeneity For more information see: Specific Lipid and Metabolic Profiles of R-CHOP-Resistant Diffuse Large B-Cell Lymphoma Elucidated by Matrix-Assisted Laser Desorption Ionization, Mass Spectrometry Imaging and in Vivo Imaging. F.P.Y. Barré, B.S.R. Claes, F. Dewez, C. Peutz-Kootstra, H.F. Munch-Petersen, K. Grønbæk, A.H. Lund, R.M.A. Heeren, C. Côme and B. Cillero-Pastor Anal Chem. 2018, 90(24):14198-14206. DOI: 10.1021/acs.analchem.8b02910*\n### Contact details\n**Node leader pre-clinical techniques:**\nMarc A.M.J. van Zandvoort, Professor in Advanced Microscopy\n[mamj.vanzandvoort@maastrichtuniversity.nl](mailto:mamj.vanzandvoort@maastrichtuniversity.nl)\n+31 (0)43 388 1998\n**Node-leader non-invasive techniques:**\nLudwig Dubois, Associate Professor Precision Medicine\n[Ludwig.dubois@maastrichtuniversity.nl](mailto:Ludwig.dubois@maastrichtuniversity.nl)\n+31 (0)43 388 2909\n**Proof of Concept Node-leader Mass Spectroscopy Imaging:**\nMichiel Vandenbosch, CORE lab leader\n[m.vandenbosch@maastrichtuniversity.nl](mailto:m.vandenbosch@maastrichtuniversity.nl)", "offer_technology_ids": [ "3cf0830c", "2fa1c4a2", "f1f735b6", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "a673b6b7", "f05d797c", "4b561f4f", "9c64e406", "fc3c255a", "4aa5d36d", "36d4a2a7", "b4a6f749", "2ce231cc", "15ef9b0e", "c41fb0d1", "4a91416e", "d74face8", "c83c6c2b", "9c814a85", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "46ccfb38", "name": "Finnish Advanced Microscopy Node", "original_id": "39c64174-2bf7-4684-bb2a-fa9ae41503b8", "description": "Sub-20nm resolution, correlative workflows, advanced sample preparation.", "documentation": "TEST BLOCK", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "d3d66a1d", "f1f735b6", "e7adfd19", "17dd34eb", "53fc2771", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "af33ff84", "4ae7143c", "de231b3c", "c9ddc22b", "eebba7a7", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0dee2953", "c60b4a73", "13e1b5d4", "c3302077", "a9f0fcad", "4b561f4f", "0534020c", "22875d0d", "4e5bcb9e" ], "country": { "id": "a9321cc5-0792-4f76-9847-a6671116bbe7", "name": "Finland", "iso_a2": "FI" } }, { "id": "3850f7eb", "name": "Finnish Biomedical Imaging Node", "original_id": "a274f0af-3c03-4932-b31e-5c792c8cf98c", "description": "Multi-modal Node: PET, MRI, MEG, optical; targets cancer, neuroscience, metabolism.", "documentation": "## FINLAND\n## Finnish Biomedical Imaging Node\n---\n**The Finnish Biomedical Imaging Node (FiBI) is a multi-sited, multimodal Node covering biomedical imaging from mouse to man. The spearhead imaging technologies of the FiBI Node include 1) preclinical and human PET imaging and PET tracer development, 2) preclinical high-field MRI, 3) magnetoencephalography (MEG), and 4) optical intravital imaging, coupled with a broad repository of imaging tracers and probes, numerous animal models from mice to pigs, and diverse stimulation systems for both animals and humans. The key expertise and main research applications focus on major challenges especially in cardiovascular and metabolic diseases, neuroscience, and cancer. With wide coverage of imaging modalities and expertise, the FiBI Node provides exceptional opportunities not only for basic research but also for translational research from small animals to larger animals to humans and to the clinic within a single Node.**\nThe Finnish Biomedical Imaging Node operates in close collaboration with the Finnish Advanced Light Microscopy Node. Together, the two Nodes form Euro-BioImaging Finland, which is on the Academy of Finland’s national roadmap for research infrastructures 2021-2024\n### Specialties and expertise of the Node\nThe expertise and the imaging modalities of the FiBI Node enable versatile basic research but also provide unique approaches especially in translational research and drug development. In addition, the research opportunities in the FiBI Node also cover development and validation of new imaging and other health care technologies, new imaging tracers and probes, and new tools for advanced image processing and analysis.\nSpecial features of the FiBI Node’s spearhead technologies are described below.\n##### **SPECIALITIES IN PET IMAGING**\n* Exceptionally broad collection of different PET tracers to study e.g., blood perfusion, glucose and fatty acid metabolism, (neuro)inflammation, and neurotransmission both in animals and humans. Just to mention a few examples, [15O]H2O, [18F]FDG, [18F]FTHA, and [11C]Acetate are among the most frequently asked tracers for cardiovascular and metabolic imaging, [11C]Methionine, [18F]rhPSMA7.3, and [68Ga]DOTANOC for cancer imaging, and [11C]Raclopride, [11C]PBR, [11C]PIB and [11C]UCB-J for neuroimaging. Our PET tracer portfolio is constantly being streamlined with new tracers developed in-house, so don’t hesitate to ask for more information about available options.\n* Numerous validated PET applications for animal and human studies:\n+ Cardiovascular PET specialties include diagnostics, characterization, and monitoring coronary artery disease, heart failure, and inflammatory processes of the cardiovascular system.\n+ Metabolic PET approaches provide various opportunities for studying key pathological processes such as insulin resistance and pancreatic beta-cell dysfunction in obesity, metabolic diseases, and T2 diabetes, and the effects of physical activity/inactivity on tissue specific and whole body metabolism.\n+ PET applications in neuroscience range from neurophysiology of aging brain, pathophysiology of neurogenerative diseases, mapping neuroreceptor systems in health and disease, molecular and functional processes (e.g. neuroinflammation) of different psychiatric and neurological disorders, to neurobiology of human behavior and emotions.\n+ Oncological PET expertise offers opportunities to assess and validate new hybrid imaging methods and image acquisition protocols in cancer diagnostics, and to develop new theranostic approaches for various types of cancers, such as prostate and breast cancer, neuroendocrine and other somatostatin receptor positive tumors, and malignant lymphoma.\n##### **SPECIALITIES IN PRECLINICAL HIGH-FIELD MRI**\n* Body movement tolerant, in-house developed technology for fMRI of awake animals. The technique allows for example diverse genetic, electrical, and pharmacologic manipulations and at the same time overcomes the interfering effects of anesthetics. It is minimally stressful to animals and it can also be combined with various brain stimulation or electrophysiological recordings providing flexible study designs.\n* Hyperpolarized MRI, a non-radioactive method for investigation of dynamic metabolic processes. The Node houses DNP-hyperpolarizer for 13C-labeled probes, such as pyruvate. Hyperpolarization increases MR sensitivity of 13C nuclei over 10000-fold for 1-2 minutes which allows real-time imaging of pathway-specific metabolic processes, where the injected probe is observed separately from its metabolites. Therefore, hyperpolarized MRI has applications in many diseases with altered metabolism including cancer, cardiovascular disease, diabetes, and a variety of inflammatory conditions.\n##### **SPECIALITIES IN MAGNETOENCEPHALOGRAPHY (MEG)**\n* Magnetoencephalography (MEG) is optimally suited for detecting neuronal dynamics in the cerebral cortex, which has made it a powerful tool in basic neuroscience research. The FiBI Node offers MEG-optimized experimental designs coupled with a wide range of sensory, motor and cognitive stimulus systems. The offered protocols can be used to study for example sensorimotor and proprioceptive brain activity related to body movements, cortical networks in language processing, and neuronal signaling of cognitive functions in health and disease. MEG is routinely combined with other complementary measures of human neurophysiology such as fMRI, EEG, TMS, and eye-tracking as well as with diverse behavioral measures.\n* Unique opportunities for MEG related imaging and neurotechnological development. New types of MEG sensors, hybrid MEG-MR systems, and next-generation MEG stimulator systems and monitoring devices are actively being developed in house.\n##### **SPECIALITIES IN OPTICAL INTRAVITAL IMAGING**\n* Multiphoton, widefield and intrinsic signal optical intravital imaging set-ups for studying e.g. ear skin vasculature, paw skin, brain, lymph node/mammary gland, tumors, and externalized internal organs such as the intestine, liver and spleen, and protocols and adapters for both anesthetized and behaving animals (brain imaging). These techniques can be used to study for example vascular networks, blood flow and leakage, cell tracking, and morphological changes in longitudinal settings. Advanced neuronal set-ups for brain imaging allow for example dynamic imaging of calcium- or voltage-sensitive proteins, micro-anatomic imaging of dendritic spines and mitochondria, and blood oxygenation and blood flow rate imaging. Brain imaging can also be performed in freely moving animals by using in-house developed home-cage device, where the animal can be exposed to cues, perform tasks or interact with other animals and coupled with physiological recordings.\n### New offer of technology\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| micro-MRI/MRS (>= 7T) | ✓ | ✓ |\n| micro-MRI/MRS (< 7T) | ✓ | ✓ |\n| micro-CT | ✓ | ✓ |\n| micro-PET | ✓ | ✓ |\n| micro-US | ✓ | - |\n| in vivo Optical Imaging | ✓ | ✓ |\n| micro-PET/MRI | ✓ | ✓ |\n| micro-PET/CT | ✓ | ✓ |\n| micro-SPECT/CT | ✓ | – |\n| Intravital microscopy (IVM) - Med | ✓ | – |\n| MRI/MRS (>= 7T) | ✓ | – |\n| MRI/MRS (< 7T) | ✓ | ✓ |\n| MRI-PET | ✓ | – |\n| MEG | ✓ | \\_ |\n| PET | ✓ | ✓ |\n| PET/CT \\* | ✓ | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ | – |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ | – |\n| micro-CT - ex-vivo | ✓ | – |\n### Additional services offered by the Node\n* User-oriented project support with study design and management\n* Synthesis and development of radiotracers and radiopharmaceuticals\n* Various animal models for human diseases (e.g. mouse, rat, rabbit, and pig models)\n* Advanced animal experiment facilities\n* Assistance in patient and subject recruitment\n* Assistance in acquiring ethical permissions\n* Blood and tissue sampling, metabolite analyses, and pharmacokinetic modelling\n* Electrophysiological and behavioral measurements such as electroencephalography (EEG), navigated transcranial magnetic stimulation (nTMS), and eye tracking\n* Wide variety of behavioural measurements\n* Basic and advanced training for using the equipment\n* Assistance in image processing, data analyses, and interpretation\n* Data storage\n### Instrument highlights\n**PET imaging:** Three whole body PET/CT scanners (GE Discovery MI, GE D690, GE Discovery VCT), human brain/animal PET scanner (CPS HRRT), simultaneous 3T PET/MRI (GE Healthcare Signa), two small animal PET/CT scanners (Siemens Inveon, Raycan), portable animal PET and CT scanners (Molecubes) and small animal PET scanner (Siemens). Simultaneous small animal 7T PET/MRI (MR Solutions) will be available in 2021. Wide repository of both in-house produced and commercial PET tracers for both animals and humans.\n**Preclinical high-field MRI:** Four high-field MRI systems (7T/16 cm Bruker, 9.4T/31 cm Bruker/Agilent, 9.4T/89 mm Agilent, 11.5 T/55 mm Bruker), a hyperpolariser (3-10 T, DTU). Simultaneous small animal 7T PET/MRI (MR Solutions) will be available in 2021.\n**Magnetoencephalography:** Two MEG systems (306-channel Elekta/MEGIN TRIUX and Elekta Neuromag devices) with compatible high-density (64-channel) EEG systems. The MEG research is supported by 3T MRI scanner (Magnetom Skyra, Siemens), TMS devices (Bistim2 & Rapid2, Magstim, Nexstim eXimia and NBS4) compatible with simultaneous EEG recordings, and a 99-channel flat-bottom SQUID magnetometer especially suitable for cardiac and fetal brain research.\n**Optical intravital microscopy:** Three upright multiphoton microscopes for imaging multiple organs/tissues (Zeiss LSM 7 with Coherent Chameleon Vision II laser with OPO equipped with isoflurane anesthesia), and for cranial window imaging in anesthetized or awake mice (Olympus FluoView1000 MP and Femtonics Femto2D-Dual microscopes, both with SpectraPhysics MaiTai lasers and mobile home cage set-ups to image freely moving mice), two widefield microscopes with electrophysiology set-ups, and optical whole-body fluorescence/luminescence imaging (Spectral Instruments Imaging Lago system with 14 LED excitation wavebands and 20 fluorescence emission filters).\n**Examples of other available instruments:** Ultrasoun systems (Accuson, VisualSonics Vevo2100, Philips Epiq 7), basic optical imaging systems (Perkin Elmer IVIS Spectrum), small animal SPECT/CT scanners (Gamma Medica, NanoSPECT/CT, Bioscan), in vivo microCT system (Perkin Elmer Guantum GX2) small animal MRI (Philips Ingenia 1.5T S), Hallmarg Standing Equine MRI (0.3 T), CT (GE Lightspeed VCT 64), small (CPI Indigo 100) and large animal x-ray (Shimadzu UD150B-40) services and Philips BV Libra C-arm for surgical imaging, near-infrared spectroscopic imaging (NIRSI) facilities, and tailored equipment for studying sensory and motor systems and cognitive functions in clinical settings. The various imaging modalities and electrophysiological and behavioral measurements are routinely integrated within FiBI Node.\n### Contact details\n**Contact the FiBI Node:**\n[contact-FiBI@eurobioimaging.fi](mailto:contact-FiBI@eurobioimaging.fi)\n", "offer_technology_ids": [ "9c64e406", "fc3c255a", "4aa5d36d", "b4a6f749", "2ce231cc", "59a33aed", "15ef9b0e", "c41fb0d1", "8fa56005", "3744dad8", "a9c43bba", "3a2f2c38", "b5cb68ca", "0f1e5f18", "4a91416e", "d74face8", "c83c6c2b", "4707da44", "4e5bcb9e" ], "country": { "id": "a9321cc5-0792-4f76-9847-a6671116bbe7", "name": "Finland", "iso_a2": "FI" } }, { "id": "0c8677f6", "name": "Flanders Bioimaging Imaging Node", "original_id": "1392c2f2-3f82-4357-9708-67c36f0b6e28", "description": "Multi-site, multi-modality: molecular to clinical imaging, 9 facilities.", "documentation": "## BELGIUM\n## Flanders Bioimaging Imaging Node\n---\n**Flanders BioImaging is a multi-sited, multi-modality Node that offers a full and complementary portfolio of biological and biomedical imaging techniques and expertise, at scales ranging from the molecular all the way up to human/clinical imaging (“molecule to man”). The node comprises 9 separate imaging facilities spread across 5 sites, all situated within a 70km radius. Whilst each facility is well equipped for imaging in either the biological or biomedical domain, our strategy is to specialise in the particular spearpoint techniques as detailed in the section below.**\nThe Flanders Bioimaging Node itself is funded by the FWO International Research Infrastructure program, in co-ordination with the Department of Economy, Science and Innovation (EWI), whilst the combined available imaging infrastructure from the constituent sites represents more than €50mi investment.\n### Specialties and expertise of the Node\nFlanders Bioimaging aims to help develop projects for a wide range of users from academia and industry to understand disease at the molecular, cellular, organ and organism levels, and to help develop and validate biomarker tools to help guide drug development and precision medicine. Whilst our sites have broad expertise, there is an especial focus on the oncology and neurodegenerative disease settings.\nOur strategy is to focus on providing access to the leading applications (‘spearpoints’) that have been developed at each site – each spearpoint is described below.\n**SPECIALTIES IN CLINICAL AND TRANSLATIONAL IMAGING:**\n●      Translation of novel CNS tracers\nThe Molecular Imaging and Research Clinic at KU Leuven (MIRaCLe) is well established in the validation and application of novel PET biomarkers to clinical populations for improved diagnosis and precision medicine for central nervous system (CNS) disease and especially neurodegeneration. The MIRaCLe platform focuses on translating novel PET candidates to first in human studies, including full quantitation and methodology development, as well as employing established markers for receptor occupancy studies in response to novel drugs in clinical populations, via interface with the UZL Clinical Trial unit.\n●      GMP production of nanobody theranostics\nThe *In vivo* Cellular and Molecular Imaging (ICMI) core facility at the VUB specialises in the development of new Nanobody-based (Nb) optical and nuclear diagnostic imaging probes and therapeutics for oncology and immuno-oncology in particular. Importantly, ICMI provides a GMP production platform for such Nb diagnostics & therapeutics, that includes selection of production vectors for (GMP-grade) Nanobody productions; Nanobody fermentation and purification protocols with qualification of in-process controls (IPCs) and analytical tests for follow-up and release; GLPgrade Nanobody batch production for *in vivo* PET imaging proof of concept studies and to support toxicity and stability studies and finally production of GMP-grade Nanobody batch that can be used for clinical translation.\n**SPECIALTIES IN PRECLINICAL IMAGING:**\n●      Multi-modality image-guided radiotherapy\nCORE ARTH (Animal facilities Radiological Techniques & Histology) Infinity at the University of Gent houses the SmART+ system for small animal irradiation, a unique system in Europe that combines multiple imaging modalities to allow the determination of biological target volumes (BTVs) for radiotherapy planning using non-uniform dose delivery protocols for automated nonhomogeneous doses.\nIn addition the facility has established pipelines for the integration of PET and MRI biomarkers to inform such higher dose delivery with the goal of targeting the more malignant or more radiation-resistant tumour areas. This comprehensive imaging biomarker platform also allows the monitoring of combination radio/chemotherapy responses and thus the validation of predictive imaging biomarkers.\n●      PET and High-field MRI characterisation of CNS disease models and therapy response\nThe *in vivo* small animal imaging facilities of the University of Antwerp consist of the Molecular Imaging Centre Antwerp and the Bio-Imaging Lab (MICA-BIL), and provides a battery of early biomarkers to evaluate neurodegenerative diseases, cancer as well as treatment response in a range of preclinical disease models. MICA-BIL makes use of PET biomarkers for the visualisation of proteinopathies, neuro-inflammation and presynaptic receptor density and combines functional connectivity and activity, structural integrity and connectivity from MRI. Fully optimised scan protocols and processing pipelines are available, including multi-modality integration to both increase predictive power and better discriminate underlying disease mechanisms and enable the early evaluation of potential treatments.\n**SPECIALTIES IN BIOLOGICAL IMAGING:**\no   Enteric Nervous System Imaging:\nThe Cell & Tissue Imaging Cluster (CIC) at KU Leuven integrates live fluorescence (single, two- and recently 3-photon), lattice light sheet and second and third harmonic imaging to provide multiplex real-time structural and physiological information on the enteric nervous system (ENS). The CIC is able to offer advanced (neuro)physiological imaging experimental setups involving (for example) the perfusion of drugs or electrical stimulation on widefield (incl. with high frame rate cameras), confocal, 2|3-photon, Abberior STED and Lattice Light sheet microscopes. Full protocols for physiological measurements in a range of sample types (including organs, tissue slices and organoids) on multiphoton/STED/LLS microscopes are available and extendable to allow pharmacological/electrical interventions at defined and accurate (ms) timepoints, with full analysis pipelines for the extraction and interpretation of valid physiological information from non-linear, superresolution and high-rate/noisy imaging data.\n* Correlative Light/Electron Microscopy:\nThe Biological Imaging Core (BIC) at the Vlaams Instituut voor Biotechnology (VIB) houses a Zeiss Elyra 7-Structured Illumination Microscope (SIM)² equipped with the LSM980 two-photon module to enable accurate correlation of super-resolution light microscopy with EM data. This allows defined region study at resolutions ranging from 60nm (SIM²) to <20nm (PALM/d STORM) to nanometre ultrastructure via SEM, with Focused Ion Beam SEM (FIB-SEM) available to allow applications under cryo conditions. This dynamic 3D/4D super-resolution microscopy platform closes the resolution gap between LM and EM, expanding *in situ* structural analysis, and enables the correlation of protein clusters/complexes with morphological domains in organelles and tissues. Imaging neurodegenerative processes at the level of organelles and identifying the initial stages of protein/peptide aggregation, transmission and organellar involvement is a key focus, with the aim to better understand neurodegenerative mechanism(s) and identify novel targets for early diagnosis and therapy.\n* Pharmacokinetic Imaging:\nThe Gent Light Microscopy Core (GLiM; [www.ugent.be/glim](http://www.ugent.be/glim)) has expertise in pharmacokinetic imaging, i.e. the study of the physicochemical properties of single molecules and nanoparticles in biological systems. This technique makes use of advanced imaging (Fluorescence Recovery after Photobleaching, FRAP; Fluorescence Correlation Spectroscopy, FCS; Single Particle Tracking, SPT) with major applications in the study of drug delivery and nanoparticle therapy (nanomedicines) in a range of biological systems. GLiM also has unique and complementary expertise in the intracellular delivery of compounds, including labels for microscopy or preclinical imaging of cells, via ‘photoporation’ (valorized at GU via the formation of the spin-off Trince). A major focus is the development of techniques to elucidate nanoparticle transport mechanisms in spheroids and patient-derived tissue fragments with the goal of informing the development of a range of nanomedicines, with special focus on improved therapeutic efficacy for the treatment of cancer. Different pharmacological and biomechanical manipulations to enhance nanoparticle transport can also be studied and developed using these model systems and readouts.\n* Dynamic Optical Microscopy:\nThe Advanced Optical Microscopy Centre (AOMC) at the University of Hasselt has unique expertise in studying molecular dynamics via Förster resonance energy transfer (FRET) and image correlation spectroscopy (ICS), two powerful fluorescence methods especially suited to study the dynamics of live biological processes, enabling 'fluorescence-based dynamic structural biology’ investigations from the single-molecule scale via e.g. super-resolution, TIRF and confocal microscopes all the way to the organoid, organs and model organism length scale via state-of-the-art light-sheet microscopy. A particular focus is the application of FRET/ICS procedures to enable dynamic optical imaging in large multicellular assemblies and thus create a framework for super-resolved multidimensional correlation imaging (ICS) methods, furthermore to map viscosity/viscoelastic properties of/ diffusive heterogeneity within biomolecular assemblies below the 200-nm optical diffraction limit. Multiplex FRET combining space-and-time-resolved data recording is available to characterise heterogenous biological environments.\n* Systems microscopy:\nThe Antwerp Centre for Advanced Microscopy (ACAM;[www.acam-uantwerpen.be](http://www.acam-uantwerpen.be/)) develops data-driven microscopy approaches, based on a diversity of imaging technologies (incl. electron microscopy, high-throughput screening, live cell and light sheet microscopy) to gain insight in and expose novel therapeutic targets for human age-related diseases. ACAM has established end-to-end pipelines to query among others, oxidative stress and mitochondrial defects in human patient cells, synaptic connectivity in primary or iPSC-derived neurons, and DNA damage in cancer cells. High-end super-resolution and expansion microscopy in combination with cyclic staining is optimized for molecular-level investigations, while deep learning-enhanced image recognition enables cell type and state recognition in more complex, physiologically relevant biological specimens such as mixed cell cultures. A systematic workflow based on tissue clearing and light sheet microscopy allows cellular phenotyping of intact tissue mimics such as cerebral organoids and whole organs such as mouse brain. Thus, together our imaging expertise allows quantitative investigation of pathological defects across scales.\n### Additional services offered by the Node\n* Full project support, experimental design, user training\n* Wide range of disease models\n* Large animal scanning (mini-pigs)\n* BSL2 animal facility\n* SPF facility for high-field MRI imaging\n* Autoradiography of ex-vivo tissue with a wide range of isotopes\n* Laser microdissection and photoablation\n* Support for patient and subject recruitment for clinical studies\n* Support for obtaining preclinical and clinical ethical permission\n* Full clinical and preclinical quantitation for PET studies\n* Image processing and data analysis for all spearpoint technologies\n* Data storage and support for metadata definitions/implementation\n### Instrument Highlights\n**Clinical PET imaging:**\nTwo PET/CT scanners (GE Discovery MI, Siemens TruePoint), a simultaneous 3T PET/MRI (GE Healthcare Signa), four SPECT/CT scanners (Symbia Intevo Bold, GE Discovery NM530s CZT, GE Discovery MI, Siemens Symbia). A wide range of 11C, 18F, 15O and 13N tracers are available for clinical research use from the associated on-site GMP production facility.\n●      Glucose metabolism/[18F]FDG\n●      Pre-synaptic density (SV2A)/ [18F]SynVesT-1/[11C]UCB-J\n●      Dopamine transporter (DAT)/ [18F]PE2I\n●      Tau/ [18F]MK6240\n●      Neuroendocrine tumours/[18F]NOTA-Octreotide\n●      Neuroinflammation (Translocator protein, TSPO)/[18F]DPA-714\n●      mGluR5/[18F]FPEB\n●      Beta-amyloid in ALZ/[11C]PiB\n●      Biomolecular labelling/[18F], [89Zr], [111In], [99mTc]\n**Preclinical Multimodality imaging:**\nOur core facilities at the Universities of Gent and Antwerp, KU Leuven and the Vrije Universiteit Brussel host a wide range of preclinical instrumentation.\nPET/SPECT/CT scanners: Dual Siemens Inveon, Dual Molecubes β-cubes (high-throughput PET-CT) are available at the Molecular Imaging Core Antwerp (MICA) and the Molecular Imaging Research and Clinic Leuven (MIRaCLe) whilst CORE ARTH Infinity houses β- and X cubes . SPECT and CT are available at these three sites and the In Vivo Cellular and Molecular Biology (ICMI) at the VUB (γ- and X-cubes, MiLabs VECTor+). MICA, MIRaCLE, CORE ARTH Infinity and ICMI all have facilities for the onsite synthesis of a range of radiotracers.\n●      Glucose metabolism/[18F]FDG\n●      Pre-synaptic density (SV2A)/ [18F]SynVesT-1\n●      Dopamine D1Receptors (D1R)/ [11C]SCH23390\n●      Dopamine D2/3Receptors (D2/3R)/ [11C]Raclopride\n●      Phosphodiesterase 10A (PDE10a)/ [18F]MNI-659\n●      Neuroinflammation (Translocator protein, TSPO) / [18F]PBR111 and [18F]DPA-714\n●      mGluR5/[11C]ABP688/[18F]FPEB\n●      mHTT using [11C]CHDI-180R/[18F]CHDI-650\n●      Beta-amyloid using [18F]AV-45/[11C]PiB\n●      Biomolecular labelling/[18F], [111In], [99mTc], [68Ga/67Ga], [64Cu]\n●      LAT transport/[18F]FET\n●      Prostate specific membrane antigen/[18F]-PSMA-11\n●      Tumoural Lipogenesis/[18F]-Choline\nCommercially available alpha/beta isotopes can be used for therapeutic biomolecule production at MIRaCLe and ICMI.\nHigh-field preclinical MRI: the Biological Imaging Lab at the University of Antwerp hosts two Bruker 7T preclinical MRI instruments and one Bruker 9.4T high-field MRI (with cryo-coil), with a wide range of available sequences:\n●      Structure analysis (volumetric and morphometry)\n●      Microstructural MRI (diffusion tensor, kurtosis, and fixel-based)\n●      Brain functional connectivity (Functional connectivity, CAPs and QPPs)\n●      Brain functional activity (stimulus-based and pharmaco-based fMRI)\n●      Susceptibility weighted Imaging (SWI and QSM)\n●      Cerebral Blood perfusion (CBF) and volume (CBV) using ASL\n●      Brain clearance (invasive and non-invasive glymphatic clearance)\n●      Manganese enhanced MRI (MEMRI)\n●      Magnetic resonance spectroscopy (MRS)\n●      Metabolic rate of O2 consumption; 31P MRS for energy metabolism\n●      Fluor-MRI; Magnetization transfer / Glutamate CEST\nOptical Imaging: Bioluminescence is available at multiple sites (Perkin Elmer IVIS Lumina LT at CORE ARTH Infinity, Biospace PhotonImager at MICA-BIL and ICMI). Intravital microscopy is available at ICMI (Leica Stellaris DIVE Dual Intravital Microscope)\nRadiotherapy delivery: The CORE ARTH Infinity core facility at the University of Gent hosts a SmART+ (Precision X-ray) platform for laboratory animal radiation research, enabling researchers to plan high-precision multimodal image-guided radiotherapy on laboratory animals using PET/MRI/BLI/CT (including longitudinal follow-up for therapy evaluation).\nImaging modalities can be integrated at all sites, with a wide range of in-vivo and ex-vivo assays available, especially in the CNS and oncology domains.\n**Biological imaging:**\nThe core facilities at the Universities of Gent, Antwerp and Hasselt along with KU Leuven and the VIB host a comprehensive imaging park for biological imaging and microscopy.\n**Light Microscopy:**\n●      Deconvolution Widefield Microscopy (DWM)\n●      Laser Scanning Confocal Microscopy (LSCM/CLSM)\n●      Spinning Disk Confocal Microscopy (SDCM)\n●      Multiphoton Microscopy\nFunctional imaging and specialised methodologies\n●      High throughput microscopy/high content screening (HTM/HCS)\n●      Fluorescence Resonance Energy Transfer (FRET)\n●      Fluorescence Recovery After Photobleaching (FRAP)\n●      Fluorescence-Lifetime Imaging Microscopy (FLIM)\n●      Multicolor Fluorescence Correlation Spectroscopy (FCS)\n●      Multicolor  Image Correlation Spectroscopy (ICS)\n●      Intravital Microscopy (IVM)\n●      Anisotropy/Polarization Microscopy\n●      Single Particle Tracking (SPT)\nSuper-Resolution Microscopy:\n●      Structured Illumination Microscopy (SIM)\n●      Image Scanning Microscopy (ISM)\n●      Single Molecule Localisation Microscopy (SMLM)\n●      Stimulated Emission Depletion Microscopy (STED).\n●      Total Internal Reflection Fluorescence Microscopy (TIRF)\nMesoscopic Imaging:\n●      Light-sheet mesoscopic imaging/ Selective Plane Illumination Microscopy (SPIM or dSLSM)\n●      Optical Projection Tomography (OPT)\nLabel-free Imaging:\n●      Second/Third Harmonic Generation (SHG/THG)\n**Electron Microscopy:**\n●      TEM of chemically fixed samples\n●      EM tomography\n●      Serial blockface SEM\n●      Focus Ion Beam SEM\n●      Immuno-gold EM on thawed cryo-section (Tokuyasu Method)\n●      Immuno-gold EM on resin sections\n●      Genetic encoded EM probes (e.g. APEX)\n●      Pre-embed CLEM\n●      Post-embed CLEM\n●      Immunolabelling on immobilized particles\n●      SEM (topography)\n**Multimodal Correlative Microscopy:**\n●      Pre-embed CLEM\n●      Post-embed CLEM\n●      Live-cell CLEM\n**Contact Flanders BioImaging:**\n[Christopher.cawthorne@kuleuven.be](mailto:Christopher.cawthorne@kuleuven.be)\n**[https://www.flandersbioimaging...](https://www.flandersbioimaging.org)**", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "d2871017", "d3d66a1d", "f1f735b6", "e7adfd19", "17dd34eb", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "d6cec7b4", "f65a70b8", "b5333ef4", "b015d920", "3a4d793f", "f05d797c", "931ee18e", "af33ff84", "4ae7143c", "df1896a3", "c9ddc22b", "eebba7a7", "e32e05f1", "3f84bc36", "04562797", "a7128dd1", "cb003121", "4b452472", "13e1b5d4", "90e98166", "73094724", "c3302077", "59bcd971", "9c64e406", "fc3c255a", "4aa5d36d", "36d4a2a7", "b4a6f749", "2ce231cc", "59a33aed", "15ef9b0e", "c41fb0d1", "8fa56005", "3744dad8", "3a2f2c38", "0f1e5f18", "4a91416e", "d74face8", "c83c6c2b", "639a72d3", "22875d0d", "a6cee2e2", "4707da44", "f45daf6b", "7add3aac", "02c9e1e3", "ae6d3c51", "4e2f1176" ], "country": { "id": "7c746ad2-6e4e-476e-9d22-0143f6002886", "name": "Belgium", "iso_a2": "BE" } }, { "id": "fc1893d4", "name": "French BioImaging Node", "original_id": "e26ee21b-84d5-45ff-a78b-17363b2a81c8", "description": "30 facilities, 80 labs, bioimage informatics, advanced microscopy methods.", "documentation": "## FRANCE\n## French BioImaging Node\n---\n**France-BioImaging (FBI) is the French national research infrastructure for biological imaging.\nAt the crossroads between molecular and cell biology, integrated physiology, biophysics and engineering, mathematics and informatics, this coordinated infrastructure gathers 30 large facilities and 80 R&D laboratories specializing in imaging in 10 regional sites (8 of which are currently open to EuBI users) and one transversal Node in bioimage informatics. FBI aims at creating the most efficient adoption of the latest advances in technologies and methods related to microscopy by the users of the imaging facilities. R&D labs agree to open their technologies and expertise to the European community either by hosting users on their own site or after technological transfer to the FBI core facilities. These technologies and methods, reinforced by a strong support in computational analysis, provide quantitative measures and integrative understanding of a wide range of cell and tissue activities in biological models, from the simplest organism, to small animals in normal and pathological situations.\nPer year, we provide our ~5,000 users immediate access to cutting-edge and innovative microscopies, powerful labeling and computing methods, and appropriate training. As such, FBI plays an essential role in enabling competitive research in many fields, from fundamental questions in cell and developmental biology to preclinical research, thereby impacting a variety of domains such as agronomy, marine biology and human health. The study of human diseases is also particularly important for FBI, with many of our users working on cancer research, host-pathogen interactions, immunity, neurodegenerative and developmental disorders, genetic diseases, aging…**\n![](upload/french_node_2024.png)\n*Main scientific fields of expertise in the 8 regional sites of FBI currently open to EuBI users*\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| Objective-couple planar illumination (OCPI) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Random Illumination Microscopy (RIM)\\* | ✓ | ✓ |\n| Lattice Lightsheet (LL) \\* | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Reversible optical fluorescence transitions (RESOLFT) | ✓ | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| Optical projection tomography (OPT) | ✓ | ✓ |\n| Macro Serial Block face Fluorecence imaging\\* | ✓ | ✓ |\n| Raman Spectroscopy (RS) | ✓ | ✓ |\n| Quantitative Phase Imaging\\* (QPI) | ✓ | ✓ |\n| Polarization microscopy (PM) | ✓ | ✓ |\n| Second/Third Harmonics Generation (SHG/THG) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Phosphorescence Lifetime imaging (PLIM) | ✓ | ✓ |\n| Intravital Microscopy (IVM) | ✓ | ✓ |\n| Voltage/pH/Ion Imaging \\* | ✓ | ✓ |\n| Microdissection \\* | ✓ | ✓ |\n| High-speed Imaging \\* | ✓ | ✓ |\n| Imaging at Biosafety Level >1 | ✓ | ✓ |\n| Photomanipulation | ✓ | ✓ |\n| Anisotropy/Polarization Microscopy | ✓ | ✓ |\n| Expansion Microscopy \\* | ✓ | ✓ |\n| Feedback microscopy \\* | ✓ | ✓ |\n| Multiplexing imaging \\*(Codex, Opal, Celldive) | ✓ | ✓ |\n| Tissue Clearing (TC)\\* | ✓ | ✓ |\n| Single molecule FRET \\* | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ | ✓ |\n| Large scale EM | ✓ | ✓ |\n| EM tomography (ET) | ✓ | ✓ |\n| serial section TEM | ✓ | ✓ |\n| Serial Blockface SEM | ✓ | ✓ |\n| STEM tomography | ✓ | ✓ |\n| Array tomography | ✓ | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| Genetic encoded EM probes | ✓ | ✓ |\n| Pre-embed CLEM | ✓ | ✓ |\n| on-section CLEM | ✓ | ✓ |\n| Cryo Electron Tomography (Cryo-ET)\\* | ✓ | ✓ |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ | ✓ |\n| pre-embeded CLEM | ✓ | ✓ |\n| in-section CLEM | ✓ | ✓ |\n| live-cell CLEM | ✓ | ✓ |\n| CXEM (Correlative X-ray and EM) \\* | ✓ | ✓ |\n| in vivo optical imaging | ✓ | ✓ |\n| Traction Force Microscopy (TFM) \\* | ✓ | ✓ |\n| Atomic Force Microscopy\\* (AFM) | ✓ | ✓ |\n| Image Analysis-bio \\* | ✓ | ✓ |\n| micro-CT | ✓ | - |\n### Instrument highlights\nAmong a number of special features offered by the France-BioImaging Node let us quote:\n* Lattice light sheet microscopes, ideal for high-resolution imaging of live samples, are available in Paris-Centre, Bordeaux and Montpellier nodes.\n* Sequential smFISH for high-resolution spatial transcriptomics is available in Montpellier.\n* Specialization in super resolution in the Bordeaux site with more than ten systems covering STED, GSD, PALM/STORM and combination of methodologies dedicated to Neurosciences and plant imaging projects\n* Several innovative correlative approaches: Correlative X-ray and Electron Microscopy (CXEM) to explore the ultrastructure of the sample at precise positions by adapted 2D or 3D electron microscopy modality, in Marseille; LM/AFM correlative microscopy for nanometric and sub-nanometric resolution, in Montpellier.\n* Imaging equipment in P3 labs for host-pathogens studies in Paris sites\n* Preclinical-biomedical imaging by innovative approaches in Marseille and Paris sites\n* A unique core facility (FB-IAS) dedicated to user projects on Bioimage Analysis\n### Additional services offered by the Node\n* Instruments\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Technical assistance to run instrument\n* Probe preparation\n* Animal preparation\n* Animal facilities\n* Wet lab space\n* Data processing and analysis\n* Training seminar rooms\n* Housing facilities\n* Regulatory affairs management service\n* Biobanking, biological material storage and processing\n![](upload/france.jpg)\n### Contact details\nRené Marc Mège (DR CNRS, PhD)\nScientific Director of the National Research Infrastructure in Biomedical Science (INBS) France-BioImaging\n**Caroline Thiriet (IE CNRS)**\nExternal Affairs Manager of France-BioImaging, Node representative, EuBI user access coordinator\n[caroline.thiriet@france-bioimaging.org](mailto:caroline.thiriet@france-bioimaging.org)\n\n[contact@france-bioimaging.org](mailto:contact@france-bioimaging.org)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "a7c09ccd", "31d30c68", "d2871017", "b51478b1", "d3d66a1d", "f1f735b6", "a42333c3", "e7adfd19", "17dd34eb", "83b4baea", "dcb85d5e", "f6b01df1", "4ba07d0c", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "d6cec7b4", "f65a70b8", "b5333ef4", "b015d920", "47c84335", "1f3001ca", "3a4d793f", "f05d797c", "a2a0f4a8", "3ba9fb09", "931ee18e", "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "995a6055", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0dee2953", "0abb2c96", "a7128dd1", "cb003121", "c60b4a73", "13e1b5d4", "90e98166", "73094724", "c3302077", "59bcd971", "a9f0fcad", "0534020c", "b4a6f749", "59a33aed", "22875d0d", "a6cee2e2", "4e5bcb9e" ], "country": { "id": "cbf249b4-f5b8-4f8e-827e-14fb60339fed", "name": "France", "iso_a2": "FR" } }, { "id": "6f0ef2b7", "name": "High Throughput Microscopy Dutch Flagship Node", "original_id": "18e9e9dc-8a5e-4d4b-b71d-02ad01a0c92d", "description": "NL flagship: high-throughput, live cell, advanced imaging, multi-site expertise.", "documentation": "## NETHERLANDS\n## High Throughput Microscopy Dutch Flagship Node\n---\n**The Dutch High Throughput Microscopy flagship Node brings together the three leading screening centers in the Netherlands that have extensive experience with cell-based screening coupled to high content imaging and advanced microscopy. The integration of these three sites in one NL-HTM center creates a world leading expertise center in high-throughput microscopy for imaging based screening. Each center offers specific strength and expertise. Each of these sites has developed a high-end infrastructure covering a broad range of screening and imaging technologies. Leiden Cell Observatory is in particular experienced in high-throughput high-end microscopy using automated live cell time-lapse confocal microscopy in combination with focused RNAi and compound screening strategies. The CSC is specialized in automated high-throughput imaging based screens using low resolution high-throughput endpoint imaging. The NKI Screening Center is highly experienced and at the forefront in whole genome RNAi screening using genome-wide shRNA as well as siRNA libraries and the NKI Advanced Microscopy Center integrates high-end microscopy approaches into medium throughput automated microscopy settings.**\n### Specialties and expertise of the Node\nThe Dutch HTM flagship Node is specialized in the development and application of cell based screening assays in 2D and 3D with image-based assays and readouts. Screening platforms compromise small molecule collections, functional genomic screening collections including CRISPR, shRNA and siRNA. Special interest and expertise lies in the use of advanced fluorescence based reporter cell lines to monitor live signaling dynamics. For automated image analysis, screen analysis and data integration we have developed relevant image analysis and bioinformatics pipelines using different open sources software for image quantification. Another area of expertise is the use of quantitative data for computational modelling to obtain a mechanistic understanding of observed phenotypes. We also have extensive experience in combining HCS with functional imaging assays, employing e.g. FRET sensors for readout of second messenger cascades, receptor activation and receptor internalization. New fast FLIM approaches have been implemented on our automated microscopes as well.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n### Additional services offered by the Node\n* Instruments\n* Technical assistance to run instrument\n* Assistance with experimental design (e.g. experimental set up, choice of technique)\n* Training in infrastructure use\n* Probe preparation\n* Animal preparation\n* Wet lab space\n* Server Space\n* Data processing and analysis\n* Training workstations\n* Training seminar room\n* Biobanking, biological material storage and processing\n* Cell culture facilities - Safety level 1 and 2\n### Instrument highlights\nSpecial features of instruments at the NL-HTM node: 1) we have both high-end confocal microscopes all equipped for automated screening and low-end HTM imagers; 2) all microscopes set-ups are equipped for live cell imaging; 3) automated robotics dedicated to perform siRNA and compound screenings are associated with the HTM imagers. We have confocal microscopes capable of adding agonists during acquisition, and we provide fast FLIM readout for FRET detection.\n### Contact details\n**Dr. Roderick L. Beijersbergen**\nAsst. Prof. Divison of Molecular Carcinogenesis and Head of NKI Robotics and Screening Center\n[r.beijersbergen@nki.nl](mailto:r.beijersbergen@nki.nl)\n+315121960\n**Dr. David A.Egan**\nLab Manager, Department of Cell Biology UMC\n[d.a.egan@umcutrecht.nl](mailto:d.a.egan@umcutrecht.nl)\n+31887555590\n**Prof. Dr. K. Jalink**\nHead of Biophysics and advanced imaging group\n[k.jalink@nki.nl](mailto:k.jalink@nki.nl)\n+31 20 512 1933\n**Prof. Dr. Bob van de Water**\nHead of division of Toxicology\n[b.water@lacdr.leidenuniv.nl](mailto:b.water@lacdr.leidenuniv.nl)\n+31715276223\n", "offer_technology_ids": [ "722bb380", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "9beefd47", "name": "Israel BioImaging", "original_id": "d091effc-c73e-4ad8-88cd-f69107c33790", "description": "Cross-modality imaging: single-molecule to clinical, advanced analysis.", "documentation": "## ISRAEL\n## Israel BioImaging\n---\n**The EUBI-Israel Node is a multi-sited, multi-modal Node including seven hosting sites across Israel. It offers access to a broad range of technologies from biological, molecular to medical imaging. The focus and unique aspect of Israel Bioimaging is facilitating and enabling cross-modality imaging spanning all scales from single-molecule to in vivo and clinical imaging. The node enables seamless correlative imaging from Electron microscopy and advanced Biological microscopy through advanced live and high throughput imaging to in vivo preclinical and clinical imaging along with the capacity for advanced image analysis and computation.**\n### Specialties and expertise of the Node\nIsrael BioImaging offers cutting edge imaging platforms and cross modality capabilities to allow multiscale imaging to enable seamless transition from cells to tissues and organs to whole body imaging. Applications range across all life forms and pathologies, from marine biology and plant science to developmental biology, infectious diseases, neuroscience, cancer and aging.\n### Offered Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ |\n| EM tomography (ET) | ✓ |\n| serial section TEM | ✓ |\n| Serial Blockface SEM | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ |\n| Cryo Scanning Electron Microscopy (Cryo-SEM)\\* | ✓ |\n| pre-embed CLEM | ✓ |\n| in-section CLEM | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ |\n| Elemental analysis \\* | ✓ |\n| micro-MRI/MRS (Field >= 7 T) (HF) | ✓ |\n| micro-CT | ✓ |\n| micro-US | ✓ |\n| in vivo optical imaging (OI) | ✓ |\n| PhotoAcoustic Imaging (PAI) - med | ✓ |\n| micro-PET/CT | ✓ |\n| Intravital microscopy (IVM) - Med | ✓ |\n| MRI/MRS (>= 7T) | ✓ |\n| MRI/MRS (< 7T) | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n| Image Analysis-bio \\* | ✓ |\n### Additional services offered by the Node\n* Project planning and methodological setup\n* Wet labs\n* Cell culture facilities\n* Animal housing\n* Imaging probes\n* Data processing and analysis\n* Data storage\n### Instrument highlights\nUnique aspects in Israel Bioimaging include high field MRI, correlative imaging across scales, advanced probe chemistry, advanced computation tools and unique applications such as marine imaging (Mediterranean and Red sea) and underwater imaging including deep water microscopy.\n### Contact details\nNode head: Prof Michal Neeman [michal.neeman@weizmann.ac.il](mailto:michal.neeman@weizmann.ac.il)\nOffice: Lili Kasumov [lili.kasumov@weizmann.ac.il](mailto:lili.kasumov@weizmann.ac.il)\n**Website is under construction**\nWeizmann Institute of Science: [https://www.weizmann.ac.il](https://www.weizmann.ac.il/pages/)\nTel Aviv University: \nTechnion: \nJerusalem: \nBen Gurion University of the Negev: \nBar Ilan University (BIU): \nBIU Light Microscopy Unit: \nBIU Electron Microscopy Unit: \nUniversity of Haifa: ", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "d3d66a1d", "f1f735b6", "e7adfd19", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "af33ff84", "4ae7143c", "df1896a3", "d169e03b", "c9ddc22b", "63775639", "e32e05f1", "0dee2953", "0abb2c96", "cb003121", "904149e2", "c60b4a73", "3965a906", "9c64e406", "fc3c255a", "b4a6f749", "2ce231cc", "59a33aed", "d54d34a2", "c41fb0d1", "3744dad8", "4a91416e", "d74face8", "c83c6c2b", "22875d0d", "6324bef6", "4707da44", "4e5bcb9e" ], "country": { "id": "7fbbd6b0-b258-44b0-91e3-536df97a806a", "name": "Israel", "iso_a2": "IL" } }, { "id": "cf8f008b", "name": "Medical and Preclinical Imaging Hungary", "original_id": "2ce2753f-e827-4bb6-8765-43c21ab5bc7f", "description": "Multi-modal Node: functional imaging, PET/CT, microCT, unique M3 concept.", "documentation": "## HUNGARY\n## Medical and Preclinical Imaging Hungary\n---\n**The Medical and Preclinical Imaging Hungary is a multi-sited, multimodal Node covering biomedical imaging, both preclinical and medical. The specialty of the Node is functional imaging. Each site specializes in at least one technique in which it has high expertise: quantitative autoradiologic measurements, microCT, PET, clinical SPECT/CT and PET/CT. Thus, users have access to a very broad scope of functional imaging techniques.**\n### Specialties and expertise of the Node\nWe are convinced that our concept of Molecules through Mice to Man (M3) concept is unique in Europe. Any user can access our full integrated line of imaging systems, and we are capable to handle the whole process from molecular level characterization through preclinical imaging to human clinical studies.\n### Offered Technologies\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Technologies | Euro-BioImaging | ISIDORe |\n| micro-MRI/MRS (>= 7T) | ✓ | ✓ |\n| micro-CT | ✓ | ✓ |\n| micro-PET | ✓ | ✓ |\n| micro-SPECT | ✓ | ✓ |\n| in vivo Optical Imaging | ✓ | ✓ |\n| micro-PET/MRI | ✓ | ✓ |\n| micro-PET/CT | ✓ | ✓ |\n| micro-SPECT/CT | ✓ | ✓ |\n| MRI-PET | ✓ | ✓ |\n| PET | ✓ | ✓ |\n| PET/CT \\* | ✓ | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ | ✓ |\n| micro-CT - ex-vivo | ✓ | ✓ |\n### Additional services offered by the Node\n* Technical assistance to run instruments\n* Cell culture facilities\n* Animal facilities\n* Wet lab space\n* Isotope laboratories\n* Data processing and analysis\n* Data storage\n* Seminar rooms\n### Additional services offered by the Node\nThe Node offers preclinical MiniPET, NanoPET-MRI and nano-SPECT-CT scanners. Beside these, clinical equipment for PET/SPECT-CT is also available. Functional Ultrasound (fUS), also coupled to SPECT/CT, can be provided. The MRI scanner is a Bruker Pharmascan 4.7T. Additional instrumentation include a Phosphore Imager and a LEICA CM3600 cryomacrotome.\nOne of the sites of the Node has all the 4 imaging modality (PET-MRI, SPECT-CT) in one room for preclinical use. Moreover, the Translation Research Center is the demo site one of the worldwide known company in the field of preclinical imaging. Besides the imaging facilities our Node have a cyclotron facility with 16 MeV medical cyclotron which can produce isotopes not only for traditional PET imaging.\n### Contact details\nViktoria Aratò, [arato.viktoria@med.unideb.hu](mailto:arato.viktoria@med.unideb.hu)", "offer_technology_ids": [ "9c64e406", "4aa5d36d", "36d4a2a7", "b4a6f749", "59a33aed", "15ef9b0e", "c41fb0d1", "8fa56005", "a9c43bba", "3a2f2c38", "0f1e5f18", "4a91416e", "c83c6c2b", "4e5bcb9e" ], "country": { "id": "ad818e51-e4da-40fd-9ced-4e0f8fb3a5b2", "name": "Hungary", "iso_a2": "HU" } }, { "id": "d2be2f9c", "name": "Molecular Imaging Italian Node", "original_id": "d90a2ef1-bafd-45ec-9f2e-924345e1740c", "description": "Italy 8-site: multi-modal, in vivo imaging, extensive tracer repository, advanced applications.", "documentation": "## ITALY\n## Molecular Imaging Italian Node\n---\n**The Multi Modal Molecular Imaging (MMMI) Italian Node is a multi-sited Node focused on biomedical imaging, and offering expertise and technical skills for the acquisition and analysis of “in vivo” images obtained by the most relevant state-of-the-art imaging technologies. The MMMI Italian Node comprises 8 research centers, each with its own specialties, located in 4 Italian cities (Turin, Milan, Naples, and Pisa). The Node provides the users with many services including a large repository of imaging agents/tracers for the available imaging technologies, and a number of cellular and animal models (mainly mice) reproducing the most relevant human pathologies. Support is available for advanced applications including quantitative assessment of biomarkers as well as “in vitro” assays for the validation of the imaging experiments.**\n### Specialties and expertise of the Node\nThe Node is well equipped with chemical instrumentation and offers support in the design, characterization and testing of imaging probes (molecular, macro- and supra-molecular, nano- and micro-sized systems) for all the Imaging Modalities. The expertise at the Node's centers covers the design of targeting and responsive imaging procedures. Several MRI (from 1T to 9.4T), Optical Imaging, PET and SPECT scanners are offered in conjunction with the proper tracers at centers excelling in research on the investigated pathologies (Milan and Naples for neurological diseases, Pisa and Naples for cardiovascular diseases, Turin and Naples for oncological diseases, and Pisa for metabolic diseases). The Node has also strong expertise in imaging procedures within the integrated diagnostic MRI-PET and PET/CT with total body and district acquisition mode, as well as on quantitative morphology by standalone CT/microCT. High frequency ultrasound technology is also available providing high-quality morphological, and functional information.A biobank service is also available, providing analysis of biochemical components (DNA extraction, RNA, proteins, etc) of different types of biological materials.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| micro-MRI/MRS (>= 7T) | ✓ | ✓ |\n| micro-MRI/MRS (< 7T) | ✓ | ✓ |\n| micro-CT | ✓ | ✓ |\n| micro-PET | ✓ | ✓ |\n| micro-US | ✓ | - |\n| in vivo Optical Imaging | ✓ | – |\n| Photoacoustic Imaging (PAI) - med | ✓ | – |\n| micro-PET/MRI | ✓ | ✓ |\n| MRI/MRS (< 7T) | ✓ | – |\n| micro-SPECT/CT | ✓ | – |\n| MRI-PET | ✓ | ✓ |\n| PET | ✓ | ✓ |\n| Terahertz Plant Imaging (THzI)\\* | ✓ | – |\n| PET/CT \\* | ✓ | – |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ | ✓ |\n| micro-MRI/MRS (< 7T) - ex-vivo | ✓ | ✓ |\n| micro-CT - ex-vivo | ✓ | ✓ |\n| Image Analysis-med \\* | ✓ | ✓ |\n![](/upload/MIIN_img1.PNG)\n![](/upload/MIIN_img2.PNG)\n###\n### Additional services offered by the Node\n* Relaxometry\n* Probe preparation\n* Animal preparation\n* Animal facilities\n* Cell culture, microscopy, histology\n* Wet lab space\n* Radiochemistry facility\n* Radionuclide production facility (cyclotron)\n* Laboratory for detector development and testing\n* Image processing and analysis\n* Biobanking\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n![](/upload/MIIN_img3.PNG)\n### Contact details\n**Enzo Terreno**\nCoordinator\nWebsite: \nPhone: +39 0116706451\ne-mail: [enzo.terreno@unito.it](mailto: enzo.terreno@unito.it)\nWebsites MMMI Italian Node partners\nUniversity of Turin:\nSan Raffaele Hospital (Milan): \nCNR Institute of Molecular BioImaging and Physiology (Milan):\nCNR Institute of Clinical Physiology (Pisa):\nG. Monasterio Foundation (Pisa):  [http://www.ftgm.it](http://www.ftgm.it/)\nUniversity of Pisa: [http://www.df.unipi.it](http://www.df.unipi.it/)\nIRCCS SDN (Naples): [http://www.sdn-napoli.it/en/home-2](http://www.sdn-napoli.it/en/home-2/)\nCNR Institute of Biostructures and BioImages (Naples): [http://www.ibb.cnr.it](http://www.ibb.cnr.it/)", "offer_technology_ids": [ "9c64e406", "fc3c255a", "4aa5d36d", "b4a6f749", "2ce231cc", "59a33aed", "d54d34a2", "15ef9b0e", "c41fb0d1", "8fa56005", "a9c43bba", "3a2f2c38", "0f1e5f18", "4a91416e", "d74face8", "c83c6c2b", "639a72d3", "4707da44", "4e5bcb9e", "b4d963a5" ], "country": { "id": "0af8a17e-b371-4f0b-a408-9ee57dc20943", "name": "Italy", "iso_a2": "IT" } }, { "id": "3e52fd14", "name": "NORMOLIM, Norwegian Molecular Imaging Infrastructure", "original_id": "66feff3a-8cda-43ee-a946-fe89e167cc96", "description": "Norwegian in vivo imaging: disease models, transgenic systems, clinical translation.", "documentation": "## NORWAY\n## NORMOLIM, Norwegian Molecular Imaging Infrastructure\n---\n**NORMOLIM focuses on imaging technologies and methods in the area of *in vivo* molecular imaging; limited to *in vivo* imaging in animal model systems (experimental models of disease and transgenic mice/rats). This research area is an important link for translation between breakthroughs in basic biomedical research and new clinical practice that can improve patient management and patient outcome. The research groups involved in the NORMOLIM infrastructure collaborate closely with the university hospitals and are directly involved in clinical research on translation of new knowledge, new therapies and new methods/technology into new clinical practice.**\n### Specialties and expertise of the Node\nThe Node is a 3-site national collaboration where the three sites have specialized in studies of brain (Trondheim), cancer (Bergen) and heart (Oslo).\nThe Node also offers some special methods and expertise:\n* Manganese Enhanced MR Imaging.\n* Tracer synthesis for PET, 18F based.\n* Multimodal MR combining in vivo MR imaging, in vivo multi-nuclear MR spectroscopy, and ex vivo MR metabolomics of intact tissue samples/biopsies.\n* Metabolomics studies using MR spectroscopy with 13C enriched substrates.\n* High-resolution MR phase contrast imaging of myocardial strain and motion.\n* High-end MRI and ultrasound-based analysis of regional myocardial function combined with advanced electrophysiological and live cell imaging techniques.\n* Multimodal imaging (MRI, PET/CT, OI, US) of tumour development and treatment effects on malignant tumours.\n* Ultrasound strain imaging and elastography.\n* Ultrasound scanning in animal models for IBD and PDAC (Microbubbles and sonoporation).\n* In vivo time-domain optical imaging of cancer, particularly with discrimination of targeted near-infrared fluorophores from endogenous background or non-targeted probe.\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| micro-MRI/MRS (Field >= 7 T) (HF) | ✓ |\n| micro-US | ✓ |\n| in vivo optical imaging (OI) | ✓ |\n| PhotoAcoustic Imaging (PAI) - med | ✓ |\n| micro-PET/MRI | ✓ |\n| micro-PET/CT | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| Mass spectrometry-based imaging (MSI) - med\\* | ✓ |\n### Additional services offered by the Node\n* Instruments\n* Technical assistance to run instruments\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Training in infrastructure use\n* Animal preparation\n* Animal facilities\n* Access to some animal models\n* Data processing and analysis\n### Instrument highlights\nAll three sites have state-of-the-art instruments and full instrument details are available through the [NORMOLIM web site](https://normolim.w.uib.no/).\nSome highlights are:\n* Coils for in vivo 1H, 13C, 23Na, 31P, 19F MR spectroscopy/imaging\n* In vivo time domain fluorescence lifetime imaging permits discrimination of fluorophores based on the fluorescence lifetime of the exogenous and endogenous fluorescence\n* PMOD software for quantification of dynamic PET scans\n* Molecular Ultrasound Imaging: The Visualsonics scanner has modules for 3D imaging, contrast imaging, Doppler and strain imaging\n![](upload/Normolim.png)\n### Contact details\n**Lili Zang**\n[lili.zhang@medisin.uio.no](mailto:lili.zhang@medisin.uio.no)\n**Jin Li**\n[jin.li@ntnu.no](mailto:jin.li@ntnu.no)\n", "offer_technology_ids": [ "4b561f4f", "9c64e406", "2ce231cc", "59a33aed", "d54d34a2", "15ef9b0e", "c41fb0d1", "4a91416e", "9c814a85", "4e5bcb9e" ], "country": { "id": "17fe4446-3b3a-4237-8bf5-d00d391e867f", "name": "Norway", "iso_a2": "NO" } }, { "id": "64543c53", "name": "No Node preference", "original_id": "fd9d5803-ec9f-4eaa-b653-5af04d608a79", "description": "Node selection assistance, tailored tech guidance, project optimization.", "documentation": "## No Node Preference\n---\nPlease select this if you are unsure of the node needed for your application and Euro-BioImaging will help you in the making the appropriate choice of technology and node for your project.\n|\n| |", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "a7c09ccd", "d2871017", "60f50c0f", "b51478b1", "d3d66a1d", "f1f735b6", "a42333c3", "f68070c5", "fc6e9ebb", "f4eef350", "83b4baea", "f6b01df1", "745fa0d0", "4ba07d0c", "d52b6d15", "e480e528", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "d6cec7b4", "f65a70b8", "b5333ef4", "b015d920", "47c84335", "1f3001ca", "3a4d793f", "f05d797c", "3ba9fb09", "931ee18e", "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "995a6055", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0dee2953", "0abb2c96", "a7128dd1", "cb003121", "904149e2", "4b452472", "c60b4a73", "3965a906", "8597af30", "13e1b5d4", "90e98166", "593e3440", "73094724", "60335007", "c3302077", "59bcd971", "a9f0fcad", "4b561f4f", "afeaed8d", "0534020c", "9c64e406", "4aa5d36d", "36d4a2a7", "2ce231cc", "59a33aed", "d54d34a2", "15ef9b0e", "c41fb0d1", "8fa56005", "6709f67e", "3744dad8", "a9c43bba", "3a2f2c38", "b5cb68ca", "0f1e5f18", "1fe88685", "4a91416e", "d74face8", "c83c6c2b", "413a548d", "9c814a85", "89bab6f3", "639a72d3", "fd0e8053", "22875d0d", "a6cee2e2", "6324bef6", "4707da44", "4e5bcb9e" ], "country": { "id": "3af7d3ae-28ec-4ebe-91c7-7cafe8faa285", "name": "Unknown", "iso_a2": "UN" } }, { "id": "a44edc42", "name": "NorMIC Oslo - Advanced Light Microscopy Node Oslo", "original_id": "cb960905-270b-434f-9086-9e3c3dcb1d80", "description": "Live imaging, sub-cellular dynamics, incubators for CO2 control.", "documentation": "## NORWAY\n## NorMIC Oslo - Advanced Light Microscopy Node Oslo\n---\n**The Norwegian advanced light microscopy Node is based on two imaging facilities, one at the University Hospital, Montebello, Oslo and one at the Department of Biosciences, Oslo University at Blindern, Oslo. Main research areas are kinetics of intracellular vesicle traffic, fusion, fission, cell division, cell migration and immune cell interactions in addition to imaging of fixed samples.**\n### Specialties and expertise of the Node\nThe platform has a focus on live imaging of tissue culture and most light microscopy units are equipped with incubators for stable temperature and CO2. The unit offers expertise and technical assistance in a range of advanced light microscopes including confocal laser scanning instruments, spinning disc confocal, TIRF, as well as access to immuno-EM techniques.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| High-speed Imaging \\* | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| Pre-embeded CLEM | ✓ | ✓ |\n### Additional services offered by the Node\n* Methodological setup\n* Training and technical assistance\n* Cell culture facilities\n* Wet lab space\n* Probe preparation\n* Data processing and analysis\n* Probe preparation\n* Housing facilities\n### Contact details\n**Oddmund Bakke**\nHead of NorMIC-Oslo facility\n[oddmund.bakke@ibv.uio.no](mailto:oddmund.bakke@ibv.uio.no)\n+4795851479\n**Andreas Brech**\nHead of CLEM/EM facility\n[andreas.brech@rr-research.no](mailto:andreas.brech@rr-research.no)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "31d30c68", "d3d66a1d", "e9910d1c", "018d2770", "d6cec7b4", "af33ff84", "e32e05f1", "3f84bc36", "143e2504", "13e1b5d4", "4e5bcb9e" ], "country": { "id": "17fe4446-3b3a-4237-8bf5-d00d391e867f", "name": "Norway", "iso_a2": "NO" } }, { "id": "d14abc55", "name": "Phase Contrast Imaging Flagship Node Trieste", "original_id": "cd6fed60-1666-472c-b573-22e092c89c67", "description": "Trieste: High-intensity phase contrast, soft tissue imaging, synchrotron source.", "documentation": "## ITALY\n## Phase Contrast Imaging Flagship Node Trieste\n---\n**The Italian Phase Contrast Imaging Flagship Node is based on the SYRMEP beamline of the Elettra Synchrotron light source (Trieste).\nThe main characteristics of Synchrotron Radiation, namely monochromaticity, high intensity and spatial coherence, allow the effective application of phase contrast techniques. Differently from conventional radiology, where the image formation relies on the absorption properties of the sample, these approaches are sensitive to the phase shifts produced by the sample on the incoming X-rays. Phase contrast is particularly effective for imaging of soft biological tissues, where the conventional technique has strong limitations due to the poor intrinsic X-ray absorption.\nThe beamline provides two stations working with monochromatic or white/pink X-ray beam for planar and Computed micro-Tomography (microCT) imaging. A CT system based on a micro-focus X-ray source, named TomoLab, is available, if required in the proposal, as auxiliary facility.\nThe Node offers full packages including image acquisition, reconstruction and data reduction tools.**\n### Specialties and expertise of the Node\nBeing part of the Elettra facility, the SYRMEP beamline is open to external users since 2000. The beamline control system has a user friendly interface, to facilitate the access by researchers without specific knowledge of Synchrotron Radiation.\nThe beamline staff has several years of expertise in X-ray techniques, image processing and analysis, matured collaborating with users and imaging groups of other laboratories.\nCompetences in application of new modalities like the low dose phase contrast CT, suited for in-vivo studies, and in dosimetry, have also been developed.\nA software package for CT reconstruction, SYRMEP Tomo Project (STP), has been specifically designed for the beamline users and offers flexible solutions to satisfy the various experimental needs.\nThe research team has also developed Pore3D, a software library for quantitative analysis of 3D images. The library includes several functions and procedures for performing filtering, segmentation, skeletonization as well as the extraction of quantitative values.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Phase Contrast Imaging | ✓ | ✓ |\n### Instrument highlights\nSpecial features of instruments at the Italian Node are:\n* The possibility to perform multi-scale Synchrotron Radiation imaging in propagation-based phase contrast modality at different resolution levels (imaging pixel sizes from 1 µm to 50 µm, according to the sample sizes and characteristics).\n* The use of a dedicated Analyzer Based Imaging setup working with a monochromatic beam in the X-ray range between 15 keV and 35 keV.\n* The possibility to optimize the imaging protocol and reconstruction workflow according to the specific application (using the different pre-processing/reconstruction algorithms available in the STP).\n* The high flexibility of the experimental station that allows to fulfill different user requirements (in-situ, implementation of new instrumentation, etc.).\n### Contact details\n**Dr. Giuliana Tromba**\nSYRMEP Beamline Coordinator\n[giuliana.tromba@elettra.eu](mailto:giuliana.tromba@elettra.eu)\n+390403758587\n**SYRMEP Beamline:**\n\n**TomoLab:**\n\n**Pore3d Library:**\n", "offer_technology_ids": [ "413a548d", "4e5bcb9e" ], "country": { "id": "0af8a17e-b371-4f0b-a408-9ee57dc20943", "name": "Italy", "iso_a2": "IT" } }, { "id": "84334573", "name": "Population Imaging Flagship Node Rotterdam", "original_id": "72a5a9d2-809d-4f02-b0c5-ac0284316cee", "description": "Epidemiological studies, imaging biomarkers, risk assessment, Rotterdam Node", "documentation": "## NETHERLANDS\n## Population Imaging Flagship Node Rotterdam\n---\n**The European Population Imaging Infrastructure is an initiative of the Dutch Federation of University Medical Centres (NFU) and the Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Centre Rotterdam. The ultimate aim of the infrastructure is to support the implementation of imaging in large, prospective epidemiological studies on the population and clinical level. Specific imaging biomarkers of (pre-)symptomatic diseases can be used to investigate causes of pathological alterations and to identify people at risk of developing disease or disease progression.**\n### Specialties and expertise of the Node\nWith the experience in data storage, image analysis and machine learning on large datasets acquired in the large population-based Rotterdam Study, the population imaging node aims at developing state of the art image analysis pipelines for both population and clinical studies. This Node provides technical support in and advice on 1) image storage and quality assurance 2) image analysis pipelines and 3) high volume image processing and machine learning. The population imaging flagship node collaborates with major groups that have extensive expertise in image analysis and machine learning. The node aims to offer centralized access to validated image-analysis tools and image-analysis pipelines. All pipelines are standardized, extensively tested, and metrics on the performance are available.\n### Offered Technologies and Services:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Population Imaging (PI) | ✓ | ✓ |\n| Image Analysis-bio \\* | ✓ | ✓ |\n| Image Analysis-med \\* | ✓ | ✓ |\n* Image storage facilities (XNAT based) for permanent or temporary storage of medical images\n* Test-retest data image data for validation and evaluation of image analysis tools and pipelines\n* Image analysis tools\n+ Cardiovascular disease (intracranial arterial calcification)\n* Image analysis pipelines\n+ Neuroimaging (gray matter, white matter, cerebrospinal fluid, white matter lesions, and hippocampus)\n+ Cardiovascular imaging (epicardial fat, left atrial volume)\n+ Musculoskeletal imaging (knee cartilage, menisci)\n![](upload/Dutch_population_imaging.png)\n### Additional services offered by the Node\n* Data processing and analysis support\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Test-retest data image data for validation and evaluation of image analysis tools and pipelines\n### Instrument highlights\nXNAT is an open source imaging informatics platform developed by the Neuroinformatics Research Group at Washington University. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data. XNAT is a hosted national service by Erasmus MC and Health-RI TraIT. It is possible to have XNAT hosted in a federated fashion, but it can also be hosted locally in your institute.\n### Testimonials\n***“We were very happy with the professional and accessible epicardial fat-analyses on our research CT-scans.”***\n- Antonio Ribeiro, M.D., Ph.D. - ELSA-Brasil | Department of Cardiology, Universidade Federal de Minas Gerais\n### Contact details\nWebsite:\n[www.populationimaging.eu](http://www.populationimaging.eu)\n**Stefan Klein**\nDepartment of Radiology and Nuclear Medicine\nErasmus MC, University Medical Center\nRotterdam, The Netherlands\n[s.klein@erasmusmc.nl](mailto:s.klein@erasmusmc.nl)\n**Prof. Dr. Wiro J. Niessen**\nDepartment of Radiology and Nuclear Medicine\nErasmus MC, University Medical Center\nRotterdam, The Netherlands\n[w.niessen@erasmusmc.nl](mailto:w.niessen@erasmusmc.nl)\n+31 10 70 41026\n**Marcel Koek**\nDepartment of Radiology and Nuclear Medicine\nErasmus MC, University Medical Center\nRotterdam, The Netherlands\n[i.vanhouwelingen@erasmusmc.nl](mailto:i.vanhouwelingen@erasmusmc.nl)", "offer_technology_ids": [ "1fe88685", "639a72d3", "fd0e8053", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "6d068cfb", "name": "Population Imaging Valencia", "original_id": "6675f5bc-1635-46b1-b18e-b9d23f355d1b", "description": "AI-driven biomarkers, predictive models, structured image repositories.", "documentation": "## SPAIN\n## Population Imaging Valencia\n---\n**The Biomedical Imaging Research Group (GIBI230) at La Fe Health Research Institute (IIS La Fe) comprises a diverse team of 39 contracted researchers and 14 associated collaborators, establishing itself as a multidisciplinary clinical and technical unit centered in medical imaging developments. Proficient in computational solutions, the group specializes in extracting robust and reproducible imaging biomarkers through the utilization of radiomic methods and artificial intelligence algorithms, primarily for enhancing observational studies.**\nStrategically, the group focuses on developing and validating predictive models while concurrently creating extensive, structured, and standardized image repositories containing associated clinical, pathological, and molecular information (Real World Data). Drawing on considerable experience from previous European projects, the group excels in cancer imaging, distributed computing, data interoperability standards, privacy-preserving synthetic data generation, and AI modeling for early diagnosis, prognosis, prediction, and monitoring. These competencies extend to the development of clinical decision support tools for managing patients with various pathologies in real-world clinical practice.\nGIBI230 actively participates in clinical trials, exemplified by the establishment of the Imaging Clinical Trials Unit in 2016 (Penadés-Blasco A, et al. Medical imaging clinical trials unit: a professional need. EJR 2022), currently overseeing more than 300 studies.\nThe group opens its technological resources to facilitate other research groups and individual researchers in achieving their objectives, thereby contributing to the overall scientific quality of diverse projects. These resources are housed within the Experimental Radiology and Imaging Biomarkers Platform (PREBI), expertly managed by the group.\n### Specialties and expertise of the Node\n**Population Imaging**\nGIBI230 is related to a Datawarehouse at our hospital and research institute, serving as a central access for the efficient storage and retrieval of data, ensuring streamlined research workflows and providing rapid access to critical information.  There is a daily ETL process in place that ensures a continuous update of the data in our systems. Our expertise extends to the integration of data from diverse disciplines such as radiology, pathology, and laboratory. This integrated approach fosters a comprehensive understanding of complex biological processes.\nCommitted to maintaining high standards, GIBI230 adheres to rigorous data standardization practices, guaranteeing uniformity in data formats. The Datawarehouse ensures that all the terms are mapped into standards ontologies such as ICD-10, SNOMED or RxNorm, and load the data into the OMOP Common data Model. In addition, this OMOP-CDM is enhanced with the extensions needed for each type of project, being GIBI230 actively involved in the development of the imaging extension with the OHDSI community. This dedication significantly enhances interoperability and facilitates collaborative research initiatives. Our commitment to standardized, up-to-date data has positioned our data warehouse as a cornerstone for evidence-based decision-making across a spectrum of biomedical research domains.\nThanks to the implementation of this standardized Datawarehouse, GIBI230 demonstrates the capability to gather data automatically and efficiently. This enables the rapid establishment of retrospective datasets comprising thousands of records, facilitating timely and comprehensive research initiatives within a matter of days.\n**Artificial Intelligence algorithms and medical imaging**\nThe research group possesses solid knowledge and experience in image processing, as well as the development of Artificial Intelligence algorithms and methodologies for extracting image biomarkers and predicting relevant clinical outcomes. This is its greatest value and contribution to society.\nSome of the main methodologies and/or research solutions that the group has established and developed include the following:\n* Solutions for the processing of MR, PET, and CT images in oncology and neurodegenerative diseases, including image harmonization, noise reduction, inhomogeneity correction, spatial resampling, intensity normalization, image registration, and lesion segmentation.\n* Image analysis algorithms applied to cancer patients, including quantification of ADC, IVIM, Kurtosis, semi-quantitative and pharmacokinetic perfusion in MR; and both radiomics in both MR and CT.\n* Tools for studying tumor heterogeneity: Histogram and unsupervised clustering algorithms for the identification and definition of tumor habitats in MR images (Fit-Cluster-Fit).\n* Radiogenomic tools for analyzing correlations between image features and genomic data, enabling the discovery of radiomic signatures that can serve as substitutes for genetic tests.\n* Deep Learning algorithms for extracting deep features from MR and/or CT images.\n* Image harmonization tools: algorithms based on Generative Adversarial Networks (GAN) for generating synthetic radiological images.\n* Convolutional Neural Networks (CNN) and Transformers for the detection and segmentation of organs and tumors from MR and/or CT images.\n* Machine Learning models for radiomics and delta-radiomics to predict treatment response in cancer patients.\n* Integrative Machine Learning models based on clinical, molecular, and medical image data for predicting overall survival, tumor grade, progression rate, and treatment response.\n* End-to-end Deep Learning models for the classification and regression of relevant clinical endpoints.\n* Visualization and explainability tools (nosological parametric maps, clustering maps, SHAP values, glyph feature distributions, UMAP projections, etc.) for a better understanding of predictive model results, facilitating their adoption in clinical practice.\n### Instruments highlights\n* 1 compute node (2 x NVIDIA® DGX A100™) and 1 storage node (SERVER SIE LADON GBT CDL 6230 A 2.1 GHz GPU V100), for processing and storing images and biological and clinical data for the development of predictive AI models.\n* 1 Multimodal PET/MR (GEHC Signa): simultaneous acquisition of PET and 3T MR with a 60cm bore, allowing rapid acquisition and high spatial resolution. For clinical trials and clinical research projects with patients.\n* 1 3T RM (Philips Achieva TX, multi-transmission) with research platforms: 60 cm central tunnel where advanced MR acquisitions are carried out with the possibility of programming special pulse sequences. Both preclinical and clinical\n* 1 High resolution multimodality equipment (micro-PET/CT, Bruker Albira) for molecular and anatomical studies in small animals and samples\n### Additional services offered by the Node\n* User-oriented project support with study design and management\n* Assistance in image processing, data analyses, and interpretation\n* Federated node for distributed analysis\n* Data storage\n* Computational resources\n* Coordination and participation in clinical trials\n* 3D printing models\n* Interventional radiology training courses in animals\nWebsite: **[https://www.acim.lafe.san.gva....](https://www.acim.lafe.san.gva.es/acim/?page_id=1229&lang=en)**\nContact:\n[carina\\_soler@iislafe.es](mailto:gibi230@iislafe.es)\n[javier\\_aquerreta@iislafe.es](mailto:gibi230@iislafe.es)", "offer_technology_ids": [ "fc3c255a", "c41fb0d1", "3a2f2c38", "1fe88685", "d74face8", "639a72d3", "fd0e8053", "4707da44", "4e5bcb9e" ], "country": { "id": "88bb821e-347c-42b2-b756-1b689acf531e", "name": "Spain", "iso_a2": "ES" } }, { "id": "e5f30cac", "name": "Portuguese Platform of BioImaging (PPBI)", "original_id": "16659688-0f13-4bd0-b1cf-a141777edcd1", "description": "Multi-sited Euro-BioImaging Node: advanced light/electron microscopy, live cell imaging, high throughput.", "documentation": "## PORTUGAL\n## Portuguese Platform of BioImaging (PPBI)\n---\n**The PPBI - Portuguese Platform of BioImaging is a multi-sited, multimodal Euro-BioImaging Node covering biological imaging. PPBI comprises several advanced microscopy core facilities, organized in 3 geographical imaging clusters. PPBI services focus on advanced microscopy and image analysis for a wide range of life science domains - from cell and developmental biology, to neurosciences, oncobiology, immunology, infection, regenerative medicine and marine biology.\nPPBI offers state-of-the-art light and electron microscopy systems, covering applications from nano to mesoscopy, and has a strong expertise in live cell imaging and high throughput microscopy. More importantly, Euro-BioImaging users can expect to work together with highly qualified staff, who support our facilities and linked services, to boost user research projects.**\n### Specialties and expertise of the Node\nAt the Euro-BioImaging PPBI Node users can expect to find expertise and resources to reach diverse research fields and projects. Each site is established on R&D institutions with a large track record of international work in biomedical areas covering specialties such as cell biology, cancer, neurodegenerative diseases, nerve regeneration, brain diseases, microbiology, host-pathogen interaction, immune response, genetic disease, chronic diseases, drug discovery, biomaterials, systems biology, organism development, and marine biology. Moreover, users will benefit from highly qualified staff with skills and expertise in project planning, imaging and bioimage data analysis.\nAt the three Euro-Bioimaging PPBI Node imaging clusters (NIC at Porto and Braga; CIC at Coimbra, Aveiro and Covilhã; and SIC at Lisbon area and Faro) the EuBI users will find expertise in analysis of 2D/3D cell cultures, small model organisms and biomaterials from advanced light microscopy techniques and transmission electron microscopy.\n![PPBI_Image](upload/PPBI_1.png \"PPBI_Image\")\nAdditionally, the PPBI NODE Node also provides access to the following flagship imaging technologies: high-throughput microscopy (HTM), correlative light and electron microscopy (CLEM), super-resolution imaging, functional imaging, and mesoscopic imaging.\nHTM services have extensive infrastructure support in all stages of a screening project including access to compound libraries. EuBI users can profit also from a tight coupling between assay development and bioimage analysis.\n![PPBI_Image](upload/PPBI_2.png \"PPBI_Image\")\nEuro-BioImaging users looking for imaging e.g. cell division, centrioles, neuronal structures, bacteria or virus at nanoscale will find at PPBI the expertise and super-resolution microscopy systems (STED, PALM, dSTORM, and SIM-SR) to support their projects. This can be complemented at the SIC by CLEM analysis.\n![PPBI_Image](upload/PPBI_3.png \"PPBI_Image\")\nPPBI sites have established expertise in functional imaging (e. g. FLIM, FLIM-FRET, FCS, FCCS, FAIM, and FRAP [plus photoactivation or photoconversion] and optogenetics techniques) for applications requiring cutting-edge fluorescence microscopy techniques, including at the single-molecule level and in the development of quantitative modeling, such as analysis of cell membrane dynamics, RNA expression or development of new fluorescent probes.\nMesoscopic imaging of live or cleared samples of multiple biological models, like 3D organoids, fish (Danio) and mammalian embryos, can be observed by SPIM, OPT, SPIM-OPT and micro-CT, including multiple Zeiss Z.1 light-sheet systems, the ultra-microscope and home-built SPIM-OPT for cm-large samples.\n![PPBI_Image](upload/PPBI_4.png \"PPBI_Image\")\nBioimaging applied to neuroscience research is also an area of specialty. Coimbra holds a consolidated expertise in calcium imaging in primary neuronal cultures, organoids, and organotypic neuronal slices. Moreover, there is a dedicated multiphoton laboratory fully equipped for intravital imaging in mice which is especially suited to perform neurotransmitter uncaging experiments.\n![PPBI_Image](upload/PPBI_5.png \"PPBI_Image\")\n### Offered Technologies\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ | ✓ |\n| Two-photon microscopy (2P) | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ | ✓ |\n| Optical projection tomorgraphy (OPT) | ✓ | ✓ |\n| Raman Spectroscopy (RS) | ✓ | ✓ |\n|\n| Second/Third Harmonics Generation (SHG/THG) | ✓ | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Intravital Microscopy (IVM) | ✓ | ✓ |\n| Microdissection \\*\\* | ✓ | ✓ |\n| Imaging at Biosafety Level >1 | ✓ | ✓ |\n| Photomanipulation | ✓ | ✓ |\n| Anisotropy/Polarization Microscopy | ✓ | ✓ |\n| Expansion Microscopy \\* | ✓ | ✓ |\n| Tissue Clearing (TC)\\* | ✓ | ✓ |\n| Single molecule FRET (smFRET)\\* | ✓ | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ | ✓ |\n| Elemental analysis including EDS in TEM (STEM)\\* | ✓ | ✓ |\n| micro-CT | ✓ | ✓ |\n| micro-US | ✓ | ✓ |\n| Atomic Force Microscopy (AFM)\\* | ✓ | ✓ |\n### Additional services offered by the Node\n* Project planning\n* Methodological set up\n* Technical Assistance to run instruments\n* Wet lab space\n* Probes\n* Cell culture facilities – Biological Safety Level 1, 2 and 3\n* Animal facilities (mice, rat, zebra fish)\n* Other model organisms (Yeast, C. elegans, Drosophila, Bacteria, Fungi, Plants, Chick embryos, Spider mites, Anopheles)\n* Workstations\n* Data storage\n* Data analysis facilities\n* Meeting/training rooms\n### Instrument highlights\nAmong the instruments and techniques available at the PPBI Node, we highlight:\n* The coherent-hybrid STED technique\n* The inducible fluorescent speckle technique\n* A system for laser microsurgery, to ablate intra-cellular structures at the sub-micron level\n* A dual-mode mesoscope allows acquisition of correlative SPIM and OPT datasets\n* A multiphoton system, fully equipment for intravital imaging in mice, equipped with two pulsed infrared lasers\n* A custom-built confocal microscope with single-molecule detection for both FCS and single-molecule FRET\n* Transmission Electron Microscope with elemental analysis in biological samples by energy-dispersive X-ray spectroscopy (STEM-EDS)\n![PPBI_Image](upload/PPBI_6.png \"PPBI_Image\")\n### Contact details\n**Gaby Martins, PPBI manager**\n[gaby@igc.gulbenkian.pt](mailto:gaby@igc.gulbenkian.pt)\n**Node page:**\n", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "d3d66a1d", "f1f735b6", "e7adfd19", "17dd34eb", "dcb85d5e", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "f65a70b8", "b5333ef4", "b015d920", "3a4d793f", "f05d797c", "a2a0f4a8", "931ee18e", "af33ff84", "3f84bc36", "143e2504", "c60b4a73", "3965a906", "a9f0fcad", "b4a6f749", "2ce231cc", "4e5bcb9e" ], "country": { "id": "7a4f7490-b813-4d9d-8c9b-21220f5f3b70", "name": "Portugal", "iso_a2": "PT" } }, { "id": "706cb740", "name": "Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node", "original_id": "55cad600-4f25-4eac-aceb-a67609b8c79b", "description": "Dual-site, multimodal small animal imaging; unique genetic models, multiphoton.", "documentation": "## NETHERLANDS\n## Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node\n---\n**The Dutch Preclinical Imaging Center PRIME – Molecular Imaging Node is a dual-sited Node that consists of the Preclinical Imaging Centre (PRIME), Radboud University Nijmegen, and the Intravital Microscopy Facility (IMF), Hubrecht Institute, Utrecht. This Node is a centralized facility for multimodality imaging of small animals, such as mice and rats. PRIME is the only centre in the Netherlands where more than four imaging modalities for small animal imaging are housed under one roof in one facility. The intravital microscopy laboratory offers advanced genetic mouse models and has heavily invested in state-of-the-art imaging of small animals using multiphoton microscopy. PRIME functions as single-site facility for small animal imaging with state-of-the-art equipment and expertise for magnetic resonance imaging (MRI), positron emission tomography (PET/CT), single photon emission computed tomography (SPECT/CT), intravital multi-photon fluorescence imaging (MPFI) and high frequency ultrasound imaging (HFUS).**\n### Specialties and expertise of the Node\nPRIME is a state-of-the-art preclinical animal imaging centre. It is housed at the Central Animal Laboratory (CDL). PRIME is run by imaging experts from the departments of Radiology (Prof. Dr. Arend Heerschap), Nuclear Medicine (Dr. Sandra Heskamp), Cell Biology (Prof. Dr. Peter Friedl), Anatomy (Dr. Amanda Kiliaan), Cognitive Neuroscience (Prof. Dr. Richard van Wezel, Dr. Jeffrey Glennon) and the Medical Ultrasound Imaging Center (Prof. Dr. ir. Chris de Korte) and the Central Animal Laboratory (Prof. Dr. Otto Boerman) of the Radboud University Medical Centre in Nijmegen and the Intravital Microscopy Facility (IMF) of the Hubrecht Institute (Prof. Dr. Jacco van Rheenen).\nThese investigators collaborate with numerous research groups in Europe and the US. More than 30% of the experiments are done in collaboration with investigators from outside the node. PRIME investigators work with both academic partners as well as with partners from industry.\nSpecial features of the Dutch PRIME Node are:\n* A facility fully equipped for small animal imaging with eight imaging modalities (MRI, PET/CT, SPECT/CT and HFUS) under one roof.\n* A durable facility for small animal imaging with state of the art equipment and expertise.\n* A facility with multi-modal equipment and fully equipped behavioral rooms integrated in one center at one location to correlate e.g. motor skills and cognition with brain imaging.\n* A center that operates essentially as a SPF/DMII unit to allow experiments with transgenic animals and with adeno, retro and lenti-viruses.\n* A center with links to clinical/human imaging facilities.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| micro-MRI/MRS (>= 7T) | ✓ | ✓ |\n| micro-CT | ✓ | – |\n| micro-PET | ✓ | – |\n| micro-SPECT | ✓ | ✓ |\n| in vivo Optical Imaging | ✓ | – |\n| micro-PET/MRI | ✓ | ✓ |\n| micro-PET/CT | ✓ | ✓ |\n| micro-SPECT/CT | ✓ | ✓ |\n| MRI-PET | ✓ | ✓ |\n| PET | ✓ | ✓ |\n| PET/CT \\* | ✓ | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ | ✓ |\n| micro-CT - ex-vivo | ✓ | – |\n### Additional services offered by the Node\n* Instruments\n* Technical assistance to run instrument\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Training in infrastructure use\n* Probe preparation\n* Animal preparation\n* Animal facilities\n* Wet lab space\n* Server Space\n* Data processing and analysis\n* Training workstations\n* Training seminar room\n* Housing facilities\n* Clinical trial insurance contracting\n* Pharmacovigilance\n* Regulatory affairs management service\n### Instrument highlights\n* microMRI/MRS - Bruker 7T Clinscan and 11.7T Biospec\n* High intensity focused ultrasound (HIFU) insert for Bruker 7T Clinscan\n* microPET/CT - Siemens Inveon\n* microSPECT/CT - Milabs U-SPECT II\n* microUS - Vevo 2100, Visualsonics\n* Optical Imaging - IVIS Lumina\n* Four near-infrared and infrared multiphoton platforms for intravital microscopy (Lavision BioTec, Leica; upright or inverted); 700-1350 nm excitation range; up to 7 channels incl. FLI\n![](upload/Prime_image_pet.jpg)![](upload/Prime_photon_5.jpg)\n### Contact details\nWilma Janssen-Kessels: [wilma.janssen-kessels@radboudumc.nl](mailto:wilma.janssen-kessels@radboudumc.nl)", "offer_technology_ids": [ "9c64e406", "b4a6f749", "2ce231cc", "59a33aed", "c41fb0d1", "8fa56005", "3744dad8", "4a91416e", "c83c6c2b", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "2103118f", "name": "SiMBION Node", "original_id": "daa1cb21-2d2c-4d98-9ed8-cb531b42c65f", "description": "Slovenian consortium: 15 centers, bioimaging access, training, TNA support.", "documentation": "## SLOVENIA\n## SiMBION NODE\n---\n**The Slovenian national consortium SiMBION consists of 15 infrastructure centres and institutional departments. It is committed to provide part of its existing bioimaging capacities to external users, including access to imaging infrastructure, imaging methodology, sample preparation, advisory help in project planning, as well as training courses for Euro-BioImaging users. The consortium partners are traditionally providing part of their research infrastructure capacities to external national and international users within numerous national and international projects, individual collaboration and commercial contracts, including Transnational Access (TNA) programme of the EU.**\n### Offered Technologies:\n* Laser scanning confocal microscopy (LSCM/CLSM)\n* Total internal reflection fluorescence microscopy (TIRF)\n* Fluorescence Recovery after Photobleaching (FRAP)\n* TEM of chemical fixed samples (TEM)\n* TEM of cryo-immobilized samples (TEM cryo samples)\\*\n* Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM)\n* Immuno-gold EM on resin sections (resin-EM)\n* Scanning Electron Microscopy (SEM)\n* micro-MRI (Field >= 7 T)(HF)\n* micro-MRI (Field <7 T)(LF)\n* ex-vivo micro-CT\n* Mass spectrometry-based imaging - bio (MSI - bio)\\*\n* Mass spectrometry-based imaging - med (MSI - med)\\*\n![](upload/Slovenia_node.png)\nCollage of light and electron microscopic images. ( S Hudoklin, A Erman, R Romih, P Veranic Institute of Cell Biology)\n![](upload/slovenia.png)\n![](upload/slovenia2.png)\nSodium (Na) distribution in flowers of Solanum lycopersicum by LA-ICP-MS (S. Bigot, P. Pongrac, M. Šala, J.T. van Elteren, J.-P. Martínez, S. Lutts and M. Quinet, Plants 2022, 11, 672).\n### Specialties and expertise of the Node\nThe consortium SiMBION was formed by merging the majority of the existing national research infrastructure resources in the field of bioimaging. The existing infrastructure, developed in the last decades within the hosting institutions by different institutional initiatives and funds, is distributed among several constitutive partners. In these circumstances, a multi-sited Node provides a framework that could at present efficiently merge this distributed research infrastructure and incorporate eventual dedicated Euro-Bioimaging infrastructure investments in the future.\nThe existing collaborative workflows between the members of the SiMBION consortium, efficiently exploit the existing state-of-the art bioimaging techniques and the available supporting laboratories and bioimaging techniques available in a very small geographical area, providing excellent conditions for the execution of complex research projects and multimodal imaging procedures. This proposed structure and the workflows can only be provided in the form of **multi-sited node**.\nThe existing collaborative workflows between the members of the SiMBION consortium, efficiently exploit the existing state-of-the art bioimaging techniques and the available supporting laboratories and bioimaging techniques available in a very small geographical area, providing excellent conditions for the execution of complex research projects and **multimodal** imaging procedures. This proposed structure and the workflows can only be provided in the form of **multi-sited node.**\n### Additional Services offered by the Node\n* Instruments\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Technical assistance to run instrument\n* Probe preparation\n* Cell and Tissue Culture facilities\n* Animal facilities\n* Wet lab space\n* Data processing and analysis\n* Training seminar rooms\n* Housing facilities\n* Regulatory affairs management service\n* Biobanking, biological material storage and processing\n* Training in infrastructure use\n* Server space\n* Training workstations\n* Biological material storage and processing\n* Training in techniques for optical clearing of biological samples\n* Sample preparation support, including latest instrumentation for cryo-fixation using High Pressure Freezing\n### Instrument highlights\nMicroanalytical centre of Jožef Stefan Institute is providing Transnational Access to ion-beam based state-of-the-art techniques for tissue chemical (elemental and molecular) imaging within EU H2020 project No. 824096 RADIATE (2019-2022). Up to 20% of total infrastructure capacity of 4000 beam hours unit of TNA access, beam hour) annually are allowed for TNA access within this EU project. From 300 to 600 beam hours (annually are provided to users of ion beams, of which 70 % are applied for chemical imaging of biological tissue. Proposal submission and evaluation are centralized (https://www.ionbeamcenters.eu/radiate/radiate-transnational-access/application-for-transnational-access/).\nAt the National Institute of Chemistry, a state-of-the-art facility features a new Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-(TOF)MS), providing high-resolution elemental imaging of biomaterials for most elements of the periodic table, and localization, sizing, and counting of metal nanoparticles in tissues.\nDue to a linear dynamic range of up to 10 orders of magnitude, and detection limits of 10’s of parts per billion, the technique can address scientific problems in many disciplines. The technique has been applied in the field of metal-labeled antibodies designed to target specific antigens, metalloproteins, drug penetration in healthy and tumor tissues, elemental and nanoparticle uptake by plants, animals, and single cells.\nThe Node also recently acquired a new EM ICE High Pressure Freezer, which allows for a superior cryo-fixation of the specimen enabling better quality results to be obtained. The system enables fast and reproducible vitrification of tissues, cultured cells and suspensions, which can be subsequently prepared for a wide range of EM applications: cryo-EM of vitreous sections (CEMOVIS), volume EM studies by freeze substitution (3D-EM tomography, FIB-SEM, SFB-SEM), ultrastructural immunohistochemistry, freeze fracturing and corelative light and electron microscopy (CLEM).\n### Contact details\n**Node contact person:**\nPrimož Pelicon\n[primoz.pelicon@ijs.si](mailto:primoz.pelicon@ijs.si)\nEsther Punzon Quijorna\n[esther.punzon-quijorna@ijs.si](mailto:esther.punzon-quijorna@ijs.si)\nFind out more details about available technologies and services on the Node website", "offer_technology_ids": [ "019f553c", "8399c5a7", "018d2770", "af33ff84", "4ae7143c", "e32e05f1", "3f84bc36", "c60b4a73", "4b561f4f", "4a91416e", "d74face8", "c83c6c2b", "9c814a85", "4e5bcb9e", "ae6d3c51", "4e2f1176", "0a49ed44", "c1a46958" ], "country": { "id": "d1479dec-3ca5-49f1-b6ac-fc26576f33e5", "name": "Slovenia", "iso_a2": "SI" } }, { "id": "151b4761", "name": "Sofia BioImaging Node - Advanced Light Microscopy Node Sofia Bulgaria​", "original_id": "e33b5cb1-63ac-4872-a8df-fa5572f6b91f", "description": "Multimodal, high-res live-cell imaging, laser disruption, open access.", "documentation": "## BULGARIA\n## Sofia BioImaging Node - Advanced Light Microscopy Node Sofia Bulgaria\n---\n**The Sofia BioImaging Node is a multimodal single-sited Node, located at the Institute of Molecular Biology, Bulgarian Academy of Science, in Sofia. **The Bulgarian Center for Advanced Microscopy at IMB-BAS is included in** [the National Roadmap for Scientific Infrastructure](https://mon.bg/bg/53) **and as part of Euro-BioImaging provides open user access to a range of state-of-the-art technologies in biological and biomedical imaging for life scientists. With a specific focus on fast and high-resolution live-cell imaging and laser-based disruptions of cells and their components, the Node provides outstanding expertise in the application of Spinning Disk microscope systems and the use of UV laser micro-irradiation and FRAP to study protein dynamics and DNA repair. For more information see** ****.**\n### Specialties and expertise of the Node\nThe research focus of the Node environment is on the molecular and cellular biology of DNA replication, repair, transcription, and chromatin dynamics. This research focus is complemented by applied research topics, such as biomedical pharmacology and drug design.\nIn the area of DNA repair, the Node has developed outstanding applications, combining live-cell recordings using spinning-disk microscopes with laser ablation to induce DNA damage or ablate other cell components. Combining this technology specialty with a large library of GFP-tagged proteins which are involved in DNA repair, and are expressed under their natural regulatory sequences, allows the recording of ultra-fast protein dynamics and interactions. The Sofia BioImaging Node offers unique expertise in screening substances for their impact on DNA repair, a topic of fundamental interest for cancer research.\nThe Node also has expertise in the development of dedicated image analysis and data visualisation software, with the [CellTool](http://dnarepair.bas.bg/software/CellTool/) software and the [DNArepairK](http://dnarepair.bas.bg/index.php/time-to-choose/) Database.\n### Offered Technologies:\n*[ISIDORe](https://www.eurobioimaging.eu/content/isidore) is a Horizon Europe funded project that brings together 154 partners from 32 countries around the world, and is designed to effectively support research on infectious diseases and increase preparedness for pandemic.*\n| Technologies | Euro-BioImaging | ISIDORe |\n| --- | --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ | ✓ |\n| Image Scanning microscopy (ISM) | ✓ | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ | ✓ |\n| Anisotropy/Polarization Microscopy (PM) | ✓ | ✓ |\n### Additional services offered by the Node\n* Instruments\n* Technical assistance to run instrument\n* Methodological setup (e.g. design of study protocol and standard operation procedures)\n* Probe preparation\n* Cell culture facilities\n* Wet lab space\n* Server Space\n* Data processing and analysis\n* Training workstations\n* Training seminar room\n* Biological material storage and processing\n* Data processing and analysis\n* Instrument highlights\n![](upload/Sofia_node_1.jpg)\n![](upload/Sofia_node_2.jpg)\nExample of a cell targeted with laser ablation (bright spot) and the subsequent analysis of protein dynamics in CellTool.\n### Instrument highlights\nAndor Revolution XD spinning disc confocal microscope system equipped with Borealis and with Nikon TiE Inverted Microscope stand. Image acquisition by two iXon3 897 EMCCD cameras. The microscope system is equipped with a FRAPPA unit for Fluorescence recovery after photobleaching (FRAP) and with Micropoint UV laser micro-irradiation device.\nAndor Dragonfly 500 spinning disk confocal microscope system for high-resolution live cell imaging, equipped with Nikon Ti2-E Inverted Microscope stand. Image acquisition by iXon 888 EMCCD camera and Zyla sCMOS camera. The microscope system is equipped with Mosaic III Duet photostimulation system and Micropoint  laser micro-irradiation device. Capable of SRRF-Stream, dSTORM, widefield, and TIRF imaging.\nZeiss Axiovert 200M motorized epifluorescence microscope with Apotome\nZeiss Axioimager A1\nXenoWork micromanipulation and microinjection system.\nAdvanced data analysis pipeline for live cell imaging data with in house built CellTool software\n![](upload/Sofia_node_3.jpg)\nThe Sofia BioImaging Node team\n### Contact details\n**Stoyno Stoynov**\nNode Contact\n[stoynov@bio21.bas.bg](mailto:stoynov@bio21.bas.bg)\n", "offer_technology_ids": [ "019f553c", "3cf0830c", "8399c5a7", "31d30c68", "f1f735b6", "e9910d1c", "018d2770", "0de0802c", "5a688552", "b015d920", "4e5bcb9e" ], "country": { "id": "8438383c-a110-42aa-93d1-dd43ce2fdc12", "name": "Bulgaria", "iso_a2": "BG" } }, { "id": "f1099f78", "name": "Swedish National Microscopy Infrastructure (NMI)", "original_id": "24b7ef61-ea66-42dc-b33c-7422c570ef54", "description": "Swedish multi-site: super-resolution, intravital, live imaging, 500+ users.", "documentation": "## SWEDEN\n## Swedish National Microscopy Infrastructure (NMI)\n---\n**The National Microscopy Infrastructure (NMI) is a distributed infrastructure of five specialized, complementary, and interlinked sites located across Sweden: Stockholm, Uppsala, Göteborg, Umeå and Lund. The mission of NMI is to provide access to innovative technologies and competence in microscopy and image analysis to all scientists that have a need for advanced imaging in fundamental and translational biomedical research projects. Annually, the NMI serves more than 500 national and international users. The Swedish Euro-BioImaging Node has strong expertise in super-resolution microscopy, correlative and multimodal microscopy, intravital microscopy, live sample microscopy and medical imaging as well as image processing and analysis. The infrastructure is coordinated by KTH (Royal Institute of Technology) which provides the single-entry point from which users are directed to the relevant imaging technologies.**\n### Specialties and expertise of the Node\nThe NMI has been designed as a multi-sited infrastructure with seven specialized imaging facilities distributed in Sweden with complementary expertise and technologies:\nAdvanced light microscopy (ALM) at the Royal Institute of Technology (KTH): Super-resolution, FCS/FCCS, lattice light-sheet and CODEX (CoDetection by indEXing) technology - high parametric imaging of cells in a tissue context.\nCentre for Cellular Imaging (CCI), at University of Gothenburg: Correlated multimodal imaging and automated high content screening microscopy for live cell imaging\nBiochemical Imaging Centre Umeå (BICU) and Umeå Core facility for Electron Microscopy (UCEM), at the University of Umeå: Correlative microscopy and electron tomography.\nIntravital Microscopy at Stockholm University (IVMSU): Intravital imaging with an integrated animal house\nBioImage Informatics Facility (BIIF) at Uppsala University: Image and data analysis\nLive Cell Imaging core facility at Karolinska Institutet (KI): 3d lattice Structured Illumination, Airy-beam light sheet, live sample microscopy in different modalities.\nLund University Bioimaging Center (LBIC): Medical imaging on all scales\nImaging with several types of microscopy, pre-clinical imaging with PET, MR and CT, and human ultra-high field MR. Image visualization and analysis.\nThe sites are supported by an administrative team at KTH that is responsible for project management, the project web portal, the website, software license servers and data handling. They also coordinate the activity of NMI to support users in finding the best technology for their research questions and help combine techniques from different sites.\nThe application experts in NMI have long experience in supporting projects in many different scientific areas, including: Neurobiology, Structural Biology, Mucosal biology and Immunology, Cardiovascular and Metabolic diseases, Cancer biology, Oral biochemistry, Virology, Cell Biology, Physiology, Endocrinology, Organotypic cultures, Dermatology and Molecular Skin Research, Pathology, Drug delivery, Developmental Biology and Regenerative medicine, Plant Biology, Botany, and Microbiology.\nAll of these research applications cover a wide spectrum of model organisms and in vitro models. There is also an increased interest from other scientific fields to utilize advanced microscopic imaging and analysis. Projects from researchers in e.g., nano- and material science, wood and fibre technology, chemistry, marine research, fuel research, food research, archaeology, palaeontology and cultural heritage have been supported.\nBioimage informatics and image analysis are another area of expertise of the Swedish Euro-BioImaging Node. The BIIF at the Uppsala site of the NMI is responsible for developing new computational technologies and provides access to expertise and state-of-the art software for processing and quantitative analysis of all kinds of microscopy image data for applications in the life sciences.\n### Technologies\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Structured illumination microscopy (SIM)\\* | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Objective-couple planar illumination (OCPI) | ✓ |\n| Lattice Lightsheet (LL) \\*\\* | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Stimulated emission depletion microscopy (STED) | ✓ |\n| Reversible optical fluorescence transitions (RESOLFT) | ✓ |\n| Second/Third Harmonics Generation (SHG/THG) | ✓ |\n| High throughput microscopy/high content screening (HTM/HCS) | ✓ |\n| Minimal Photon Fluxes Microscopy (MINFLUX)\\* | ✓ |\n| Polarization microscopy (PM) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n| Intravital Microscopy (IVM) | ✓ |\n| Voltage/pH/Ion Imaging \\*\\* | ✓ |\n| Microdissection \\*\\* | ✓ |\n| Imaging at Biosafety Level >1 | ✓ |\n| Photomanipulation | ✓ |\n| Anisotropy/Polarization Microscopy | ✓ |\n| Phosphorescence Lifetime imaging (PLIM) \\* | ✓ |\n| Feedback microscopy \\* | ✓ |\n| Expansion Microscopy \\* | ✓ |\n| Feedback microscopy \\* | ✓ |\n| High-speed Imaging \\* | ✓ |\n| Spatial transcriptomics (ST) | ✓ |\n| Photomanipulation | ✓ |\n| Tissue Clearing (TC)\\* | ✓ |\n| TEM of chemical fixed samples (TEM) | ✓ |\n| TEM of cryo-immobilized samples (TEM cryo samples)\\* | ✓ |\n| serial section TEM | ✓ |\n| EM tomography (ET) | ✓ |\n| FIB-SEM | ✓ |\n| Array tomography | ✓ |\n| Immuno-gold EM on thawed cryo-sections (Tokuyasu-EM) | ✓ |\n| Immuno-gold EM on resin sections (resin-EM) | ✓ |\n| Pre-embedding immunolabelling (pre-embed IL) | ✓ |\n| Genetic encoded EM probes | ✓ |\n| Pre-embed CLEM | ✓ |\n| Cryo Electron Tomography (Cryo-ET)\\* | ✓ |\n| Cryo Transmission Electron Microscopy (Cryo-TEM)\\* | ✓ |\n| Cryo Focussed Ion beam (Cryo-FIB)\\* | ✓ |\n| Scanning Electron Microscopy (SEM) | ✓ |\n| Elemental analysis including EDS in TEM (STEM)\\* | ✓ |\n| CAT | ✓ |\n| live-cell CLEM | ✓ |\n|\n| micro-MRI/MRS (>= 7T) | ✓ |\n|\n| micro-CT | ✓ |\n| micro-PET/CT | ✓ |\n| micro-SPECT/CT | ✓ |\n| MRI/MRS (>= 7T) | ✓ |\n| MRI/MRS (<7T) | ✓ |\n| micro-MRI/MRS (>= 7T) - ex-vivo | ✓ |\n| micro-CT - ex-vivo | ✓ |\n| Atomic Force Microscopy (AFM)\\* | ✓ |\n| Mass spectrometry-based imaging\\* (MSI) | ✓ |\n| Image Analysis-bio \\* | ✓ |\n| Image Analysis-med \\* | ✓ |\n### Additional services offered by the Node\nBioImage Informatics\n* Guidance on image analysis assay development, including image processing algorithm development and software engineering to address challenging project goals.\nAll NMI nodes have supporting routines and infrastructure for tissue, cell and molecular biology laboratory work including:\n* Wet lab\n* Cell culture facilities\n* Probes\n* Animal facilities\n* Other model organisms\n* Biosafety level BSL-2\n* Workstations\n* High-performance computers\nAll nodes also offer:\n* Methodological setup (e.g. sample preparation, design of study protocols and standard operation procedures\n* Technical assistance to run instruments\nThe Live Cell Imaging core facility offers pedagogy-based Train-the-trainer training as well as an Imaging-by-staff service.\n### Instrument highlights\nSpecial feature of the Intravital microscopy facility at the Stockholm University (IVMSU): This facility operates as an “open access” facility, by combining state-of-the-art imaging and animal facility together, to enable users from academy and industry to visualize biological processes at the molecular and cellular levels within intact living rodent models. Being “open access” makes this facility unique both at the national and international levels. To enable this unique feature, IVMSU is localized within its own biological containment barrier integrated into the state-of-the-art animal facility (Experimental Core Facility) at Stockholm University.\nTo guarantee highest-quality service and access to cutting-edge instrumentation the NMI nodes are constantly implementing and development new technology and methods:\n* Lattice light-sheet microscopy for single cell fast volumetric imaging of biological processes\n* CODEX (CoDetection by indEXing) technology - high parametric imaging of cells in a tissue context\n* Correlated multimodal imaging: laser scanning confocal microscopy and matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS)\n* Cryo-CLEM integrated in the Focused Ion Beam scanning electron microscopy\n* Developing new techniques for high-throughput/high content imaging and analysis of zebrafish embryos, an important model organism in large-scale studies of e.g. cardiovascular disease. Building up a set of state-of-the art learning-based analysis and visualization tools for whole-slide tissue images/digital pathology.\n* Airy-beam light sheet for subcellular resolution images (1um isotropic) of samples up from 500um to several cm.\n* 3D lattice Structured Illumination for SIM imaging in thick samples.\n### Contact details\n[contact@nmisweden.se](mailto:contact@nmisweden.se)\n", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "a7c09ccd", "d2871017", "d3d66a1d", "f1f735b6", "a42333c3", "fc6e9ebb", "e7adfd19", "4ba07d0c", "d52b6d15", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "a673b6b7", "b5ef918c", "d6cec7b4", "f65a70b8", "b5333ef4", "b015d920", "47c84335", "1f3001ca", "3a4d793f", "f05d797c", "af33ff84", "4ae7143c", "df1896a3", "d169e03b", "eebba7a7", "63775639", "e32e05f1", "3f84bc36", "143e2504", "04562797", "0abb2c96", "a7128dd1", "cb003121", "4b452472", "c60b4a73", "3965a906", "8597af30", "13e1b5d4", "90e98166", "c3302077", "a9f0fcad", "4b561f4f", "9c64e406", "b4a6f749", "c41fb0d1", "8fa56005", "4a91416e", "c83c6c2b", "22875d0d", "a6cee2e2", "6324bef6", "4707da44", "4e5bcb9e", "02c9e1e3" ], "country": { "id": "239b5262-49ee-4a0b-aee6-afe45eb56dda", "name": "Sweden", "iso_a2": "SE" } }, { "id": "09122290", "name": "The UK Node", "original_id": "1ec3ed9f-d654-4197-9b22-f47f84d3535b", "description": "UK multi-site: super-resolution, correlative, high-content imaging, open-access.", "documentation": "## UNITED KINGDOM\n## The UK Node\n---\n**The UK Node offers open-access to a wide range of advanced biological imaging techniques including correlative, multi-modal, high-content and super-resolution. It is a multi-sited national infrastructure hosted by the following seven leading institutions spread across the UK: Edinburgh Super-Resolution Imaging Consortium (ESRIC), the Francis Crick Institute, King’s College London, Liverpool University, Octopus at Harwell, Oxford Brookes University and York University. They all offer state-of-the-art imaging equipment, expertise, training and image data services. The technologies can be applied to a wide range of fundamental and translational research projects at molecular to cellular resolutions, in single cells to 3D, in vitro models and whole organisms.**\nThe Euro-BioImaging [UK Node Manager](mailto:georgina@rms.org.uk) acts as the single point of contact who can direct potential users to the relevant imaging technology and site to undertake their experiments. We welcome applications from all biological and biomedical research disciplines. Projects will be prioritised based on technical feasibility and scientific merits. Support will be provided for the entire experimental pipeline including (where appropriate) initial user consultation, experimental planning, full hands-on training, assistance with sample preparation, gathering highest quality imaging data and data analysis.\n### Specialities and Expertise of the Node\n**[ESRIC:](https://www.esric.org/)** SIM, dSTORM, PALM, spt-PALM, SRRF, STED, FLIM-FRET,\nTIRF, Spinning Disk Confocal\nESRIC comprises open access advanced imaging facilities specialising in super-resolution techniques. As well as cutting-edge equipment, we bring together a broad spectrum of knowledge and expertise in extending the boundaries of biological imaging beyond the diffraction limit. Current technologies include dSTORM/PALM/DNA-PAINT on Nikon N-STORM and Olympus Cell Excellence systems, gSTED, Tau STED and FLIM-FRET on a Leica SP8 with FALCON FLIM, Structured Illumination Microscopy on a Nikon N-SIM /SoRa hybrid system, and SRRF on an Andor Dragonfly spinning disk. Our equipment enables us to image objects in 3D at super-resolution in up to 4 colours, with resolutions ranging from 120nm down to 10nm.\n**[Francis Crick Institute:](https://www.crick.ac.uk/research/platforms-and-facilities/light-microscopy)** Lightsheet microscopy (from live organoids and embryos to\nfixed whole mouse organs), High Resolution                                                     Episcopic\nMicroscopy (HREM), Optical Projection Tomography (OPT)\nWe offer two methods for imaging thick samples, Lightsheet microscopy and High Resolution Episcopic Microscopy (HREM), with support for the entire experimental workflow, including sample prep, clearing, image analysis, and data management.\nOur Lightsheet systems cover two distinct application spaces: Larger fixed samples (10 - 20 mm) can be imaged with the LaVision Ultramicroscope whereas smaller living or fixed samples (50 - 500 µm) can be imaged with either the Luxendo MuVi or Viventis LS1. The Ultramicroscope can be used in combination with antibody labelling and tissue clearing to image many sample types, including whole mouse organs, later-stage embryos, tumors, and tissue sections. In contrast the MuVi and LS1 are suitable for live imaging of small samples such as spheroids, organoids, and early-stage embryos. The LS1 offers higher throughput whereas the MuVi can image thicker samples, and has been adapted with a pulsed IR laser for photo-stimulation.\nHREM is a simple block-face approach for imaging tissue and organ morphology that does not require endogenous tissue fluorescence or any form of antibody labelling. It was originally developed to characterise embryonic lethal mouse mutations and has been used to study cardiovascular, skeletal, and neurological defects in a wide variety of mouse models (eg: Vanyai et al, Development 2020.)\n[*King’s College London:*](https://www.kcl.ac.uk/research/facilities/euro-bioimaging-uk-node) STORM ,SIM, Lightsheet, FLIM, CLEM,Volume EM,\nLA-ICP-MS, Raman\nAt the atomic and nano scales, we support volume EM and CLEM workflows, cryo SEM and cryo TEM and are experts in freeze fracture. We provide cryo-focused ion beam SEM and are developing a complete pipeline from live cell to cryo ET leading to sub-tomographic averaging of proteins in situ.\nMoving down the resolution scale, we provide access and support in, super-resolution and low-toxicity live cell imaging (N-STORM 5.0 and SoRa, plus single and multi-photon lightsheet capability), as well as high-content and throughput spinning disc (Opera Phenix).\nExtending beyond optical imaging, we deliver analytical multi-modal imaging in the form of 2D or 3D spatial quantitative elemental and molecular imaging of both endogenous elements and metal tagged antibodies in cells and tissues using a multiplexing methodology whilst identifying associated lipids and biomolecules in a label free approach. Routine LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry) has been integrated with DESI (Desorption electrospray ionisation)-MS and Raman Spectroscopy as a single unique correlative workflow. Together with integration of IR, this workflow will enable high resolution spatial mapping of lipid, nucleic acids and protein phosphorylation.\n[*Liverpool:*](https://cci.liv.ac.uk/index.html) Automated Live Cell Imaging, STORM, PALM, Bio AFM-TIRF, SIM2, Lightsheet, Cytometry, volume EM, TEM, MicroCT,                                Photoacoustic\nWe provide an integrated ensemble of imaging modalities in one place for imaging across scales from single molecule to cells and model organisms. Example projects include cell biology, surface science, biochemistry, and microbiology. Of particular note is our unique Bio AFM-TIRF imaging system for atomic force microscopy combined with dual fluorescence total internal reflection. We support the entire experimental workflow for each technique with dedicated staff, and we use an OMERO server for data management.\n[*Octopus:*](https://www.clf.stfc.ac.uk/Pages/Octopus-new.aspx) MINFLUX, CLEM with superresolution and cryoFIB-SEM,\nSIM, STORM/PALM, STED, Lightsheet, Multiphoton,\nFIB-SEM,                             FLIM/PLIM, Optical Trapping, TIRF, Raman, Single\nMolecule Tracking\nWe offer multiple microscopy techniques on a suite of commercial and custom-built systems, including MINFLUX, light sheet, single molecule localisation microscopy (PALM/STORM, including cryo-STORM), STED, single molecule methods including tracking and Fluorophore Localisation Imaging with Photobleaching (5 nm precision), confocal (including two photon and FRET/FLIM), optical trapping, and cryo focused ion beam SEM.\nThe microscopes are co-located with extensive preparation facilities including laboratories for biochemistry, cell biology, and chemistry. Facility users have access to a dedicated support team including microscopists, cell and molecular biologists, chemists, and data analysis experts. Users are provided with assistance at all stages of the experiment, including sample preparation and labelling, collection of data, and data analysis and interpretation. Custom data analysis packages are available and can be tailored to the requirements of a particular experiment. Accommodation and catering facilities are available on campus.\n[Oxford Brookes:](https://www.brookes.ac.uk/research/units/hls/centres/centre-for-bioimaging) SBF-SEM, SEM (tomography), CLEM, Cellular Electron\nTomography, High Pressure Freezing\nWe focus on providing volumeEM and CLEM workflows, including dual axis serial section cellular electron tomography and serial block face-scanning electron microscopy (SBF-SEM). We can work with fixed or high pressure frozen samples and have extensive expertise in eukaryotic parasite work and insect vectors. The centre is equipped with CATII culturing facilities within the Centre, as well as a SAPO licence to support these projects.\n[*York:*](https://www.york.ac.uk/biology/technology-facility/imaging-cytometry/) SIM, Multiphoton, Spatial Transcriptomics (GeoMX), Phase\nImaging /Holography, Confocal, Slide Scanner, cryoTEM,\ncryoSEM\nCurrent technologies include PALM/STORM/SIM2 via the Zeiss ELYRA 7, Spatial-omics via Nanostring GeoMX-DSP and 10X Visium, Label-free imaging via PhaseFocus LiveCyte and Tomocube and multiphoton imaging via Zeiss LSM980 AiryScan2 along with the more routine confocal, slide scanning and scanning and electron microscopy. The team have a wide breadth of biological expertise spanning plant sciences through to biomedicine, and are familiar with most sample types and sample preparation methods.\n### Additional services offered by the Node\n* Project planning and management\n* Wet lab\n* Cell culture facilities\n* Methodological setup\n* Facility induction\n* Technical assistance to prepare experiments and run instruments\n* Workstations\n* Data storage\n* Image acquisition\n* Image processing and analysis\n**Probes**\nAll sites within the EuBI UK Node operate within leading edge academic institutions and as such, many different types of probes, including plasmids, antibodies and chemical reagents are available within individual researcher labs. Additionally, a number of facilities maintain their own in-house reagents, including pre-labelled antibodies for super-resolution (STORM) and spatial transcriptomics.\n**Other model organisms**\nAll sites within the EuBI UK Node operate within leading edge academic institutions that host labs working with a broad range of different model organisms, including zebrafish, Drosophila and c.elegans. Facilities to support users working with such organisms would therefore be possible, subject to discussions and agreements with the appropriate academics.\n**High biological safety level**\nBSL2 facilities are available within a number of the laboratories at the host institutions for the EuBI UK Node facilities and can be made available to users following consultation with the site leads. Of note, Oxford Brookes holds a SAPO license for culturing Trypanosoma brucei within the imaging facility itself.\n### Instrument Highlights\n[***ESRIC:***](https://www.esric.org/)dSTORM/PALM/DNA-PAINT on Nikon N-STORM and Olympus Cell Excellence systems, gSTED, Tau STED and FLIM-FRET on a Leica SP8 with FALCON FLIM, SIM on a Nikon N-SIM /SoRa hybrid system, and SRRF on an Andor Dragonfly spinning disk. Our equipment enables us to image objects in 3D at super-resolution in up to 4 colours, with resolutions ranging from 120nm down to 10nm.\n[***Francis Crick Institute:***](https://www.crick.ac.uk/research/platforms-and-facilities/light-microscopy)Our Lightsheet systems cover two distinct application spaces: Larger fixed samples (10 - 20 mm) can be imaged with the LaVision Ultramicroscope whereas smaller living or fixed samples (50 - 500 µm) can be imaged with either the Luxendo MuVi or Viventis LS1. The Ultramicroscope can be used in combination with antibody labelling and tissue clearing to image many sample types, including whole mouse organs, later-stage embryos, tumors, and tissue sections. In contrast the MuVi and LS1 are suitable for live imaging of small samples such as spheroids, organoids, and early-stage embryos. The LS1 offers higher throughput whereas the MuVi can image thicker samples, and has been adapted with a pulsed IR laser for photo-stimulation.\nHREM is a simple block-face approach for imaging tissue and organ morphology that does not require endogenous tissue fluorescence or any form of antibody labelling. It was originally developed to characterise embryonic lethal mouse mutations and has been used to study cardiovascular, skeletal, and neurological defects in a wide variety of mouse models (eg: Vanyai et al, Development 2020.)\n[***King’s College London:***](https://www.kcl.ac.uk/research/facilities/euro-bioimaging-uk-node) At the atomic and nano scales, we support volume EM and CLEM workflows, cryo SEM and cryo TEM and are experts in freeze fracture. We provide cryo-focused ion beam SEM and are developing a complete pipeline from live cell to cryo ET leading to sub-tomographic averaging of proteins in situ.\nMoving down the resolution scale, we provide access and support in, super-resolution and low-toxicity live cell imaging (N-STORM 5.0 and SoRa, plus single and multi-photon lightsheet capability), as well as high-content and throughput spinning disc (Opera Phenix).\nExtending beyond optical imaging, we deliver analytical multi-modal imaging in the form of 2D or 3D spatial quantitative elemental and molecular imaging of both endogenous elements and metal tagged antibodies in cells and tissues using a multiplexing methodology whilst identifying associated lipids and biomolecules in a label free approach. Routine LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry) has been integrated with DESI (Desorption electrospray ionisation)-MS and Raman Spectroscopy as a single unique correlative workflow. Together with integration of IR, this workflow will enable high resolution spatial mapping of lipid, nucleic acids and protein phosphorylation.\n[***Liverpool:***](https://cci.liv.ac.uk/index.html)We provide an integrated ensemble of imaging modalities in one place for imaging across scales from single molecule to cells and model organisms. Example projects include cell biology, surface science, biochemistry, and microbiology. Of particular note is our unique Bio AFM-TIRF imaging system for atomic force microscopy combined with dual fluorescence total internal reflection. We support the entire experimental workflow for each technique with dedicated staff, and we use an OMERO server for data management.\n[***Octopus:***](https://www.clf.stfc.ac.uk/Pages/Octopus-new.aspx) We offer multiple microscopy techniques on a suite of commercial and custom-built systems, including MINFLUX, light sheet, single molecule localisation microscopy (PALM/STORM, including cryo-STORM), STED, single molecule methods including tracking and Fluorophore Localisation Imaging with Photobleaching (5 nm precision), confocal (including two photon and FRET/FLIM), optical trapping, and cryo focused ion beam SEM.\nThe microscopes are co-located with extensive preparation facilities including laboratories for biochemistry, cell biology, and chemistry. Facility users have access to a dedicated support team including microscopists, cell and molecular biologists, chemists, and data analysis experts. Users are provided with assistance at all stages of the experiment, including sample preparation and labelling, collection of data, and data analysis and interpretation. Custom data analysis packages are available and can be tailored to the requirements of a particular experiment. Accommodation and catering facilities are available on campus.\n[***Oxford Brookes****:*](https://www.brookes.ac.uk/research/units/hls/centres/centre-for-bioimaging) We focus on providing volumeEM and CLEM workflows, including dual axis serial section cellular electron tomography and serial block face-scanning electron microscopy (SBF-SEM). We can work with fixed or high pressure frozen samples and have extensive expertise in eukaryotic parasite work and insect vectors. The centre is equipped with CATII culturing facilities within the Centre, as well as a SAPO licence to support these projects.\n[***York:***](https://www.york.ac.uk/biology/technology-facility/imaging-cytometry/)\nCurrent technologies include PALM/STORM/SIM2 via the Zeiss ELYRA 7, Spatial-omics via Nanostring GeoMX-DSP and 10X Visium, Label-free imaging via PhaseFocus LiveCyte and Tomocube and multiphoton imaging via Zeiss LSM980 AiryScan2 along with the more routine confocal, slide scanning and scanning and electron microscopy. The team have a wide breadth of biological expertise spanning plant sciences through to biomedicine, and are familiar with most sample types and sample preparation methods.\n![](upload/ukyork.png)\n![](upload/ukyork1.png)\n*Left: Cyanobacteria imaged on the Zeiss Elyra7, Luke Mackinder Group. Right: Algae imaged on the Tomocube, Luke Mackinder Group*\n### Contact details\n**Georgina Fletcher**\nEuBI UK Node Manager\n[georgina@rms.org.uk](mailto:georgina@rms.org.uk)", "offer_technology_ids": [ "019f553c", "3cf0830c", "ff8ab803", "8399c5a7", "2fa1c4a2", "31d30c68", "d2871017", "d3d66a1d", "f1f735b6", "fc6e9ebb", "e7adfd19", "17dd34eb", "f4eef350", "83b4baea", "dcb85d5e", "f6b01df1", "745fa0d0", "4ba07d0c", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "f65a70b8", "b5333ef4", "47c84335", "3a4d793f", "f05d797c", "931ee18e", "af33ff84", "4ae7143c", "de231b3c", "df1896a3", "d169e03b", "c9ddc22b", "eebba7a7", "995a6055", "63775639", "e32e05f1", "3f84bc36", "143e2504", "0dee2953", "a7128dd1", "cb003121", "904149e2", "4b452472", "c60b4a73", "90e98166", "593e3440", "73094724", "c3302077", "a9f0fcad", "4b561f4f", "4e5bcb9e", "f45daf6b", "7add3aac", "02c9e1e3" ], "country": { "id": "2010e3be-2193-406c-9a37-a5c296102a49", "name": "United Kingdom", "iso_a2": "GB" } }, { "id": "c4b25263", "name": "The Van Leeuwenhoek Center for Advanced Microscopy (LCAM) - Functional Imaging Flagship Node Amsterdam", "original_id": "007b7281-7600-4fb7-8d52-2daa95fc8281", "description": "Advanced live cell imaging, FRET, FCCS, FLIM, custom fluorophores.", "documentation": "## NETHERLANDS\n## The Van Leeuwenhoek Center for Advanced Microscopy (LCAM) - Functional Imaging Flagship Node Amsterdam\n---\n**The Dutch LCAM – Functional Imaging flagship Node in Amsterdam in the Netherlands focuses on advanced life cell- and functional imaging and on technically challenging high-end experiments. This Node develops equipment, software and molecular constructs (fluorophores, small-molecule dyes and FRET sensors) to enable novel types of experiments. LCAM presents the single largest concentration of microscopy experts in the Dutch biomedical field with world-class specialists in e.g. FRET, FCCS, FLIM and instrumentation.**\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Deconvolution widefield microscopy (DWM) | ✓ || Laser scanning confocal microscopy (LSCM/CLSM) | ✓ || Spinning disk confocal microscopy (SDCM) | ✓ || Two-photon microscopy (2P) | ✓ || Total internal reflection fluorescence microscopy (TIRF) | ✓ || Single Molecula localisation microscopy (SMLM) | ✓ || Light-sheet mesoscopic imaging (SPIM or dSLSM) | ✓ || High throughput microscopy/high content screening (HTM/HCS) | ✓ || Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ || Fluorescence Resonance Energy Transfer (FRET) | ✓ || Fluorescence Recovery After Photobleaching (FRAP) | ✓ || Fluorescence Lifetime Imaging Microscopy (FLIM) | ✓ |\n![](upload/lcam.jpg)\n### Contact details\n**Dr. Mark Hink**\nManager LCAM-FNWI\n[m.a.hink@uva.nl](mailto:m.a.hink@uva.nl)\n\n**Prof Dr. Kees Jalink**\n*Manager LCAM-NKI*\n[k.jalink@nki.nl](hhttp://www.lcam.nl/)", "offer_technology_ids": [ "7cb8eeaf", "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "d3d66a1d", "e7adfd19", "722bb380", "e9910d1c", "018d2770", "0de0802c", "5a688552", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } }, { "id": "66b1f7ec", "name": "Wageningen Imaging and Spectroscopy Hub (WISH) - ALM and Molecular Imaging Node Wageningen", "original_id": "1022b15d-6d57-43bd-a0ff-5a99aeeee957", "description": "Ultrafast fluorescence, in vivo photosynthesis, single-cell chloroplast imaging.", "documentation": "## NETHERLANDS\n## Wageningen Imaging and Spectroscopy Hub (WISH) - ALM and Molecular Imaging Node Wageningen\n---\n**The WISH – ALM and Molecular Imaging Node in Wageningen joins the outstanding scientific and technical excellence of three participating expertise groups specialized in light microscopy, microspectroscopy, and magnetic resonance. This Node applies advanced imaging technologies to plant research within a multidisciplinary research environment of cell & developmental biologists, (bio-) physicists and biochemists. Advanced instrumentation has been developed for the particular purpose of studying photosynthesis in vivo with the use of ultrafast fluorescence at the level of individual cells and chloroplasts.**\n### Specialties and expertise of the Node\nSpectroscopic investigations of energy transfer within photosynthetic complexes; functional imaging of membrane associated protein complexes involved in plant signaling and photosynthesis; and the visualization of plant developmental processes like cell division.\n### Offered Technologies:\n| Technologies | Euro-BioImaging |\n| --- | --- |\n| Laser scanning confocal microscopy (LSCM/CLSM) | ✓ |\n| Spinning disk confocal microscopy (SDCM) | ✓ |\n| Total internal reflection fluorescence microscopy (TIRF) | ✓ |\n| Two-photon microscopy (2P) | ✓ |\n| Single Molecula localisation microscopy (SMLM) | ✓ |\n| Fluorescence Resonance Energy Transfer (FRET) | ✓ |\n| Fluorescence Recovery After Photobleaching (FRAP) | ✓ |\n| Fluorescence (cross)-correlation spectroscopy (FCS/FCCS) | ✓ |\n| Fluorescence Lifetime Imaging (FLIM) | ✓ |\n### Contact details\n**Johannes Hohlbein**\nAssociate Professor, Laboratory of Biophysics\nWageningen University & Reserach\n[johannes.hohlbein@wur.nl](mailto:johannes.hohlbein@wur.nl)+31317482635", "offer_technology_ids": [ "019f553c", "3cf0830c", "8399c5a7", "2fa1c4a2", "d3d66a1d", "e9910d1c", "018d2770", "0de0802c", "5a688552", "4e5bcb9e" ], "country": { "id": "e7d114bc-58ca-41a3-aa37-eeb089983090", "name": "Netherlands", "iso_a2": "NL" } } ], "website_pages": [ { "id": "b5de18fa", "url": "https://www.eurobioimaging.eu", "title": "Euro-BioImaging", "description": "Access imaging technologies, expert training, data services across 41 Nodes in Europe.", "documentation": "© Umeå University, photo by Mattias Pettersson © Heiti Paves, Optika & Diagnostika © Multi-Modal Molecular Imaging Italian Node The gateway to European biological and biomedical imaging Euro-BioImaging offers open access to biological and biomedical imaging technologies, training and data services across 41 Nodes, comprised of 247 facilities, in 18 countries and the EMBL. Apply for access See funding options Image life, discover the future Euro-BioImaging’s mission is to provide you with imaging services that bridge biological and biomedical imaging and facilitate innovative and world-class research. Whatever the scale of your imaging, Euro-BioImaging will give you the tools and support to explore and answer your research questions. Read more about our mission Access to imaging technologies We offer access to a range of imaging technologies to allow you image across the scales at one of our 41 Nodes, located in 18 countries and the European Molecular Biology Laboratory, EMBL. Discover our technologies Expert training and support Each Node is staffed with expert personnel who can provide the support required to maximise the output of your research project. Guidance is available for all aspects of the imaging pipeline, from study design to image capture and analysis. In addition, we provide access to training courses for all different levels of expertise. Explore our training Image data management We help you extract meaningful conclusions from your image data through image analysis support, develop tools for handling large image datasets, and support you in making your data FAIR and sharing it widely. Image copyright (right): Tejada-Arranz et al., 2020. View our data services Latest news June 30, 2025 Deuterium Metabolic Imaging to measure hepatic fructose metabolism Chronic intake of high amounts of fructose has been linked to the development of metabolic disorders caused by the almost complete clearance of fructose… June 30, 2025 VISITING THE PRIME NODE With the occasion of the Board meeting which took place in Amsterdam last May, the Med-Hub section Director Linda Chaabane and the Med-Hub Head… June 24, 2025 EU Project CANDLE starts building National Cancer Data Nodes The EU-funded project CANDLE – National CAncer data Node DeveLopErs – officially kicked off on 1st of June 2025, launching its three-year mission to… June 20, 2025 AgroSERV's 4th call for access is open AgroServ is a transdisciplinary initiative supported by the European Union through the Horizon Europe program and will continue until 2027. It supports the research… Show all news Upcoming events Meeting ISCaM Annual Meeting July 2–4, 2025 Brussels, Belgium Meeting PET is Wonderful July 2–4, 2025 Edinburgh, United Kingdom Meeting FEBS Congress 2025 July 5–9, 2025 Istanbul, Turkey Meeting International Congress of Immunology August 17–22, 2025 Vienna, Austria Show all events Join the Virtual Pub A weekly virtual meeting where the entire imaging community is invited to meet to discuss hot topics, showcase success stories, and explore new technologies. Register Sign up for our newsletter Sign up to get the latest news from the world of bioimaging right in your inbox, every two to three months. Sign up Key figures 19 Members (Countries & EMBL) 41 Nodes 247 Imaging Facilities 86 Biological Imaging Technologies 24 Biomedical Imaging Technologies 862 Cumulative User projects as of December 2024", "headings": [ "The gateway to European biological and biomedical imaging", "Image life,\ndiscover the future", "Access to imaging technologies", "Expert training and support", "Image data management", "Latest news", "Deuterium Metabolic Imaging to measure hepatic fructose metabolism", "VISITING THE PRIME NODE", "EU Project CANDLE starts building National Cancer Data Nodes", "AgroSERV's 4th call for access is open", "Upcoming events", "ISCaM Annual Meeting", "PET is Wonderful", "FEBS Congress 2025", "International Congress of Immunology", "Join the Virtual Pub", "Sign up for our newsletter", "Key figures" ], "page_type": "general" }, { "id": "49348cd7", "url": "https://www.eurobioimaging.eu/our-events/image-data-events/", "title": "Image data events - Euro-BioImaging", "description": "Events on image data management, FAIR principles, and innovative solutions for researchers.", "documentation": "Image data events Euro-BioImaging offers several events all around image data which are designed to cover a comprehensive range of topics including image data management, data formats and standards and the implementation of FAIR principles in the biological and biomedical imaging domain. By bringing together experts at the Nodes, researchers, and the imaging community, these events aim to foster the exchange experiences, invite collaboration, enhance technical skills, and promote innovative approaches in the dynamic field of image data. Take a look at the different events we offer: Image data community days The 'Euro-BioImaging Image Data Community Days' bring together Euro-BioImaging Node staff, researchers and other experts from across the globe to explore and discuss the latest advancements in the field of image data. Learn more Guide to FAIR BioImage Data In 2023, we launched the 'Euro-BioImaging's Guide to FAIR BioImage Data' series of yearly events, which aims to introduce the FAIR principles in the context of bioimaging and provide you with simple yet effective steps for a smooth start to your FAIR journey. Learn more User Forum on Data In 2024, this edition of the User Forum highlighted innovative image analysis and image data management solutions at Euro-BioImaging Nodes. It featured user presentations as well as presentations from image data and image analysis experts from the Nodes, focusing on the technical aspects of the work. Learn more Webinar on Data Management of Preclinical Image Datasets The \"Webinar on Data Management of Preclinical Image Datasets\" showcases the tools developed to improve the discoverability, access, interoperability, and reusability of preclinical image datasets, consequently providing a solid step towards the adoption of the FAIR principles of our imaging community. Learn more Special Edition Virtual Pub on Data In 2022, we ran a two-part Special Edition of the Virtual Pub to cover the topic of “DATA” in Biological & Biomedical Imaging. Each event featured short presentations from academics and industry showcasing a range of image data management and analysis solutions for Biological & Biomedical imaging. Learn more", "headings": [ "Image data events", "Image data community days", "Guide to FAIR BioImage Data", "User Forum on Data", "Webinar on Data Management of Preclinical Image Datasets", "Special Edition Virtual Pub on Data" ], "page_type": "homepage" }, { "id": "2624ded3", "url": "https://www.eurobioimaging.eu/sme-industry/", "title": "SME and Industry Access - Euro-BioImaging", "description": "Access 240+ imaging facilities, 120+ technologies, expert consultations, competitive pricing.", "documentation": "Industry Access to Biological and Biomedical Imaging Do you work for a company in Biotech, Pharma, Health or Agricultural Research and are looking for access to cutting-edge imaging technologies? Whether your company is looking for single or regular access to a specific instrument or technology in your geographical region or for high-profile scientific and technical experts for international collaborations, we will help you find the best R&D partner for your research focus and business model. By working with Euro-BioImaging, you can get fast access to instrumentation and skilled service staff, thereby saving on investments and focusing on your core expertise. Euro-BioImaging offers Single entry point to almost 240 imaging facilities Free and confidential consultation Simple access procedure and support Flexible service Competitive pricing for research services high-throughput screening of cells - spheroids and organoids - super resolution and electron microscopy - molecular imaging and tracer development - clinical and preclinical PET/CT, PET/MRI and (ultra) high field MRI - imaging under BSL1 to BSL3 - advan ced image analysis tools - population imaging...and more! We help you find the right solution! You could not find the service you are looking for? Euro-BioImaging is offering access to more than 120 distinct imaging technologies covering all scales from atomic resolution to whole human body imaging. We also provide related services such as sample preparation, cell culture, animal husbandry and image data analysis. Work in a quality-managed environment fully compliant with regulatory requirements Independently validate new technologies across multiple sites and in real-life environments Collect data for internal use without publication delay - whether for your research, marketing or investor relations Minimize disruption risk through backup facilities with common standards and identical workflow protocols Access a larger network of key opinion leaders and experts to identify new application use cases for your products Gain visibility and the chance to acquire diverse user data and customer feedback on new technologies pre- and post market-entry Contact our scientific experts directly to discuss your imaging needs. Case study 1 – Organ-on-a-chip Confocal laser scanning microscopy was used for the quality control and characterisation of a blood-brain-barrier model developed at a partner SME. Learn more Case study 2 – Drug delivery Correlative Coherent Anti-Stokes Raman Scattering (CARS) microscopy can be used for high-resolution, chemically specific imaging of drug nanoparticles in cell culture and tissues, or to analyze drug crystallization and its influence in dissolution of tablets. Learn more Case study 3 – Tissue perfusion and oxygenation Photo Acoustic Imaging (PAI) is a label-free technology with high spatial resolution in tissues up to centimetres thick that can be used to monitor tumor hypoxia. Learn more How does it work? Our process is adapted to the needs of industry users. You can contact us directly to arrange a first consultation with our technology experts and discuss your imaging needs. Euro-BioImaging will identify (a) suitable imaging facility/-ies that can provide the technical services you require and put you in direct contact with the responsible access manager. You will need to provide sufficient details on your research project to the facility to be able to assess whether your project is technically feasible and provide an estimate of time and costs. Confidentiality of your proposal is guaranteed throughout the matchmaking process. We can provide you with a Non-Disclosure Agreement (NDA) if needed or start with your own template. After you have agreed on a service or collaboration with one or more of our facilities, you will sign a Service Level Agreement or Collaboration Agreement with the facility (depending on the nature of your project) and can schedule your visit. Euro-BioImaging will work with you closely to set up an effective collaboration with our partners and support you through the administrative and contractual process. Specific provisions for SMEs Are you working in non-commercial, pre-competitive research at an SME? You might be eligible to benefit from our funding opportunities if your project fulfils certain eligibility criteria. Please check out our funding page or contact us directly to discuss your project.", "headings": [ "Industry Access to Biological and Biomedical Imaging", "Do you work for a company in Biotech, Pharma, Health or Agricultural Research and are looking for access to cutting-edge imaging technologies?", "Euro-BioImaging offers", "high-throughput screening of cells - spheroids and organoids - super resolution and electron", "microscopy - molecular imaging and tracer development - clinical and preclinical PET/CT, PET/MRI", "and (ultra) high field MRI - imaging under BSL1 to BSL3 -advanced image analysis tools -", "population imaging...and more!", "We help you find the right solution!", "Case study 1 – Organ-on-a-chip", "Case study 2 – Drug delivery", "Case study 3 – Tissue perfusion and oxygenation", "How does it work?", "Confidentiality of your proposal is guaranteed throughout the matchmaking process.", "Specific provisions for SMEs" ], "page_type": "access" }, { "id": "405363bb", "url": "https://www.eurobioimaging.eu/news/", "title": "News - Euro-BioImaging", "description": "Updates on imaging projects, job openings, AI events, and new imaging techniques.", "documentation": "News Subscribe to our newsletter June 30, 2025 Deuterium Metabolic Imaging to measure hepatic fructose metabolism Chronic intake of high amounts of fructose has been linked to the development of metabolic disorders caused by the almost complete clearance of fructose… June 30, 2025 VISITING THE PRIME NODE With the occasion of the Board meeting which took place in Amsterdam last May, the Med-Hub section Director Linda Chaabane and the Med-Hub Head… June 24, 2025 EU Project CANDLE starts building National Cancer Data Nodes The EU-funded project CANDLE – National CAncer data Node DeveLopErs – officially kicked off on 1st of June 2025, launching its three-year mission to… June 20, 2025 AgroSERV's 4th call for access is open AgroServ is a transdisciplinary initiative supported by the European Union through the Horizon Europe program and will continue until 2027. It supports the research… June 19, 2025 We are hiring! Scientific Project Manager for the IMAGINE project Are you passionate about scientific project management in the field of advanced imaging? Would you like to contribute to an exciting new initiative at… June 18, 2025 Euro-BioImaging at TiM2025: Sharing Knowledge and Celebrating Open Data This spring, three members of the Euro-BioImaging Hub team participated in the Trends in Microscopy 2025 (TiM2025) conference, held from March 17–21 in Münsingen,… June 18, 2025 Euro-BioImaging Hiring: Communications Officer Location: Turku, Finland (Euro-BioImaging ERIC Statutory Seat)Full-time position | Fixed term until 31 August 2027 | Starting salary: €3,200–€4,200/month Join a cutting-edge European research… June 12, 2025 AI4Life Community Event Celebrating AI Innovation in Life Sciences held in Helsinki May 28, 2025 – Helsinki, Finland — The AI4Life project, a Horizon Europe-funded project advancing artificial intelligence (AI) in life science research, and… June 4, 2025 Laser Speckle Contrast Imaging Showcase at Euro-BioImaging We are happy to announce that showcasing of Laser Speckle Contrast Imaging is now launched. Used in biomedical research at both preclinical and clinical… June 4, 2025 EVOLVE call supporting Node participation in conferences targeting new user groups is now open We are thrilled to announce that Euro-BioImaging opened the EVOLVE call for Node participation in conferences targeting new user groups. This initiative is intended… June 4, 2025 RE-IMAGINE-CROPS Project Kicks Off to Transform Sustainable Agriculture with Real-Time Imaging On May 6th, 2025, the RE-IMAGINE-CROPS project officially launched with a kickoff meeting that brought together leading researchers and industry experts from across Europe. June 2, 2025 Proteintech joins Euro-BioImaging Industry Board Euro-BioImaging is pleased to welcome Proteintech as the newest member of the Euro-BioImaging Industry Board (EBIB). A global leader in antibody and reagent production,… Country All Austria Belgium Bulgaria Czechia Denmark EMBL Finland France Hungary Israel Italy Netherlands Norway Poland Portugal Slovenia Spain Sweden United Kingdom Node All Advanced Light and Electron Microscopy Node Prague Advanced Light Microscopy Node Poland Advanced Light Microscopy Node Sofia Advanced Microscopy and Molecular Imaging Node - AMMI Maastricht Austrian BioImaging/CMI B-Min - Mesoscopic Imaging Node Barcelona Barcelona Live and Intravital - Advanced Light Microscopy Node (BLivIN) Brain Imaging Network (BIN) Cellular Imaging Hungary Node Center for Advanced Preclinical Imaging (CAPI) Challenges Framework Flagship Node Correlative Light Microscopy Dutch Flagship Node Danish BioImaging Node Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED Dutch High Field Imaging Hub Erasmus MC OIC - Advanced Light Microscopy Rotterdam Node Euro-BioImaging EMBL Node Finnish Advanced Light Microscopy Node Finnish Biomedical Imaging Node Flanders BioImaging France-BioImaging Israel BioImaging Italian Advanced Light Microscopy Node LCAM - Functional Imaging Flagship Node Amsterdam Medical and Preclinical Imaging Hungary Multi Modal Molecular Imaging (MMMI) Italian Node Multimodal Imaging Node Brno NL-BioImaging NorMIC - Advanced Light Microscopy Node Oslo NORMOLIM - Norwegian Molecular Imaging Infrastructure Phase Contrast Imaging Flagship Node Trieste Population Imaging Flagship Node Rotterdam Population Imaging Node Valencia Portuguese Platform of BioImaging (PPBI) Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node SiMBION SLN@BCN - Barcelona Super-resolution Light and Nanoscopy Node Swedish National Microscopy Infrastructure (NMI) The UK Node WISH - ALM and Molecular Imaging Node Wageningen Show more Technology All 3D Imaging AFM - Atomic Force Microscopy CARS - Coherent anti-Stokes Raman scattering Correlated Imaging cryo-EM Cryo-ET Electron Microscopy Energy-dispersive X-ray spectroscopy EPR - Electron Paramagnetic Resonance Expansion Microscopy FIB-SEM FLIM fMRI Innovation Intravital Microscopy Laser Speckle Contrast Imaging Light Micr", "headings": [ "News", "Deuterium Metabolic Imaging to measure hepatic fructose metabolism", "VISITING THE PRIME NODE", "EU Project CANDLE starts building National Cancer Data Nodes", "AgroSERV's 4th call for access is open", "We are hiring! Scientific Project Manager for the IMAGINE project", "Euro-BioImaging at TiM2025: Sharing Knowledge and Celebrating Open Data", "Euro-BioImaging Hiring: Communications Officer", "AI4Life Community Event Celebrating AI Innovation in Life Sciences held in Helsinki", "Laser Speckle Contrast Imaging Showcase at Euro-BioImaging", "EVOLVE call supporting Node participation in conferences targeting new user groups is now open", "RE-IMAGINE-CROPS Project Kicks Off to Transform Sustainable Agriculture with Real-Time Imaging", "Proteintech joins Euro-BioImaging Industry Board", "Country", "Node", "Technology", "Category" ], "page_type": "news" }, { "id": "ea1e2fc2", "url": "https://www.eurobioimaging.eu/how-to-access/funding/", "title": "Funding - Euro-BioImaging", "description": "Funding for researchers, including i4A, canSERV, AgroServ; application details available.", "documentation": "Funding Euro-BioImaging is a publicly funded, non-profit research infrastructure. Hence, the costs for scientists to access Euro-BioImaging services are kept to their minimum, with the sole aim to allow running the infrastructure. The costs vary depending on the scale and complexity of the access and the required support. In order to access Euro-BioImaging technologies, you may also need some financial support for travel and accommodation expenses. The first thing you should do is look into the funding instrument that currently supports your research: more and more funding authorities regard access to public research infrastructures as eligible costs! For instance, if you are an ERC grant-holder, you can freely use your funds to access Euro-BioImaging. In the future, you may want to check this aspect beforehand, when applying for a grant, and consider whether it is beneficial to indicate that you will want to use European Research Infrastructure services to support your research. Funding opportunities If your access is not already funded, you may need to look into other opportunities: we are doing our best to continuously list the ones that are currently available to researchers in the tables below. Please note that we are updating these lists regularly, so come back to this page in the future if you have not found what serves your purposes for now. Euro-BioImaging is also constantly working to make new funding opportunities available. Imaging 4 All - funding for researchers in low- and middle-income countries Imaging for All (i4A) coordinated by Global BioImaging provides funding for low- and middle-income country researchers to access imaging infrastructures and training opportunities. All Euro-BioImaging Node facilities are eligible to host these projects. Applications are open until August 15. More info EU & other funding Finally, Euro-BioImaging has been awarded a number of important Horizon Europe and other grants to provide funding for User Access at Euro-BioImaging Nodes. Below you will find information about currently open funding for user projects for researcher from anywhere in the world. Topic-specific Access funding CanServ - Supporting Cancer Research If your project is cancer related, you can apply for funding through the canSERV project, which supports research on cancer by facilitating access to European Research Infrastructures. 28 out of 41 Euro-BioImaging Nodes provide services in canSERV, spanning from biological to preclinical to human imaging services. Regular calls for free access to these services are open throughout 2024 and special challenge calls will launch soon. More information on the currently open calls and deadlines here . More information on how to apply to a Euro-BioImaging Node here . AgroServ - Supporting agro-ecology research projects For researchers in the field of agroecology, plant biology, soil or marine microorganisms, crop sciences or related topics, funding opportunities are available via the AgroServ project. The project will provide researchers in the field with access to relevant Research Infrastructure services from a broad range of participating infrastructures, including a spectrum of imaging services from nine participating Euro-BioImaging Nodes. The available imaging services range from plant-adapted electron and super-resolution microscopy to plant phenotyping, elemental detection and application of medical imaging technologies, such as PET and MRI, on plant samples. Click for the full catalogue of Euro-BioImaging's AgroServ services . Find out how the project application works here . ISIDORe - Supporting infectious disease research - TNA Calls closed -CALLS CLOSED-NO LONGER ACCEPTING APPLICATIONS - ISIDORe is a Horizon Europe-funded project that provides free of charge access to cutting-edge technology platforms and resources across a wide spectrum ranging from characterisation of pathogens to vaccine development. Eighteen Euro-BioImaging Nodes participate in the ISIDORe project, offering state-of-the-art imaging expertise to enhance basic research, drug discovery, diagnostics, vaccines, and clinical disease management. Please visit the following webpages to see if ISIDORe could support your research on infectious diseases, vaccine development, pathogens of concern, or related topics. Find out how the project application works here . COMULISglobe - Supporting correlative multimodal imaging COMULISglobe is a project funded by the Chan Zuckerberg Initiative (CZI) and one of the Euro-BioImaging partner communities. The are currently no Open Call for Access via this project. Funding instruments available at specific Euro-BioImaging Nodes This table reports the funding instruments supporting access exclusively to a specific Euro-BioImaging Node (and not applicable to all Nodes). Continuous funding programmes at Nodes Funding instrument Node For whom For what Expiry date Additional information SEELIFE call for free access at Italian Nodes Molecular Imaging I", "headings": [ "Funding", "Funding opportunities", "Imaging 4 All - funding for researchers in low- and middle-income countries", "EU & other funding", "Topic-specific Access funding", "Funding instruments available at specific Euro-BioImaging Nodes", "Continuous funding programmes at Nodes", "International funding instruments", "National funding instruments" ], "page_type": "homepage" }, { "id": "43a17e65", "url": "https://www.eurobioimaging.eu/events/febs-congress-2025/", "title": "FEBS Congress 2025 - Euro-BioImaging", "description": "49th FEBS Congress, Istanbul, July 5-9, 2025; poster sessions, bursary for early-career researchers.", "documentation": "FEBS Congress 2025 When July 5–9, 2025 Where Istanbul, Turkey The 49th FEBS Congress will take place in Istanbul from July 5-9. It aims to provide an outstanding international forum in the area of Europe and neighbouring regions for the face to face exchange of knowledge and ideas across the molecular life sciences. The core scientific programme comprises inspiring plenary lectures from distinguished researchers working in areas of high topical interest, and a range of themed symposia providing focused updates from leading experts in each field. The contribution of participants towards the scientific discussion at the event is encouraged by the opportunity to present work through extensive poster sessions, and submitted abstracts may also be considered for oral presentations. The broad subject coverage of the Congress and its size provide an excellent setting for participants to gain valuable insight into progress in research areas beyond their own. Furthermore, additional activities or special sessions aim to engage participants on wider issues, such as teaching in the molecular life sciences. A commercial exhibition provides additional interest. The FEBS Congress has a strong emphasis on support, education and inspiration for the next generation of scientists, with a bursary scheme for early-career researchers, a satellite Young Scientists’ Forum, and activities to encourage interaction with peers and experts. Altogether FEBS Congresses aim to be an exemplary cross-discipline gathering in the molecular life sciences for research presentation, discussion, learning, inspiration and encouragement, with participants leaving with new research knowledge and ideas, and perhaps the beginnings of international collaborations and friendships. Generally, Euro-BioImaging Hub team members attend this event with research infrastructure partners. More information", "headings": [ "FEBS Congress 2025", "When", "Where" ], "page_type": "homepage" }, { "id": "171032e0", "url": "https://www.eurobioimaging.eu/our-events/tech-exchange/", "title": "Tech Exchange webinar for companies - Euro-BioImaging", "description": "Monthly Tech Exchange webinars for imaging tech; register for updates and presentations.", "documentation": "Tech Exchange Tech Exchange – the webinar for presentations from leading companies in the imaging field! Approximately once  a month, directly after the Virtual Pub at 14:00h CE(S)T, we offer the floor to companies that want to showcase their technologies and exciting applications in biological and biomedical imaging – whether they offer systems solution or tailored parts, tools, workflows or software! We welcome large and small companies alike – please get in touch if you are a company with a new technology or product and would like to present. Priority is given to current and prospective Industry Board members. We are looking forward to exciting presentation of innovative technologies from our Industry Board and other companies that address the imaging needs of our research community. When : Please check our calendar for the next episode. We aim to have monthly webinars, but the exact date will vary depending on the overall technology focus of the event, to ensure that community interest and company offer are a match. How to join : Everyone is free to join, but registration is required. Just sign up for the Tech Exchange and Euro-BioImaging’s Virtual Pub scientific seminar series once, and you will get automatic reminders for upcoming events. Register here . Recordings: Some of our Tech Exchange events have been recorded. Visit our YouTube channel. Next episodes No scheduled events All events How to join? The TechExchange follows straight after the Virtual Pub - you can register for both at the same time. Register Are you a company with an innovative imaging solution? Do you want to present your technological developments to a large network of imaging enthusiasts? Contact us Recordings Recordings of previous Tech Exchange events are available to watch. Our YouTube channel", "headings": [ "Tech Exchange", "Tech Exchange – the webinar for presentations from leading companies in the imaging field!", "Next episodes", "How to join?", "Are you a company with an innovative imaging solution?", "Recordings" ], "page_type": "homepage" }, { "id": "a7f92ac1", "url": "https://www.eurobioimaging.eu/who-we-are/our-team/", "title": "Our Team - Euro-BioImaging", "description": "Team roles, contact info, training management, legal services, imaging tools development.", "documentation": "Our Team Euro-BioImaging ERIC is coordinated by its Hub Team. The Euro-BioImaging Hub consists of the Statutory Seat in Finland (Turku), the community-specific Bio-Hub for biological imaging at EMBL, and the community-specific Med-Hub for biomedical imaging in Italy (Torino). Meet our team! John Eriksson Director General Euro-BioImaging Statutory Seat\n |\n Turku john.eriksson@eurobioimaging.eu Works closely in the Directorate with the Section Directors to prepare and implement Euro-BioImaging ERIC tasks. Is the legal representative of Euro-BioImaging ERIC and promotes the research infrastructure at the national and international level. Responsible for the day-to-day management and coordination of Euro-BioImaging ERIC in collaboration with the Section Directors. Antje Keppler Section Director Bio-Hub Euro-BioImaging Bio-Hub\n |\n EMBL antje.keppler@eurobioimaging.eu Prepares and implements Euro-BioImaging ERIC tasks as part of the Directorate. Represents the interests of the biological imaging community within Euro-BioImaging ERIC and promotes the research infrastructure at the national and international level. Responsible for the day-to-day management of the Bio-Hub team. Linda Chaabane Section Director Med-Hub Euro-BioImaging Med-Hub\n |\n Torino linda.chaabane@eurobioimaging.eu Prepares and implements Euro-BioImaging ERIC tasks as part of the Directorate. Represents the interests of the biomedical imaging community within Euro-BioImaging ERIC and promotes the research infrastructure at the national and international level. Responsible for the day-to-day management of the Med-Hub team. Victoria Lucia Alonso Scientific Project Manager Euro-BioImaging Med-Hub\n |\n Torino victoria.alonso@eurobioimaging.eu Manages and coordinates training activities for Euro-BioImaging. Collaborates with all Hubs on growing training activities, improving visibility and community building. Amaranta Amador Bernal Head of Legal Services and International Relations Euro-BioImaging Statutory Seat\n |\n Turku amaranta.amador.bernal@eurobioimaging.eu Provides high-level advice to the Directorate on strategy, legal, governance, scientific policy and international relations. Ensures the legal compliance of the ERIC operations. Supports the Directorate in shaping and implementing the international relations strategy with key stakeholders. Anna-Elena Bitetti Image Data Scientist Euro-BioImaging Med-Hub\n |\n Torino Develops tools for the management and processing of preclinical images. Daniela Aviles Huerta Scientific Project Manager Euro-BioImaging Bio-Hub\n |\n EMBL daniela.aviles@eurobioimaging.eu Manages user access to Euro-BioImaging services and supports skill-building at the Euro-BioImaging Nodes by training program implementation. Johanna Bischof Head of Bio-Hub Operations Euro-BioImaging Bio-Hub\n |\n EMBL johanna.bischof@eurobioimaging.eu Supports user access and our Nodes at the scientific and technical level, including community engagement and integration of new technologies. Erika Cerutti Scientific Project Manager Euro-BioImaging Med-Hub\n |\n Torino erika.cerutti@eurobioimaging.eu Supports the Med-Hub team in managing its contribution to international Horizon Europe projects. Marianna Childress Poli External Communication Officer Euro-BioImaging Bio-Hub\n |\n EMBL marianna.poli@eurobioimaging.eu Increases Euro-BioImaging ERIC visibility via publishing our news stories, social media contributions and community engagement. Sudeep Das AI and Biomedical Data Strategy Officer Euro-BioImaging Statutory Seat\n |\n Turku sudeep.das@eurobioimaging.eu Promoting adoption of AI-driven solutions, compliance to FAIR data and sustainability of infrastructures. Managing EU projects whose partnerships extend globally and creating a vibrant community for scientists. Rafael Diaz Junior Scientific Officer Euro-BioImaging Statutory Seat\n |\n Turku rafael.diaz@eurobioimaging.eu Supports various administrative tasks while actively participating in the planning, application, funding acquisition, and execution phases of Horizon Europe projects. Giuseppe Digilio Operations Advisor Euro-BioImaging Med-Hub\n |\n Torino giuseppe.digilio@eurobioimaging.eu Coordinates and supports Nodes operation and integration; fosters engagement of the biomedical imaging community at large. Dorothea Dörr Scientific Project Manager Euro-BioImaging Statutory Seat\n |\n Turku dorothea.dorr@eurobioimaging.eu Involved in the planning and implementation of international Horizon Europe projects and administers activities of the Statutory Seat. Ayoub El Ghadraoui EU Project Manager Euro-BioImaging Bio-Hub\n |\n EMBL ayoub.elghadraoui@eurobioimaging", "headings": [ "Our Team", "John Eriksson", "Antje Keppler", "Linda Chaabane", "Victoria Lucia Alonso", "Amaranta Amador Bernal", "Anna-Elena Bitetti", "Daniela Aviles Huerta", "Johanna Bischof", "Erika Cerutti", "Marianna Childress Poli", "Sudeep Das", "Rafael Diaz", "Giuseppe Digilio", "Dorothea Dörr", "Ayoub El Ghadraoui", "Solveig Eriksson", "Jiri Funda", "Camilo Guzmán", "Anne-Charlotte Joubert", "Pasi Kankaanpää", "Isabel Kemmer", "Dale Lawson", "Anting Li", "Dario Longo", "Rakesh Mahato", "Aastha Mathur", "Maria Mirza", "Susan Muchai", "Buǧra Özdemir", "Claudia Pfander", "Ilari Pulli", "Feriel Ramdhane", "Zorica Ruohonen", "Arina Rybina", "Jaanus Saarnak", "Beatriz Serrano-Solano", "Susanne Vainio", "Alessandra Viale", "Aman Yadav" ], "page_type": "homepage" }, { "id": "6013fa00", "url": "https://www.eurobioimaging.eu/our-events/conferences/", "title": "Conferences - Euro-BioImaging", "description": "Upcoming conferences: mmc 2025, FEBS, Immunology Congress, SPAOM 2025; contact for more info.", "documentation": "Conferences Euro-BioImaging attends a number of conferences, engaging with researchers, imaging facility staff from our Nodes and beyond, industry partners, as well as other research infrastructures, around both academic and policy-making related topics. We hope to see you at some of these upcoming events! Where to meet Euro-BioImaging staff Join us on our booths at the following conferences: Euro-BioImaging will have a booth, talk or special event at the following upcoming meetings. We would delighted to meet you there and our Nodes are invited to join us at the booth for meet & greet sessions. Email us if you would like to know more about the opportunity. July 1-3, Manchester, UK - Microscience Microscopy Congress (mmc) 2025 July 5-9, Istanbul, Türkiye - 49th FEBS Conference August 17-22, Vienna, Austria - International Congress of Immunology August 19-25, Gothenburg, Sweden - BNMI 2025 October 8-11, EMBL Heidelberg - Seeing is Believing November 5-7, Braga, Portugal - SPAOM 2025 We are part of the community ... Join us! Community events Below is the Events database powered by MicroscopyDB ! If you want to see the upcoming conferences, please use the filter function to select \"Conference/Meeting ad hoc\" or \"Conference/Meeting annual.\" If you have events, tools, training/education resources, or jobs to share, please add them to the relevant MicroscopyDB databases . (“$” associated with a registration fee)", "headings": [ "Conferences", "Join us on our booths at the following conferences:", "We are part of the community ...", "Join us!", "Community events" ], "page_type": "homepage" }, { "id": "8c85202b", "url": "https://www.eurobioimaging.eu/for-companies/", "title": "How companies can engage with us - Euro-BioImaging", "description": "Access 120+ imaging technologies, expert consultations, industry board, and collaboration opportunities.", "documentation": "For companies New imaging technologies have, and will continue to, revolutionise Life Sciences and the understanding of health and disease. As the open research infrastructure for imaging technologies in Europe, Euro-BioImaging ERIC (Euro-BioImaging) enables biological and medical researchers to access cutting-edge equipment and expertise needed for their projects. In this regard, close collaboration between Euro-BioImaging ERIC and Industry is key to the success of the infrastructure: On one hand to continuously include the latest technology developments from leading companies in the sector, and on the other hand to provide cutting-edge imaging, image analysis and non-tech services tailored to the specific needs of SME and industrial users. There are a number of ways in which companies engage with Euro-BioImaging - whether you are a manufacturer developing new imaging technologies or leading a company R&D project in need of imaging expertise and the latest instruments. Download overview Access Services Euro-BioImaging gives you access to 120+ cutting -edge biological and biomedical imaging technologies across all scales. We also offer Image Data Analysis as a Service to help you make the most of your image data. Fully confidential consultation by our technology experts Attractive fee-for-service model with services tailored to your research needs Service agreement with full IP Collaborate Are you looking for competent partners for your imaging project Technology development Methods development National or European funding programmes We can help you identify the right experts and set up a collaboration ! Contact us to discuss your imaging needs! Consult with experts Share your expertise, best practices & ideas and in return learn  from some of the best in their field. More than 10 expert groups on image data, remote access and training, imaging technologies and more Online workshops Stakeholder consultations Join the community Participate in one of our many free and open events organized for imaging enthusiasts Virtual Pub (scientific highlights in imaging) Tech Exchange (commercial imaging solutions) Online workshops User Forum Subscribe to our newsletter! Industry Board Become a member of our Industry Board for a small annual fee and benefit from Regular meetings with other companies in the imaging sector Annual meeting with experts from 190+ pan‑European imaging facilities Access to information on trends and latest developments in imaging Visibility for your technology or career opportunities Tailored opportunities for companies Support We work with different initiatives and programmes globally on training, career development and capacity building for imaging scientist and core facilities. If you want to support emerging imaging communities or offer opportunities to early career imaging specialists, get in touch with us! Contact us to learn more", "headings": [ "For companies", "Access Services", "Collaborate", "Consult with experts", "Join the community", "Industry Board", "Support" ], "page_type": "homepage" }, { "id": "8bc4f0d5", "url": "https://www.eurobioimaging.eu/training/mentoring/", "title": "Mentoring - Euro-BioImaging", "description": "Mentoring Program: Apply for peer support in career development, data management, and soft skills.", "documentation": "Mentoring We are delighted to introduce a new training pillar within the framework of EVOLVE , our Mentoring Program! Euro-BioImaging’s Mentoring Program will strengthen our Node Community by forging relationships with members from other Nodes, with the Global BioImaging network and industry. These mentoring relationships aim to benefit both mentors and mentees and support skill building, career development and daily operations. Apply Why join Euro-BioImaging's Mentoring Program? Staff in imaging facilities usually work closely in small teams and sometimes even by themselves, which means they might miss out on different viewpoints, expertise in different areas, and career perspectives. While having a direct supervisor is important, sometimes you need advice from outside your usual crew – maybe someone with different skills or a fresh outlook. By fostering peer-to-peer support , Euro-BioImaging’s Mentoring Program aims to fill this gap. How does it work? Mentoring pairs are carefully matched based on their skills and experience , rather than merely seniority level. The specific areas of professional development that mentees have highlighted as important are central for the selection of the mentor. Pairs are encouraged to meet at least once a month for a six-month period, during which they establish concrete goals to strive towards. These relationships can be short-term, focused on achieving specific objectives, or they can pave the way to longer-term collaborations, including the participation in our Job Shadowing Program . Who can be your mentor? Members at the: Euro-BioImaging Nodes Global Imaging Network Euro-BioImaging Industry Board and Industry partners Potential Areas of Mentoring Career Development User service support Data Management Soft Skill Development (leadership, negotiation, conflict resolution, team building) Business Strategy and Planning Technical advice Guidance on Green Sustainable Practices and more… Who can apply? All imaging core facility staff from Euro-BioImaging and the Global BioImaging network are welcome to apply. How to apply? First track Both mentors and mentees are encouraged to fill out the application form linked below. Our training team will go through the applications and reach out with your proposed match. Euro-BioImaging’s training team will support pairs for a set duration. Second track Dual program targeted to participants of the Euro-BioImaging Job Shadowing Program. If you have any questions, please write to: info@eurobioimaging.eu Next call: Fall 2025 . Apply here The Mentoring initiative is made possible through EU funding as part of the EVOLVE project.", "headings": [ "Mentoring", "Why join Euro-BioImaging's Mentoring Program?", "How does it work?", "Who can be your mentor?", "Potential Areas of Mentoring", "Who can apply?", "How to apply?" ], "page_type": "training" }, { "id": "58f7e252", "url": "https://www.eurobioimaging.eu/news/eu-project-candle-starts-building-national-cancer-data-nodes/", "title": "EU Project CANDLE starts building National Cancer Data Nodes - Euro-BioImaging", "description": "CANDLE project builds EU cancer data nodes, enhancing research and data sharing.", "documentation": "EU Project CANDLE starts building National Cancer Data Nodes Published June 24, 2025 Category Funded Projects The EU-funded project CANDLE – National CAncer data Node DeveLopErs – officially kicked off on 1st of June 2025, launching its three-year mission to build a robust cancer research infrastructure across EU Member States. This project is coordinated by Health-RI and with a consortium of 40 partners from 20 European countries. CANDLE will support Member States in setting up National Cancer Data Nodes which will be able to manage and share cancer data nationally and across borders, connecting different national actors. Euro-BioImaging ERIC will assist in the design of national nodes, support their user communities, develop a network resource kit, and provide guidance on best practices for data use. We will work closely with the Euro-BioImaging Radiology and Medical Imaging Valencia Node in Valencia , the European Research Infrastructure Consortiums (ERICs) in Life Sciences and the Finnish National Cancer Center (FICAN) to support the development  of National Cancer Data nodes in Europe. CANDLE is a continuation of our commitment to support the EU Mission on Cancer as we started through over  key initiatives like canSERV, EOSC4Cancer and EUCAIM which complement our mission in enabling cutting-edge research, open access to advanced imaging technologies, data services, and collaborative research infrastructure, and fosters the development of AI tools for improved diagnosis and treatment. The National Cancer Data Nodes implemented in CANDLE will closely link to other European cancer data projects as recommended in the UNCAN blueprint: 1) the UNCAN.eu platform, UNCAN-CONNECT, a federated cancer data infrastructure being developed under the upcoming EU project , and 2) the European Cancer Patient Digital Centre (ECPDC). Driving Integration Across Europe CANDLE will strategically support the European Health Data Space (EHDS) by creating a federated network of national cancer data nodes, acting as disease-specific EHDS demonstrators. This initiative also implements the EU Mission on Cancer and Europe's Beating Cancer Plan nationally. The CANDLE Consortium, including Euro-BioImaging, will ensure the adoption of best practices in data sharing, enhance data access maturity, and foster cross-domain collaboration, directly contributing to EHDS goals. More news from Euro-BioImaging June 30, 2025 Deuterium Metabolic Imaging to measure hepatic fructose metabolism Chronic intake of high amounts of fructose has been linked to the development of metabolic disorders caused by the almost complete clearance of fructose… June 30, 2025 VISITING THE PRIME NODE With the occasion of the Board meeting which took place in Amsterdam last May, the Med-Hub section Director Linda Chaabane and the Med-Hub Head… June 20, 2025 AgroSERV's 4th call for access is open AgroServ is a transdisciplinary initiative supported by the European Union through the Horizon Europe program and will continue until 2027. It supports the research… See all news", "headings": [ "EU Project CANDLE starts building National Cancer Data Nodes", "Driving Integration Across Europe", "More news from Euro-BioImaging", "Deuterium Metabolic Imaging to measure hepatic fructose metabolism", "VISITING THE PRIME NODE", "AgroSERV's 4th call for access is open" ], "page_type": "news" }, { "id": "8a985e6c", "url": "https://www.eurobioimaging.eu/data-services/", "title": "Data services - Euro-BioImaging", "description": "Image Data Services, IDA, FAIR support, technical assistance, community initiatives.", "documentation": "Data services To support production of quality data, analysis methods and an extended data life cycle, Euro-BioImaging offers Image Data Services for the benefit of the whole imaging community. Together with our expert Nodes staff, we support adoption practices that yield FAIR (Findable, Accessible, Interoperable and Reusable) image data and analysis workflows. User Data Services Euro-BioImaging offers its users Image Data Analysis (IDA) as a Service through expert Image Analysts at the Nodes. Discover our Services Community Data Services Community initiatives are responsible for a lot of valuable work around developing training materials and standards for data, metadata and tools. Euro-BioImaging serves as a central coordinating point, participating in various community initiatives and consolidating their efforts. Discover our Services FAIR Data Services At Euro-BioImaging, we support development of an ecosystem of FAIR bioimage data and tools. Discover our Services Technical Support Euro-BioImaging offers technical assistance to users in the form of tool and workflow development which facilitate FAIR image data management and analysis. To this end, a particular focus is laid on developing tools that support the OME-zarr file format. Discover our Services Digital image data produced by biological and biomedical imaging technologies is a growing and valuable resource. Storing, annotating, processing, visualizing and analyzing image data helps researchers understand physiological and pathological processes that drive life. A well curated dataset with quality metadata can augment the study with information that elevates its utility beyond a single use, and following standardised nomenclatures and methods makes the data and analysis easier to share and adapt. Here’s a schema to demonstrate how Euro-BioImaging empowers the Community with FAIR and Open Image Data and Analysis Services. Read our article: https://link.springer.com/article/10.1007/s00418-023-02203-7", "headings": [ "Data services", "User Data Services", "Community Data Services", "FAIR Data Services", "Technical Support" ], "page_type": "services" }, { "id": "5eaeed05", "url": "https://www.eurobioimaging.eu/our-events/", "title": "Our events - Euro-BioImaging", "description": "Events: All Hands Nodes Meeting, User Forum, Tech Exchange, image data events.", "documentation": "Our events Euro-BioImaging organizes a number of flagship events for key stakeholders, namely Nodes, users, researchers, and members of the biological and biomedical imaging communities. We also attend a number of conferences, with researchers and research infrastructure (RI) partners and policy makers. We invite you to join us at the events we have listed below. All Hands Nodes meeting Each year, the Euro-BioImaging Hub team organises the \"All Hands Nodes Meeting.\" The aim of the annual All-Hands Nodes meeting is to bring together scientists from the Euro-BioImaging Nodes to meet each other, encourage interdisciplinary collaborations, and to discuss most relevant topics for Euro-BioImaging operation and developments in imaging. More Virtual Pub A weekly virtual meeting where Node staff, Friends of Euro-BioImaging, and our Hub team discuss hot topics, showcase success stories, and explore new technologies. More User Forum Designed to highlight the importance of imaging to different research areas, the Euro-BioImaging User Forum takes place online twice a year and features keynote presentations from prominent scientists as well as presentations from users at our Nodes. More Image Data Events Euro-BioImaging offers several events all around image data bringing together imaging experts at the Nodes with researchers and the imaging community. More Tech Exchange Approximately once  a month, directly after the Virtual Pub, the Euro-BioImaging Industry Board offers the floor to companies that want to showcase their technologies and exciting applications in biological and biomedical imaging. This is a great opportunity for the imaging community to learn about latest technical developments and new innovations from instrument manufacturers and image software developers. More Conferences & Meetings Discover a selection of the conferences & meetings we or members of the Euro-BioImaging community will attend with researchers, research infrastructure partners and policy makers. More Past events May 7, 2025 Euro-BIoImaging at the SEE-LIFE Symposium in Italy The Euro-BioImaging Med-Hub section director, Linda Chaabane, was invited to participate in the Symposium on ‘Empowering Italian Euro-BioImaging infrastructure’ organised by the Italian nodes… April 25, 2025 Czech-BioImaging celebrates its 10 year anniversary! In 2025, Czech-BioImaging celebrates its 10th anniversary. Czech-BioImaging is the national infrastructure that brings together 16 leading imaging centers across the Czech Republic,… April 9, 2025 Wonderful All Hands Nodes Meeting at EMBL Heidelberg From March 25-28, Euro-BioImaging Hub team was delighted to host our Node community & industry partners. The Euro-BioImaging All Hands Meeting is the occasion… March 13, 2025 FAIR Image Analysis: Insights from BioHackathon Europe 2024 At this year’s BioHackathon Europe 2024 in Barcelona, a dedicated group of enthusiasts developed FAIR  image analysis workflows in the Galaxy platform. Led by… February 21, 2025 Join Euro-Bioimaging at EMIM 2025 in Bilbao: Outstanding Opportunity to Connect, Learn, and Collaborate! Euro-Bioimaging is delighted to be part of the prestigious event that is the European Molecular Imaging Meeting (EMIM) again in 2025, in the vibrant… February 3, 2025 Join us for the Euro-BioImaging Image Data Community Days 2025 Euro-BioImaging is proud to announce that we will be hosting the first Euro-BioImaging Image Data Community Days during the week of 7-11 April 2025. January 31, 2025 Programme's out for the All Hands Nodes meeting We are looking forward to the Euro-BioImaging All Hands Nodes meeting! This event takes place in person at EMBL Heidelberg from March 25-28, 2025. January 16, 2025 The UK’s Light Microscopy Core Facilities staff meeting kicks off 2025 The UK Light Microscopy Facility meeting, organised by the RMS and a local host, is always a bright way to start the year in… December 10, 2024 Euro-BioImaging attends ICRI 2024 The International Conference on Research Infrastructures (ICRI) took place in Brisbane, Australia, in December 2024. Organised jointly by Australia’s national science agency, CSIRO, the… December 9, 2024 Euro-BioImaging and Nodes at ANERIS General Assembly Meeting Earlier last week, two Euro-BioImaging Nodes, along with Euro-BioImaging hub members Ayoub El Ghadraoui and Susanne Vainio, took part in the ANERIS General Assembly… See all events", "headings": [ "Our events", "All Hands Nodes meeting", "Virtual Pub", "User Forum", "Image Data Events", "Tech Exchange", "Conferences & Meetings", "Past events", "Euro-BIoImaging at the SEE-LIFE Symposium in Italy", "Czech-BioImaging celebrates its 10 year anniversary!", "Wonderful All Hands Nodes Meeting at EMBL Heidelberg", "FAIR Image Analysis: Insights from BioHackathon Europe 2024", "Join Euro-Bioimaging at EMIM 2025 in Bilbao: Outstanding Opportunity to Connect, Learn, and Collaborate!", "Join us for the Euro-BioImaging Image Data Community Days 2025", "Programme's out for the All Hands Nodes meeting", "The UK’s Light Microscopy Core Facilities staff meeting kicks off 2025", "Euro-BioImaging attends ICRI 2024", "Euro-BioImaging and Nodes at ANERIS General Assembly Meeting" ], "page_type": "homepage" }, { "id": "141899a8", "url": "https://www.eurobioimaging.eu/training/cross-node-job-shadowing/", "title": "Cross-Node Job Shadowing - Euro-BioImaging", "description": "Job shadowing program details: application deadlines, funding, training plans, contact info.", "documentation": "Cross-Node Job Shadowing We are excited to announce the Cross-Node Job Shadowing program! This is an opportunity for Node Staff to work with other Euro-BioImaging Node outside their country of residence to keep learning and to exchange ideas and best practices. Whether you're interested in scientific and technical fields, facility operations, or data management and analysis , this program is for you! Funded by the EU project EVOLVE, this initiative supports Node Staff in expanding their expertise and fostering collaboration. Benefits For Individual Node Staff Network with people in a similar field to your own Attain new technical and operational skills and abilities Experience a new work environment For Nodes Promoting technical/operational development at Nodes Stimulating participation in collaborative projects Improving and harmonizing operational and administrative procedures Overview of the Node-to-Node exchanges from the first round of the shadowing program - EVOLVE 2024 How does it work? To participate, both the visitor and the host must be active staff members at a Euro-BioImaging Node at different member states. While not a requirement, preference may be given to applicants who have not previously received support through EVOLVE Training opportunities . The program is open to all Euro-BioImaging Node Staff, including technicians, administrative employees, and Node managers. Application Rounds The program runs an annual call each Spring during the EVOLVE project (starting in 2024). First round: Opened on May 10, 2024 | Deadline: June 14, 2024 Second round: Opens on March 24, 2025 | Deadline: May 16, 2025 Selected applicants are entitled to reimbursement for visit expenses including travel, accommodation and meals upon invoice submission. Need help finding the right Node? If you know what you want to learn but aren’t sure where to go, our training team will connect you with a suitable host. Visit Duration Minimum 3 days, maximum 2 weeks. We encourage covering multiple topics for a well-rounded experience. How to apply? There are two ways to apply. A. You already have a Node in mind Contact your chosen host Node. Work together to create a Training Plan. Submit the official Application Form. B. You need help finding the right Node Fill out the request for form for the host-pairing service. We will connect you with a suitable host. Collaborate with the host to develop a Training Plan before applying. If you need assistance to be paired with a host, apply early! Late requests may not be accommodated before the deadline. If you are working at our Euro-BioImaging Node you should have received the link to the official application and our host-pairing submission forms. If you have any questions, please reach out to: info@eurobioimaging.eu The Job Shadowing initiative is made possible through EU funding as part of the EVOLVE project.", "headings": [ "Cross-Node Job Shadowing", "Benefits", "How does it work?", "Application Rounds", "Need help finding the right Node?", "Visit Duration", "How to apply?" ], "page_type": "training" }, { "id": "cf5eaec8", "url": "https://www.eurobioimaging.eu/contact-us/", "title": "Contact us - Euro-BioImaging", "description": "Contact info, virtual meetings, newsletter sign-up for bioimaging updates.", "documentation": "Contact us Any questions or comments about Euro-BioImaging, its services or this web portal? Use the form at the right or email us at: info@eurobioimaging.eu Postal Address: Euro-BioImaging ERIC P.O. Box 123, Tykistökatu 6 FI-20521, Turku, FINLAND Name E-mail Please leave this field empty. Subject Message I accept that my contact information will be stored for the purpose of contacting you within the scope of this request. More information can be found in our privacy policy . Join the Virtual Pub A weekly virtual meeting where the entire imaging community is invited to meet to discuss hot topics, showcase success stories, and explore new technologies. Register Sign up for our newsletter Sign up to get the latest news from the world of bioimaging right in your inbox, every two to three months. Sign up", "headings": [ "Contact us", "Join the Virtual Pub", "Sign up for our newsletter" ], "page_type": "contact" }, { "id": "c0c28a84", "url": "https://www.eurobioimaging.eu/training/euro-bioimaging-training-courses/", "title": "Euro-BioImaging Training Courses - Euro-BioImaging", "description": "Training for Node staff: skills, financial support, Train-the-Trainer course details.", "documentation": "Euro-BioImaging Training Courses In addition to promoting the excellent Training Courses offered by our Nodes, the EVOLVE project now allows us to directly provide Node staff with access to dedicated instruction and guidance to support them in their scientific activities as well as in the management and coordination of their Nodes. The Training Course pillar is made up of two branches: Euro-BioImaging Training Courses for the Professional Development of Node Staff. This structured approach is dedicated to comprehensive skill development tailored to the specific needs of facility staff. Support to attend course organized by our Nodes, and potentially those outside of the Euro-BioImaging community. Euro-BioImaging Training Courses These courses aim to satisfy the Training needs of Node staff, and consultations with them are currently ongoing. Announcements with specifics details of course titles and contents will be made in due course. The general areas that will be covered are: Technical, operational and management skills for imaging core facilities Image data management and analysis Provision of services and support to users Dimensions of gender and sex in research Support to attend externally organized courses Financial support to facilitate Node staff's attendance at Node courses is also to be provided. The aim is to allow access to the widest range of events to expand expertise and knowledge. Those interested are invited to check the Training opportunities offered by our Nodes before considering external courses. For information, please write to info@eurobioimaging.eu EVOLVE Train-the-Trainer course The Train-the-Trainer course is tailored specifically for imaging core facility staff working at Euro-BioImaging Nodes who are involved in user support, training, and course organization. This course is not about imaging techniques , but rather about how to teach them effectively . This program provides a comprehensive toolkit for developing and delivering impactful training sessions, user courses, and collaborative workshops. Location: Imaging Center, EMBL Heidelberg Dates: 20–24 October 2025 Format: On-site Eligibility: Node staff More information Euro-BioImaging Training Courses are made possible through EU funding as part of the EVOLVE project.", "headings": [ "Euro-BioImaging Training Courses", "Euro-BioImaging Training Courses", "Support to attend externally organized courses", "EVOLVE Train-the-Trainer course" ], "page_type": "training" }, { "id": "1fe54112", "url": "https://www.eurobioimaging.eu/special-edition-virtual-pubs/", "title": "Special Edition Virtual Pubs - Euro-BioImaging", "description": "Special Edition Virtual Pubs on imaging tech, applications in research, and collaboration opportunities.", "documentation": "Special Edition Virtual Pubs Several times a year, the Euro-BioImaging Hub team in collaboration with the Euro-BioImaging Industry Board or other partner organisation, organises a Special Edition Virtual Pub. These events feature short format talks from multiple speakers on specialised topics related to imaging technologies, image analysis, data management, or other themes. These events are recorded if possible and can be watched on Euro-BioImaging's YouTube channel. Please find below useful links to learn more about our Special Edition Virtual Pubs! Register In this Special Edition Virtual Pub, we focus on the role imaging tools play in research in Art and Archaeology . Join us to explore potential applications and a wide range of imaging technologies that can be used in these research areas. Programme In this Special Edition Virtual Pub, we explored new trends and novel model systems for biomedical research with colleagues from Infrafrontier ERIC, Euro-BioImaging Nodes and other experts. Programme Watch recordings In this Special Edition Virtual Pub, organised in collaboration with the Euro-BioImaging Industry Board, we discussed some of the issues that innovators should be aware of and heard use cases from our network about successful tech transfer and translation from the lab. Programme & Abstracts Watch recordings This Special Edition Virtual Pub event in collaboration with EBRAINS highlighted the expertise of selected Euro-BioImaging Nodes in the Neuroscience domain and explored the potential areas of collaboration with EBRAINS. Programme & Abstracts This Special Edition Virtual Pub “Open Hardware in Imaging,” organised in collaboration with the Euro-BioImaging Industry Board, featured presentations from scientists and companies who are committed to making imaging hardware and software solutions openly available to a wide audience. Programme & Abstracts Watch recordings This Special Edition Virtual Pub in collaboration with the ISIDORe project, highlighted the researchers' experience, science and preliminary findings in a number of biological or biomedical imaging projects on infectious diseases which were supported by our Euro-Bioimaging Nodes and the ISIDORe project . Programme From open and modular hardware framework for light microscopy to adapting legacy commercial microscope frames to new modalities in order to obtain super-resolution performance, the Special Edition Virtual Pub “Open Hardware in Microscopy” highlights these developments, by featuring presentations of a number of open hardware projects in light and electron microscopy. Programme & abstracts Watch recordings In 2022, we ran a two-part Special Edition of the Virtual Pub to cover the topic of “DATA” in Biological & Biomedical Imaging. Each event featured short presentations from academics and industry showcasing a range of image data management and analysis solutions for Biological & Biomedical imaging. Programme On 10th December 2021, Euro-BioImaging together with the Euro-BioImaging Industry Board organised a Special Edition of the Virtual Pub, focused on the theme of “COLD.” This event captures evoked a seasonal, celebratory spirit with exciting talks from our community. Programme This Special Edition Virtual Pub \"Speed in biological & biomedical imaging,\" organised in collaboration with the Euro-BioImaging Industry Board, included Flash presentations from academics and industry. From in vivo imaging to high-speed cameras and image compression, there was something for everyone and even a prize for the best flash talk. Programme", "headings": [ "Special Edition Virtual Pubs" ], "page_type": "homepage" }, { "id": "554ab121", "url": "https://www.eurobioimaging.eu/events/iscam-annual-meeting/", "title": "ISCaM Annual Meeting - Euro-BioImaging", "description": "ISCaM2025: July 2-4, 2025, Brussels; focus on tumor metabolism, networking, and presentations.", "documentation": "ISCaM Annual Meeting When July 2–4, 2025 Where Brussels, Belgium Following the success of the 11th Annual Meeting of the International Society for Cancer Metabolism (ISCaM) , which gathered more than 200 participants from all over the world, we are pleased to announce that the 12th edition will be held again at the BEL Congress Centre, in Brussels from July 2nd to 4th, 2025. The ISCaM2025 symposium ( www.iscam2025.org ) will bring together experts in the tumor metabolism field to discuss new concepts in the regulation and role of cancer metabolism in tumor growth, as well as strategies for targeting tumor metabolism for therapeutic benefit. A combination of basic, translational and clinical studies will be presented, with the goal of identifying promising avenues in tumor metabolism that impact our understanding, diagnosis and treatment of cancer. In addition to a stellar line-up of invited speakers, short talks and poster presentations will provide opportunities for researchers at all levels, with a special support for junior scientists, to discuss their most current work in this field. This meeting will represent an excellent opportunity to share knowledge and methodology in tumor metabolism research and to network in a collegial and social atmosphere, during the breaks, reception and conference dinner.", "headings": [ "ISCaM Annual Meeting", "When", "Where" ], "page_type": "homepage" }, { "id": "8da7c083", "url": "https://www.eurobioimaging.eu/data-services/community-services/", "title": "Community services - Euro-BioImaging", "description": "FAIR data services, technical support, training, tools, and community coordination.", "documentation": "Community services FAIR image data is a valuable resource for the scientific community. It not only ensures rigorous and reproducible science, but holds the potential to enable novel scientific discoveries and promote development of advanced analysis methods. At Euro-BioImaging, we support development of an ecosystem of FAIR bioimage data and tools. We provide coordination and policy support, as well as guidelines, tools, and direct support for producing FAIR image data and making it openly available. Our data services for the imaging community at large are supported by many data-centric European projects including those related to the European Open Science Cloud (EOSC). Representation in the European landscape Euro-BioImaging represents needs and interests of the image data community towards European funding and policy agencies through its membership in the EOSC-Association and its task forces. We also raise the visibility of image data research by participating in various cross-domain data projects. You can find more information about our involvement in various EU projects here . Coordination with community initiatives Community initiatives are responsible for a lot of valuable work around developing training materials and standards for data, metadata and tools. Euro-BioImaging serves as a central coordinating point, participating in various community initiatives and consolidating their efforts. Technical support Large and complex datasets require specialised solutions, including those supported by cloud resources, for efficient image data management and analysis. Euro-BioImaging, supported by European projects, provides technical solutions for cloud compatible image data formats and workflows for the global community. You can access out latest tools here. You can access out latest tools on GitHub . You can access our data workflows on WorkflowHub . FAIR Image Data Stewardship Euro-BioImaging promotes and facilitates the adoption of FAIR practices which get implemented at our Nodes and the Hub. We offer resources, training and 1-on-1 guidance to FAIRify user data in all stages of the data lifecycle – from project planning to data deposition and reuse.", "headings": [ "Community services", "Representation in the European landscape", "Coordination with community initiatives", "Technical support", "FAIR Image Data Stewardship" ], "page_type": "services" }, { "id": "56d1794d", "url": "https://www.eurobioimaging.eu/training/euro-bioimaging-training/", "title": "Training for Node Staff - Euro-BioImaging", "description": "Training for Node staff under EVOLVE project; focuses on skill development and service quality.", "documentation": "Training for Node Staff As part of the Horizon Europe project EVOLVE , the Training Program at Euro-BioImaging is geared towards providing training opportunities for Node staff, with the goal of supporting them in the provision of their high quality services to users, in the management and coordination of their facilities, and in their own skill and career development. Euro-BioImaging's Training Plan operates on three pillars: Training for Node staff is made possible by funding from the European Union as part of the EVOLVE project.", "headings": [ "Training for Node Staff" ], "page_type": "training" }, { "id": "ec39fc98", "url": "https://www.eurobioimaging.eu/our-events/user-forum/", "title": "User Forum - Euro-BioImaging", "description": "User Forum events on imaging in immunology, plant biology, and cardiovascular research.", "documentation": "User Forum Designed to highlight the importance of imaging to different research areas, the Euro-BioImaging User Forum takes place twice a year and brings together the imaging community - Euro-BioImaging Users and prospective users, our Nodes, Core facility staff, experts from different domains, technology developers and more. Everyone is welcome at these virtual events to learn more about the diverse applications of imaging. Audience: Our User Forum attracts researchers from both academia or industry, Master’s and PhD students, post-doctoral fellows, people interested in the diverse ways in which biological and biomedical image technologies, image data analysis & management solutions are used to address different research questions. In the past, our events have attracted attendees from 25+ countries around the world. Key figures 1,100+ Attendees to date 8 User Forum events 30+ Node & User presentations Past: The Euro-BioImaging User Forum “Focus on Immunology” took place on October 15, from 2-5 pm . The event explored how imaging can support immunology research and will feature keynote speakers as well as presentations from Euro-BioImaging Nodes & Users, covering both scientific & technical aspects of Immunology-focussed research projects. Learn more Recordings The Euro-BioImaging User Forum “Image Data” took place on Tuesday, March 26th, 2024 from 14:00-17:00 CET . This event highlighted innovative image analysis and image data management solutions at Euro-BioImaging Nodes. It featured user presentations as well as presentations from image data and image analysis experts from the Nodes, focusing on the technical aspects of the work. Learn more Recordings The Euro-BioImaging User Forum \"Understanding plant biology\" took place on Thursday, October 12, 2023, from 2 pm-5 pm CEST. This event highlighted how cutting-edge imaging technologies can support research into the structure and function of plants, shed light on plant health, resilience and adaptability, and help answer agroecology-related research questions. Specific expertise available at our Nodes across Europe was showcased through case studies presented in tandem with the research community. Learn more Recordings Euro-BioImaging’s fifth online User Forum took place on Tuesday, March 21, 2023, from 14:00-17:00 CET. The topic was “Cardiovascular research.” This event highlighted the importance of cutting-edge imaging technologies in support of cardiovascular health, disease, diagnostics and the development of therapies. We will showcase the specific expertise available at our Nodes across Europe through case studies presented in tandem with the research community. Learn more Recordings This event highlighted the importance of cutting-edge imaging technologies in support of pandemic preparedness, finding treatments and understanding the underlying biology of infectious agents. We showcased the specific expertise available at our Nodes across Europe through case studies presented in tandem with the research community. Learn more Highlights Recordings This event highlighted the importance of cutting-edge imaging technologies in support of brain research and showcase the specific expertise available at our Nodes across Europe through case studies presented in tandem with the research community. Learn more Highlights Recordings This event highlighted the importance of cutting-edge imaging technologies in support of cancer research and showcased the specific expertise available at our Nodes across Europe through case studies presented in tandem with the research community. Learn more Highlights Recordings This event highlighted the importance of cutting-edge imaging technologies in support of cancer research and showcased the specific expertise available at our 25 Nodes across Europe through case studies presented in tandem with the research community. Learn more Highlights", "headings": [ "User Forum", "Audience:", "Key figures", "Past:" ], "page_type": "homepage" }, { "id": "41a3855d", "url": "https://www.eurobioimaging.eu/eu-projects/", "title": "EU projects - Euro-BioImaging", "description": "Details on 12 EU projects enhancing imaging, AI, and data access in life sciences.", "documentation": "EU projects Euro-BioImaging is engaged in a large number of collaborative projects funded by the European Union under the Horizon Europe funding framework program. In these projects, we work together with other Research Infrastructures from the Life Sciences and beyond, as well as other partner organisations. The projects cover a wide range of topic areas - from facilitating and funding user access to Research Infrastructures to building digital spaces for FAIR life science data. Find out more about our different projects below. Euro-BioImaging's EU Project Timeline List of projects May 1, 2025–Apr 30, 2028 RE-IMAGINE-CROPS RE-IMAGINE-CROPS will develop the first multimodal imaging mobile device, enhancing agricultural sustainability and efficiency within crop management. Mar 1, 2025–Feb 29, 2028 RI-SCALE RI-SCALE aims to empower Research Infrastructures (RIs) with scalable AI-driven solutions and advanced data exploitation platforms, enhancing the accessibility, interoperability, and impact of research data across multiple scientific domains. Mar 1, 2025–Feb 28, 2027 OSCARS: FAIR Image Analysis Across Sciences The project will develop reusable image analysis workflows across disciplines (bioimaging, environmental sciences, and astrophysics). Oct 1, 2024–Apr 30, 2029 ILLUMINATE ILLUMINATE will provide the first clinical translation of MeMRI, with application to castrate resistant metastatic prostate cancer. Mar 1, 2024–Aug 31, 2027 EVOLVE EVOLVE aims to enhance Euro-BioImaging ERIC by strengthening its administration, upgrading the user access portal, and expanding its network of Nodes and Hubs. Jan 1, 2024–Jun 30, 2026 foundingGIDE foundingGIDE lays the foundation for a Global Image Data Ecosystem for sharing bioimage data. Sep 1, 2023–Aug 31, 2027 ERIC Forum 2 The ERIC Forum Implementation Project, now in its second edition, brings together the ERIC community to strengthen its coordination and enhance its collaborations. May 1, 2023–Apr 30, 2028 IMAGINE Supporting community adoption and validation of innovative tools for imaging across scales. Feb 1, 2023–Jan 31, 2028 IMPRESS Developing new tools and applications in Transmission Electron Microscopy and training. Jan 1, 2023–Dec 31, 2026 ANERIS Developing image analysis tools for underwater imaging and training. Jan 1, 2023–Dec 31, 2026 EUCAIM Deploying a digital federated infrastructure of FAIR cancer-research related images. Sep 1, 2022–Feb 28, 2025 EOSC4Cancer Providing a European-wide foundation to accelerate data-driven cancer research. Sep 1, 2022–Aug 31, 2025 canSERV Funding user access to imaging services in cancer research. Sep 1, 2022–Aug 31, 2027 AgroSERV Enhacing agroecology research by funding access to imaging services. Sep 1, 2022–Aug 31, 2025 AI4Life Developing advanced AI methods for image analysis and making them easily available to life scientists. Jun 1, 2022–Nov 30, 2024 eRImote Solutions for digital and remote service provision across research infrastructures. Feb 1, 2022–Jan 31, 2025 ISIDORe ISIDORe effectively supports research on infectious diseases and increases pandemic preparedness. Oct 1, 2021–Sep 30, 2024 BY-COVID BY-COVID tackles data challenges for effective pandemic response. Apr 1, 2021–Sep 30, 2023 EOSC Future EOSC Future builds on EOSC to deliver a durable platform for researchers. Mar 1, 2021–Nov 30, 2023 HealthyCloud Supplying image data and management tools for the health research and innovation cloud. Mar 1, 2019–Aug 31, 2023 EOSC-Life Building cloud-based tools and solutions for bioimaging data and promoting interoperability. Jan 1, 2019–Dec 31, 2022 ERIC Forum The ERIC Forum advances operations of ERICs and contributes to the development of ERIC-related policies. CORBEL CORBEL facilitated access to multiple research infrastructures to support advanced interdisciplinary research.", "headings": [ "EU projects", "Euro-BioImaging's EU Project Timeline", "List of projects", "RE-IMAGINE-CROPS", "RI-SCALE", "OSCARS: FAIR Image Analysis Across Sciences", "ILLUMINATE", "EVOLVE", "foundingGIDE", "ERIC Forum 2", "IMAGINE", "IMPRESS", "ANERIS", "EUCAIM", "EOSC4Cancer", "canSERV", "AgroSERV", "AI4Life", "eRImote", "ISIDORe", "BY-COVID", "EOSC Future", "HealthyCloud", "EOSC-Life", "ERIC Forum", "CORBEL" ], "page_type": "homepage" }, { "id": "f59cac35", "url": "https://www.eurobioimaging.eu/upcoming-events/", "title": "Upcoming events - Euro-BioImaging", "description": "Events: Training, meetings, virtual pubs on imaging, cancer metabolism, and more.", "documentation": "Upcoming events All events Image Data User Forum Meeting Training Virtual Pub Tech Exchange EBIB events July 2025 Jul 2 2025 July 2–4, 2025 Meeting ISCaM Annual Meeting Brussels, Belgium Jul 2 2025 July 2–4, 2025 Meeting PET is Wonderful Edinburgh, United Kingdom Jul 5 2025 July 5–9, 2025 Meeting FEBS Congress 2025 Istanbul, Turkey August 2025 Aug 17 2025 August 17–22, 2025 Meeting International Congress of Immunology Vienna, Austria Aug 19 2025 August 19–22, 2025 Meeting BNMI 2025 Symposium Gothenburg September 2025 Sep 5 2025 September 5, 2025 13:00–14:00 CEST Virtual Pub Metabolic MR Imaging in an experimental and clinical setting online Rene' In't Zandt, Lund University Sep 8 2025 September 8–12, 2025 Training Advanced Course on Preclinical Imaging Prague and Brno Sep 12 2025 September 12, 2025 13:00–14:00 CEST Virtual Pub Title TBD online TBD Sep 19 2025 September 19, 2025 13:00–14:00 CEST Virtual Pub Cancer Metabolism Series with ISCaM The ironic role of iron in acute myeloid leukemia: from disease mechanisms to therapy online Delfim Duarte, i3s, University of Porto Sep 26 2025 September 26, 2025 13:00–14:00 CEST Virtual Pub Correlated Imaging Series Correlated Imaging Series with COMULIS Title TBD online TBD October 2025 Oct 3 2025 October 3, 2025 13:00–14:00 CEST Virtual Pub Title TBD Online Adam Istvan Horvath, Eötvös Loránd University Oct 10 2025 October 10, 2025 13:00–14:00 CEST Virtual Pub Shining light on tissue mechanics with subcellular resolution using Brillouin microscopy online Luis Alonso Baez, Norwegian University of Science & Technology Oct 17 2025 October 17, 2025 09:00–October 18, 2025 13:00 CEST foundingGIDE Community Event 2025 Brisbane, Australia Oct 17 2025 October 17, 2025 13:00–15:00 CEST Virtual Pub Special Edition Special Edition Virtual Pub on Food Science Online Multiple speakers Oct 20 2025 October 20, 2025 09:00–October 24, 2025 16:00 CEST Training EVOLVE EVOLVE Train-the-Trainer course Imaging Center, EMBL Heidelberg Oct 24 2025 October 24, 2025 13:00–14:00 CEST Virtual Pub Exploring super-resolution imaging (Title TBC) online Ilaria Testa, SciLifeLab All events", "headings": [ "Upcoming events", "ISCaM Annual Meeting", "PET is Wonderful", "FEBS Congress 2025", "International Congress of Immunology", "BNMI 2025 Symposium", "Metabolic MR Imaging in an experimental and clinical setting", "Advanced Course on Preclinical Imaging", "Title TBD", "The ironic role of iron in acute myeloid leukemia: from disease mechanisms to therapy", "Title TBD", "Title TBD", "Shining light on tissue mechanics with subcellular resolution using Brillouin microscopy", "foundingGIDE Community Event 2025", "Special Edition Virtual Pub on Food Science", "EVOLVE Train-the-Trainer course", "Exploring super-resolution imaging (Title TBC)" ], "page_type": "homepage" }, { "id": "a0f8dc59", "url": "https://www.eurobioimaging.eu/evolve/evolve-news/", "title": "EVOLVE News - Euro-BioImaging", "description": "News on training, job openings, mentoring masterclasses, and Node participation calls.", "documentation": "EVOLVE News Learn more about the what's going on in the EVOLVE project by Euro-BioImaging. EVOLVE News June 18, 2025 Euro-BioImaging at TiM2025: Sharing Knowledge and Celebrating Open Data This spring, three members of the Euro-BioImaging Hub team participated in the Trends in Microscopy 2025 (TiM2025) conference, held from March 17–21 in Münsingen,… June 18, 2025 Euro-BioImaging Hiring: Communications Officer Location: Turku, Finland (Euro-BioImaging ERIC Statutory Seat)Full-time position | Fixed term until 31 August 2027 | Starting salary: €3,200–€4,200/month Join a cutting-edge European research… June 4, 2025 EVOLVE call supporting Node participation in conferences targeting new user groups is now open We are thrilled to announce that Euro-BioImaging opened the EVOLVE call for Node participation in conferences targeting new user groups. This initiative is intended… May 19, 2025 EVOLVE Mentoring Masterclass: Insights from Daphna Link-Sourani In the latest edition of Euro-BioImaging’s EVOLVE Mentoring Masterclass series, Dr. Daphna Link-Sourani brought a wealth of experience, insight, and authenticity to a powerful… May 14, 2025 Register for the EVOLVE Train-the-Trainer course! We are excited to announce a new Train-the-Trainer course tailored specifically for imaging core facility staff working at Euro-BioImaging Nodes who are involved in… April 17, 2025 Ilaria Testa lights up EVOLVE Mentoring Masterclass on interdisciplinary science, SMART microscopy and team building In a compelling EVOLVE Mentoring Masterclass hosted by Euro-BioImaging, Professor Ilaria Testa offered a multifaceted look into her scientific journey, from her interdisciplinary path… April 4, 2025 Warm welcome to Euro-BioImaging's new Scientific Ambassadors In early 2024 the first cohort of Euro-BioImaging Scientific Ambassadors was onboarded. Twelve highly enthusiastic researchers were chosen to represent Euro-BioImaging and raise awareness… March 24, 2025 Second call for our EVOLVE Job Shadowing Program Now Open! Are you a Euro-BioImaging Node staff member eager to broaden your professional horizons, exchange innovative ideas, and enhance your expertise? The second call for… March 14, 2025 Peter O'Toole Leads Inspiring EVOLVE Mentoring Masterclass on Imaging Core Facility Leadership The EVOLVE Team2025 Mentoring Masterclass series kicked off with an engaging session featuring Peter O’Toole, President of the Royal Microscopical Society and Director of… This work is made possible by funding from the European Union as part of the EVOLVE project.", "headings": [ "EVOLVE News", "EVOLVE News", "Euro-BioImaging at TiM2025: Sharing Knowledge and Celebrating Open Data", "Euro-BioImaging Hiring: Communications Officer", "EVOLVE call supporting Node participation in conferences targeting new user groups is now open", "EVOLVE Mentoring Masterclass: Insights from Daphna Link-Sourani", "Register for the EVOLVE Train-the-Trainer course!", "Ilaria Testa lights up EVOLVE Mentoring Masterclass on interdisciplinary science, SMART microscopy and team building", "Warm welcome to Euro-BioImaging's new Scientific Ambassadors", "Second call for our EVOLVE Job Shadowing Program Now Open!", "Peter O'Toole Leads Inspiring EVOLVE Mentoring Masterclass on Imaging Core Facility Leadership" ], "page_type": "news" }, { "id": "1d6a8109", "url": "https://www.eurobioimaging.eu/who-we-are/strategic-goals/", "title": "Strategic Goals - Euro-BioImaging", "description": "Strategic goals for 2024-2028: imaging services, FAIR data, training, stakeholder engagement.", "documentation": "Strategic Goals With its Strategic Plan for 2024-2028, Euro-BioImaging enters a new phase of its development, aiming to significantly influence the future of imaging and facilitate access to imaging technology, data and expertise. Over the past four years, Euro-BioImaging has made significant progress towards building an internationally recognised, pre-eminent, open-access imaging research infrastructure. This 2024–2028 strategic plan outlines the vision for the continued contributions of Euro-BioImaging to the life sciences through six strategic goals and their planned implementation. This page provides an overview of Euro-BioImaging's six strategic goals for 2024-2028. The entire Strategic Plan can be downloaded here , and the summary can be downloaded here . Below, you can access the embedded version of the entire Strategic Plan. Euro-BioImaging Strategic Plan Strategic goal 1: Provide cutting-edge imaging services, contribute to scientific excellence and promote Open Science > Our aim To be increasingly attractive to users, Euro-BioImaging aims to ensure the competitiveness of its imaging technology portfolio and will continue to adapt its services regularly to evaluate and adapt its services regularly based on user feedback, research into advanced imaging technologies, and data processing and analysis. The approach to meeting this first strategic goal is divided into three essential tasks: Advancing the services at Euro-BioImaging by continually including innovative imaging technologies Providing FAIR image data services Offering a broad training portfolio for users and staff > How do we plan to achieve it? Euro-BioImaging's readiness relies on its capacity to adapt and update its portfolio of services and technologies to upcoming scientific needs. We plan to continuously assess upcoming innovations, technologies, and methods that fit the needs of our Nodes and user communities. The feedback loops we have built during the last three years will be determinant in adopting innovations and quickly filtering out non-anymore-relevant technologies or methods. On the data front, we will reinforce and scale up Euro-BioImaging capabilities to meet the upcoming growth in image data generation and storage and support our stakeholder's needs. We will maintain the high-quality service we have been providing since the creation of the infrastructure while establishing new guidelines, knowledge transfer, stewardship and processes to support FAIRness, enhance FAIRification of our data, and increase expertise among our staff, our Nodes and the imaging community. We will continue developing our efforts towards cloud-compatible and machine-ready data formats to match ever-growing imaging data needs. Our position as a European Landmark research infrastructure gives us the unique capacity to connect and interact with various stakeholders. Our Nodes and existing communities are fundamental to us: we aim to strengthen our relations with these two critical groups through dedicated events, projects and initiatives and reinforce bidirectional collaboration. We will also increase contact points with our Nodes to enhance dialogue, feedback, and interaction by implementing new expert groups to increase user access. We want these efforts to generate benefits and increase funding opportunities for the Nodes and Euro-BioImaging. Relying on our central position as an imaging research infrastructure, we also aim to widen our community of users by offering remote access tailored to cover the unmatched needs of the European Research Area. We plan to boost our staff skills and knowledge to support our Nodes and users better. Through managerial and technical support training, we aim to continually update our knowledge on crucial issues related to topics as diverse as governance or AI. We strive to launch and coordinate a modular system of advanced, feedback-based training and a coordinated career path to ensure that core facility staff can advance their knowledge and careers. In addition, we will establish a job-shadowing programme across Nodes in Europe and beyond to increase capacity in facility management and operations. Strategic goal 2: Engage with national and international stakeholder networks and increase synergy with other research infrastructures > Our aim Maintaining, strengthening, and enlarging our stakeholder network is fundamental to Euro-BioImaging's success. As a pan-European research infrastructure, international collaboration and partnerships to advance the field of biological and biomedical imaging are paramount. > How we plan to achieve it Euro-BioImaging will continue to build solid and sustainable partnerships with existing member states and funding agencies and engage with key stakeholders to secure the infrastructure's long-term development and growth. We are in dialogue with potential new members, especially countries in the European widening area. Through dedicated outreach channels, we aim to better engage with th", "headings": [ "Strategic Goals" ], "page_type": "homepage" }, { "id": "d86b29a7", "url": "https://www.eurobioimaging.eu/who-we-are/governance/", "title": "Governance - Euro-BioImaging", "description": "Governance structure, 41 Nodes, 192 imaging facilities, contact for membership queries.", "documentation": "Governance Euro-BioImaging ERIC operates through the dedicated efforts of a diverse group of stakeholders spanning multiple countries, actively engaged in guiding, deciding, and advising on our daily operations. Explore below to learn more about our Operational Structure , Governing Bodies , and Advisory Bodies . Operational Structure Hubs The coordination of Euro-BioImaging is divided into a tripartite Hub: the Statutory Seat in Turku, Finland, a community-specific Bio-Hub for biological imaging at EMBL in Heidelberg, and a community-specific Med-Hub for biomedical imaging in Torino, Italy. The tripartite Hub jointly provides general supporting services, including the management of user access, policy and lobbying, community and skill-building activities, and services for image data. Member States Euro-BioImaging comprises 18 Member states and the EMBL. Countries are continuously invited to consider supporting and becoming members of Euro-BioImaging ERIC, and if you have questions about this, please feel free to contact us directly. Countries can join the ERIC in an observing role first if they prefer to. You can find a list of our member states here . Nodes Our distributed infrastructure is built on existing national and international facilities of excellence in imaging technologies. These facilities are bundled into collections called Nodes. Member countries host either a single or several Nodes. You can find a comprehensive list of our 41 Nodes here . Facilities The Nodes provide access to 192 specialised imaging facilities located in Europe and beyond. These facilities provide physical or remote access to imaging technologies, deliver training, and, with their experienced staff, support users at all stages of their research projects. You can find a list of the current facilities accessible through our infrastructure here. Governing Bodies Euro-BioImaging Board The Euro-BioImaging Board is the principal governing body of Euro-BioImaging ERIC, approving all strategic and financial decisions in addition to overseeing the performance of the Hub and Nodes with input from the Scientific Advisory Board and the Hub Directorate. It is composed of representatives of Member and Observer countries, where only the former have the right to vote. Directorate The Euro-BioImaging Tripartite Hub is managed by a Directorate consisting of a Director-General, who is the legal representative of Euro-BioImaging ERIC at the Statutory Seat, a Section Director of the Bio-Hub and a Section Director of the Med-Hub. John Eriksson is the Director General based at the Statutory Seat in Turku, Finland. Antje Keppler is the Section Director of the Bio-Hub, based at the EMBL in Heidelberg, Germany. Linda Chaabane is the Section Director of the Med-Hub, based in Turin, Italy. Our Directorate promotes the research infrastructure at a national and international level. The Director General is responsible for the day-to-day management and coordination of Euro-BioImaging ERIC in collaboration with the Section Directors. The Section Directors represent the interests of biological and biomedical communities, respectively. Advisory Bodies Scientific Advisory Board (SAB) Chair: Ian Smith , Emeritus Professor, Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne, Australia The 12 members of the SAB oversee the scientific, ethical, technical, and management quality of Euro-BioImaging ERIC activities. The SAB members are highly qualified, internationally recognised scientists and ethical experts chosen based on their competencies by the Directorate, in consultation with Euro-BioImaging Members, and appointed by the Euro-BioImaging Board. Panel of Nodes (PoN) Chair: Sebastian Munch , VIB Technologies, VIB, Ass. Prof. Department of Neuroscience KU Leuven, & spokesperson Flanders BioImaging Vice-Chair: Ilva van Houwelingen , Process Coordinator Imaging Office, Department of Radiology & Nuclear Medicine, Erasmus University Medical Center Rotterdam The Euro-BioImaging Panel of Nodes comprises an official representative of each of the Euro-BioImaging Nodes. The Euro-BioImaging Panel of Nodes is constituted to provide advice to the Directorate concerning Euro-BioImaging ERIC activities, especially all matters related to service delivery at the Nodes, such as physical user access, training activities, testing new imaging technologies, image data management, and Euro-BioImaging Hub activities and services supporting Nodes in their role as access providers. To do so, the Panel of Node Co-Chairs, Marc van Zandvoort and Julia Fernandez-Rodriguez hold monthly meetings with the Euro-BioImaging Directorate. Euro-BioImaging Industry Board Advisory Panel The Euro-BioImaging Industry Board (EBIB) Advisory Panel constitutes an Advisory Body to the Euro-BioImaging Directorate. Its primary function is to provide expert, strategic advice from an industry point of view on issues such as its Strategic Plan, service and technology priorities, colla", "headings": [ "Governance", "Hubs", "Member States", "Nodes", "Facilities", "Euro-BioImaging Board", "Directorate", "Scientific Advisory Board (SAB)", "Panel of Nodes (PoN)", "Euro-BioImaging Industry Board Advisory Panel" ], "page_type": "homepage" }, { "id": "0b3d4d4a", "url": "https://www.eurobioimaging.eu/sponsorship/", "title": "Sponsorship Programme - Euro-BioImaging", "description": "Sponsorship for events enhancing biomedical imaging; application link included.", "documentation": "Sponsorship Programme Euro-BioImaging is proud to support events that advance imaging by fostering collaboration across disciplines, encouraging scientific exchanges and engaging the community in meaningful dialogue. Through our Sponsorship Programme, we aim to support and empower organisers of conferences, workshops, and educational activities that align with our mission across Europe and beyond. The Sponsorship Programme is open to any legal entity worldwide. It focuses on supporting events that improve biological or biomedical imaging awareness, support the diffusion and circulation of biological or biomedical imaging knowledge, contribute to building biological or biomedical imaging communities, or enhance biological or biomedical imaging impact. If your event aligns with the above criteria, we invite you to submit a request by clicking on the link below. Please note that Euro-BioImaging evaluates sponsorship applications at its discretion, and all decisions are final and not subject to discussion. Access the sponsorship request form (please note once again that requests from individuals will not be granted): https://forms.gle/fUTdMEuV3EzPMaTY6", "headings": [ "Sponsorship Programme" ], "page_type": "homepage" }, { "id": "d31aa4c2", "url": "https://www.eurobioimaging.eu/documents/", "title": "Documents - Euro-BioImaging", "description": "Access annual reports, equality plan, statutes, strategic plan, and policies.", "documentation": "Documents On this page, you will find documents related to Euro-BioImaging governance, such as our Annual Reports, Equality Plan, Status and more. You can access the material needed for outreach in the box on the right: our logos, style tile and brochure. The documents are in alphabetical order. If you need something that you cannot find here, send a message to communications@eurobioimaging.eu Annual Reports All our annual reports are all in one place! You can access the 2020 , 2021 , 2022 , and 2023 annual reports. Equality Plan The Euro-BioImaging Equality Plan, released in September 2022, fosters diversity and equality within the organisation. It aims to create a safe, healthy, inclusive workplace culture through open communication, training, and regular audits. You can access the Euro-BioImaging Equality Plan here . List of Nodes All the Euro-BioImaging Nodes at one glance! Access the list here . Statutes Read or download the Statutes of the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences. Access the integral document here . Strategic Plan In the next four years, Euro-BioImaging and its community will embark on a new development phase for a critical mission: shaping the future of imaging in Europe. Read all the details in the Euro-BioImaging Strategic Plan. Access the full version here and the summary here . Terms and Conditions + General Policies Access our policies below: Terms and Conditions of our services here . Terms and Conditions of our events here . Privacy Policy here . User Access Policy here . ELSI Policy here . Personal Data Policy here .", "headings": [ "Documents" ], "page_type": "homepage" }, { "id": "b6dde532", "url": "https://www.eurobioimaging.eu/frequently-asked-questions/", "title": "FAQ - Euro-BioImaging", "description": "Access imaging technologies, training, proposal submission, contact info for assistance.", "documentation": "FAQ Regarding Usage Why should I use Euro-BioImaging? You get quality-controlled, validated services that significantly improve your chances of getting high-quality, reliable research data successfully and cost-effectively. You get expert help at every step of the way, we process applications quickly and do everything we can to make sure your imaging needs will be met - it's in our interest as much as yours, because we are here to serve the life science research community, not to make profit. Through Euro-BioImaging you are able to access numerous imaging technologies and other services that you might not easily find otherwise. The image data and metadata acquired during User access at a Euro-BioImaging Node belong to the User. We also constantly collect feedback and improve our services, and update the technologies we focus on. Having your imaging done as a Euro-BioImaging project can also aid you in funding acquisition and publishing. Finally, nearly all our users have been very happy with the services they have received, and have reported them to have concretely benefited their work. How do I apply to Euro-BioImaging? That depends on what services you want to use. If you wish to obtain access to imaging technologies, click on the “Technologies” tab, choose the service(s) you are interested in and submit a proposal. See here for more information. If you wish to apply for training, click on the “Training” tab to learn more. Use of general Euro-BioImaging data services does not require applying, but if you wish to get your data, analysis tool or workflow included in these services, you need to contact us first. Click on the “Data” tab to learn more. Please remember that after using Euro-BioImaging services, you may be required to submit feedback, such as always after accessing imaging technologies. What do I do if I do not know the most suitable imaging technology for my project? You can either contact us beforehand at info@eurobioimaging.eu , and we can help you identify the suitable technology, and/or you can submit a technology access proposal without specifying any technology (in the “Technologies” tab, click “Others” and then choose “Unknown service/technology”, and then proceed to submit your proposal). We will then identify a suitable technology for you when processing your application. I am not working in a Euro-BioImaging member country. Can I still apply? Yes. Anyone is welcome to apply to use Euro-BioImaging services. How do I acknowledge Euro-BioImaging? To ensure that Euro-BioImaging can continue to stay in operation, please credit us in any work that includes data and results obtained with Euro-BioImaging services. To do so, please properly cite us or include a sentence similar to the following in any publication, thesis, presentation or poster. \"The authors acknowledge Euro-BioImaging ERIC ( https://ror.org/05d78xc36 ) for providing access to imaging technologies and services via the -Node in , ( – if available ).\" Please also remember to report to us any publications or other significant outputs (e.g. patent, software release, technology transfer) to which Euro-BioImaging technology access, services or training contributed using our output reporting form . Thank you for helping to demonstrate the value of Euro-BioImaging in this way! Regarding Funding Are there any funding opportunities for user access? Check here for possible funding opportunities. Regarding Membership Is my country a member in Euro-BioImaging ERIC? You can check on the “About us” tab. There, under “Who We Are” you will find a map that shows all the current members. The map may also indicate countries which are in the process of becoming members, but have not yet completed the process, shown as Observer countries. How can my facility participate in Euro-BioImaging? First your country needs to be a member of Euro-BioImaging. See the map in “Who We Are” (under the “About us” tab) to see if it is. If it is, contact us at info@eurobioimaging.eu and we will tell you more about how your facility can join. If your country is not a member, you need to convince your government to join. We can help with that as well, contact info@eurobioimaging.eu for more information. Regarding Services Does Euro-BioImaging offer training courses on imaging technologies? Yes. Click on the “Training” tab to see a list of available courses. Note, however, that Euro-BioImaging training activities are still under development, and a full training module will become available on this portal later on. Note also that if you visit a Node to access imaging technologies, the Node will provide you with the necessary training to use the said technologies Can Euro-BioImaging help me with my image data? Yes. The Node that you conducted your experiment at will help you with the image data acquired there. If you haven’t acquired your data at any Node, you can still contact us at info@eurobioimaging.eu and we can see what we can d", "headings": [ "FAQ", "Regarding Usage", "Regarding Funding", "Regarding Membership", "Regarding Services", "Regarding Errors" ], "page_type": "homepage" }, { "id": "3d22f118", "url": "https://www.eurobioimaging.eu/who-we-are/", "title": "Who are we? - Euro-BioImaging", "description": "Access cutting-edge imaging services, training, and support across Europe.", "documentation": "Who are we? Enabling science & innovation through imaging Euro-BioImaging is a state-of-the-art research infrastructure established in November 2019 to provide world-class biological and biomedical imaging services to life science researchers across Europe. Its primary objective is to enable groundbreaking research and drive technological advancements that will significantly influence the future of imaging. Euro-BioImaging is crucial in promoting Open Science and contributing to scientific excellence by providing cutting-edge imaging services. For researchers, innovators, industry partners, and European stakeholders in life sciences, biomedicine, and beyond, Euro-BioImaging offers unparalleled access to an extensive array of cutting-edge imaging technologies, expertise, dedicated training programs, data services, innovation support, and industrial collaboration across Europe. Euro-BioImaging provides a centralized, coordinated infrastructure that significantly enhances research capabilities, supports innovation, accelerates scientific discovery, and builds proficiency in imaging technologies and sophisticated data management. Importantly, Euro-BioImaging boosts community networking, expert training, dynamic industry collaboration, and strategic stakeholder engagement. Through Euro-BioImaging, life scientists can access state-of-the-art imaging instruments, expertise, training opportunities and data management services. All scientists, regardless of their affiliation, area of expertise or field of activity, can benefit from these pan-European open-access services, which are provided with high-quality standards by leading imaging centres. Euro-BioImaging was awarded landmark status by ESFRI in 2018 and was established as an ERIC at the end of 2019. A fully distributed infrastructure Euro-BioImaging is a fully distributed infrastructure managed by a Hub . The Hub is divided into three activity-based sections: the Seat , located in Turku (Finland) and headed by John Eriksson , Director General; the Bio-Hub , located at the EMBL in Heidelberg (Germany) and headed by Antje Keppler , Section Director of the Bio-Hub; the Med-Hub , located in Turin (Italy) and headed by Linda Chaabane , Section Director of the Med-Hub. The Hub Sections work together to promote Euro-BioImaging at a national and international level, prepare the Euro-BioImaging ERIC tasks and implement common strategic goals. The Bio-Hub represents the interests of the biological imaging community within Euro-BioImaging, while the Med-Hub represents the interests of the biomedical imaging community. The distributed Euro-BioImaging infrastructure builds on existing national and international facilities of excellence in imaging technologies: the Euro-BioImaging Nodes . The Nodes provide physical or remote access to imaging technologies across 237 imaging facilities in 18 countries and the EMBL. In addition to access, the Nodes deliver training and support to users at all stages of their research projects. Euro-BioImaging members are shown in green. The three Hub hosts (Finland, EMBL and Italy) are outlined in dark green.", "headings": [ "Who are we?" ], "page_type": "homepage" }, { "id": "70d0fdd6", "url": "https://www.eurobioimaging.eu/our-nodes/", "title": "Our Node list per member state - Euro-BioImaging", "description": "41 renowned imaging nodes across Europe with diverse services and training opportunities.", "documentation": "Our Nodes Most Euro-BioImaging services are provided by 41 Euro-BioImaging Nodes , which are internationally renowned imaging facilities in the member countries. To become a Euro-BioImaging Node, facilities go through a rigorous application and review process in the Call for Nodes. They are evaluated by our Scientific Advisory Board on a wide variety of factors, including: Scientific and technical excellence European and national significance Technology maintenance and updates Access and service package Quality assurance User training Other technology-specific factors Following successful evaluation and approval by the Board, the Nodes join the Euro-BioImaging family by signing service level agreements that outline the services to Euro-BioImaging users. In addition to supporting user projects, our Nodes are active in European-funded research projects, support and develop technological breakthroughs, organise outstanding training courses and conferences, and make science accessible to the public through their outreach efforts. Discover the current list of the Nodes categorised by member state below. Our Nodes can also be searched and accessed via the Technologies tab on the Euro-BioImaging Access Portal . Austria Austrian BioImaging Node/CMI Belgium Flanders BioImaging Node Bulgaria Sofia BioImaging Node - Advanced Light Microscopy Node Czechia Advanced Light and Electron Microscopy Node Prague Multimodal Imaging Node Brno Center for Advanced Preclinical Imaging (CAPI) Denmark Danish BioImaging Node EMBL Euro-BioImaging EMBL-Node Finland Finnish Advanced Microscopy Node Finnish Biomedical Imaging Node France French BioImaging Node Hungary Cellular Imaging Hungary Medical and Preclinical Imaging Hungary Israel Israel BioImaging Italy Advanced Light Microscopy Italian Node Molecular Imaging Italian Node Phase Contrast Imaging Flagship Node Trieste Digital Imaging Multimodal Platform Neuromed - DIMP NEUROMED Netherlands Correlative Light Microscopy Dutch Flagship Node Dutch High Field Imaging Hub Erasmus MC OIC - Advanced Light Microscopy Rotterdam Node Facility of Multimodal Imaging - AMMI Maastricht High Throughput Microscopy Dutch Flagship Node Preclinical Imaging Centre (PRIME) - Molecular Imaging Dutch Node Population Imaging Flagship Node Rotterdam The Van Leeuwenhoek Center for Advanced Microscopy (LCAM) - Functional Imaging Flagship Node Amsterdam Wageningen Imaging and Spectroscopy Hub (WISH) - ALM and Molecular Imaging Node Wageningen Challenges Framework Flagship Node Norway NorMIC Oslo - Advanced Light Microscopy Node Oslo NORMOLIM - Norwegian Molecular Imaging Infrastructure Poland Advanced Light Microscopy Node Poland Portugal Brain Imaging Network (BIN) Portuguese Platform of BioImaging (PPBI) Slovenia SiMBION Node Spain Barcelona Live and Intravital Barcelona Mesoscopic Imaging Node Barcelona Super-Resolution Light and Nanoscopy Node Radiology and Medical Imaging Valencia Advanced Light Microscopy Node Bilbao (ALM@BIO) Sweden Swedish National Microscopy Infrastructure (NMI) United Kingdom The UK Node", "headings": [ "Our Nodes" ], "page_type": "nodes" }, { "id": "ce0faa17", "url": "https://www.eurobioimaging.eu/training/from-our-nodes/", "title": "From our Nodes - Euro-BioImaging", "description": "Training in imaging tech, sample prep, data analysis; courses taught in English, remote options.", "documentation": "From our Nodes With the advances in imaging technology, more and more new technologies are available to users, making training in the correct use of the technologies and the connected sample preparation and data analysis crucial. The Euro-BioImaging Nodes offer a wide range of training opportunities. Training opportunities at Euro-BioImaging Nodes cover the full spectrum of technologies available from biological to biomedical imaging as well as sample preparation and handling, and image data analysis. Some courses are taught remotely and virtually, increasing their accessibility. As a general rule, the courses combine theory and hands on learning. The training courses at the Euro-Bioimaging Nodes are: Available for users, students and facility staff Taught in English Open for anyone to apply to Training at Euro-BioImaging Nodes Below is a curated list of training courses available at Euro-BioImaging Nodes. If you would like to see a list of all of the training courses and events in the database powered by MicroscopyDB , please visit the From our partners page. If you have events, tools, training/education resources, or jobs to share, please add them to the relevant MicroscopyDB databases . (“$” associated with a registration fee)", "headings": [ "From our Nodes", "The training courses at the Euro-Bioimaging Nodes are:", "Training at Euro-BioImaging Nodes" ], "page_type": "training" }, { "id": "7006b8fe", "url": "https://www.eurobioimaging.eu/the4seasons/", "title": "The Four Seasons of the Invisible - Euro-BioImaging", "description": "Imaging contest details: eligibility, submission rules, quarterly sessions, prizes up to €1000.", "documentation": "The Four Seasons of the Invisible Participate in the Four Seasons of the Invisible, Euro-BioImaging’s first imaging contest! Join us to celebrate the four seasons seen through the prism of imaging devices: electron micrographs of flu virus or changes in chloroplast structure in decaying leaves for autumn , ice crystal images or brown fat depletion during hibernation for winter , microscopic pollen tubes or CT images of lungs affected by hay fever for spring, and plankton blooms or heat shock proteins for summer , and much more!  Only your imagination is the limit. Who can participate? This image contest is open to all members of the Euro-BioImaging Community and beyond. Any imaging scientist involved in scientific imaging and research fields worldwide. The contest has four quarterly sessions, each corresponding to a season. The dates for each session are indicated below. Register, fill out the form and upload your entries! You can submit as many entries as you want per season. All scientific imaging techniques and research fields are welcome. To qualify for the contest, submitted images must be captured using a microscope or another imaging device. Macrophotography is not allowed. Individual images or image stacks (of spatial, temporal, or higher dimensionality) can be submitted and must follow the technical requirements below. What can I win? At the end of each seasonal session, a panel chooses one quarterly winner and one runner-up. Quarterly winners get their travel expenses reimbursed for the next science conference or event they attend up to the limit of 1000€ (upon presentation of expense receipts). Quarterly runner-ups get their travel expenses reimbursed for the next science conference or event they attend up to the limit of 500€ (upon presentation of expense receipts). The selected images will be published on the Euro-BioImaging website and on the organization’s social media channels. Image requirements Each entry must include: A descriptive title. A narrative explanation of how the image aligns with the seasonal theme. Technical details and appropriate metadata regarding the imaging technology utilised and the sample; including magnification, imaging method, sample description, stains, labels, tracers etc. The entrants title, first name, and last name. Affiliation details (e.g., research institution, Euro-BioImaging Node). Acknowledgements, if applicable (e.g., funding sources, collaborators). All submitted images must follow the following technical specifications: Still images: Resolution not exceeding 1500 pixels in width; JPEG format. Videos: Resolution not exceeding 720 pixels in width; MP4 format. Contest timeline Spring Session: 31 March – 20 June 2025 Summer Session: 21 June – 21 September 2025 Autumn Session: 22 September – 20 December 2025 Winter Session: 21 December 2025 – 20 March 2026 Detailed rules can be found here . The Four Seasons of the Invisible / Spring 2025 Submissions for this contest have now closed. You can submit your entry below. Please read carefully the contest rules here . We remind you that if your entry is a still image, it should be 1500 px wide at the maximum in JPEG format. Moving images should be 720 px wide at the maximum in MP4. Good luck!", "headings": [ "The Four Seasons of the Invisible", "The Four Seasons of the Invisible / Spring 2025" ], "page_type": "homepage" }, { "id": "b2a39ac1", "url": "https://www.eurobioimaging.eu/evolve/evolve-job-shadowing-series/", "title": "EVOLVE Job Shadowing series - Euro-BioImaging", "description": "Job shadowing insights, Node collaborations, imaging advancements, and unique experiences shared.", "documentation": "EVOLVE Job Shadowing series What an exciting and rewarding journey it has been to follow the visits of our Job Shadowing Fellows from the first 2024 call of the Euro-BioImaging Job Shadowing Program! While many fellows are still in the midst of their visits—or eagerly anticipating theirs—we’re delighted to share some truly inspiring stories with our community. Through our EVOLVE Job Shadowing Series , we highlight the voices of both our talented fellows and hosts. From implementing cutting-edge image analysis pipelines to exploring the latest advancements in imaging technologies and facility management, this series showcases some inspiring stories. Stay tuned for more—you won’t want to miss it! March 12, 2025 EVOLVE Job Shadowing Series: Paula Jiménez Gómez visits the DIMP NEUROMED - Leadership & Exploring the challenges of Project Coordination The EVOLVE Job Shadowing program is a fantastic opportunity for Node staff to immerse in the daily life and operations of other Nodes of… March 12, 2025 EVOLVE Job Shadowing Series: Mahlet Birhanu on her visit to the Radiology and Medical Imaging Valencia Node - Job roles, Health data management tools, and seeing your blind spots. The EVOLVE Job Shadowing program is a fantastic opportunity for Node staff to immerse in the daily life and operations of other Nodes of… February 13, 2025 EVOLVE Job Shadowing Series: A Week of Discovery at the IMG Light and Electron Microscopy Node in Prague In the picturesque city of Prague, science meets artistry at the Institute of Molecular Genetics (IMG) Light and Electron Microscopy Node. From October 14th… January 10, 2025 Insights from a job shadowing host: Julien Colombelli and seeding long-term collaborations to inspire new projects The EVOLVE Job Shadowing programme is a fantastic opportunity for Node staff to immerse in the daily life and operations of other Nodes of… January 7, 2025 Insights from a job shadowing visit: Sebastian Munck at the Mesoscopic Imaging Node Barcelona and the importance of evolving workflows The EVOLVE Job Shadowing programme is a fantastic opportunity for Node staff to immerse in the daily life and operations of other Nodes of… November 12, 2024 My Job Shadowing visit to the Electron Microscopy Unit in Finland EVOLVE: Job Shadowing Series František Kitzberger Affiliation and Node: Laboratory of Electron…", "headings": [ "EVOLVE Job Shadowing series", "EVOLVE Job Shadowing Series: Paula Jiménez Gómez visits the DIMP NEUROMED - Leadership & Exploring the challenges of Project Coordination", "EVOLVE Job Shadowing Series: Mahlet Birhanu on her visit to the Radiology and Medical Imaging Valencia Node - Job roles, Health data management tools, and seeing your blind spots.", "EVOLVE Job Shadowing Series: A Week of Discovery at the IMG Light and Electron Microscopy Node in Prague", "Insights from a job shadowing host: Julien Colombelli and seeding long-term collaborations to inspire new projects", "Insights from a job shadowing visit: Sebastian Munck at the Mesoscopic Imaging Node Barcelona and the importance of evolving workflows", "My Job Shadowing visit to the Electron Microscopy Unit in Finland" ], "page_type": "homepage" }, { "id": "9d522de2", "url": "https://www.eurobioimaging.eu/training/masters-programmes/", "title": "Master’s programmes - Euro-BioImaging", "description": "MSc programs in imaging, internships, contacts for Cell Biology, Imaging, and Biomedical Imaging.", "documentation": "Master’s programmes Education is the greatest gift we can give to the next generation, which is why Euro-BioImaging is collaborating with several dedicated Master’s degree programs in biological or biomedical imaging. The collaboration includes supporting student mobility between and from these MSc programmes. In addition, to provide practical training to these young imaging scientists, the Euro-BioImaging Industry Board (EBIB) initiated a pilot Internship program for master’s students in 2021. Learn about Industry Internships Euro-BioImaging is collaborating with the following MSc degree programmes an supports student mobility between and from these members. Please contact Euro-BioImaging if you would like to add your programme in this list. CELL BIOLOGY AND ADVANCED MICROSCOPY, Amsterdam, Netherlands 120 ECTS, 2 years The master track Cell Biology and Advanced Microscopy is a collaborative effort by the University of Amsterdam (UvA) the Academic Medical Centre (AMC) and the Netherlands Cancer Institute (NKI), who collaborate in the van Leeuwenhoek Center for Advanced Microscopy (LCAM). The major objective of this track is the understanding of fundamental cell biological research in relation to human disease with special emphasis on the use of advanced microscopy techniques. Student's skill sets Cell imaging and molecular cell biology Internship opportunities 1st: year 6-9 months (December-May/July) 2nd: year 6-9 months (September-March/June) Contact Jürgen Seppen , Director Master Biomedical Sciences General inquiry , General email for asking questions from international students Dorus Gadella , Track coordinator Cell Biology and Advanced Microscopy at Science faculty Eric Reits , Track coordinator Cell Biology and Advanced Microscopy at Science faculty Learn more MASTER IN CELL IMAGING, Rouen, France 120 ECTS, 2 years The Master in Cell Imaging offers innovative multidisciplinary knowledge in High technologies in cell imaging, Cell biology, Physics applied to imaging and Image processing, as well as transversal skills in Sales & Marketing, Law and company management, project management and communication. Thanks to a English course including intensive lab work on PRIMACEN's high-tech equipment, students acquire a scientific and technical expertise in cell imaging which offers various French and international career opportunities. Student's skill sets Cell imaging Internship opportunities 1st year : 2 months (April-May) 2nd year : 5-6 months (February-August) Contact Delphine Burel , Course Director & Responsible for the 2nd year Oana Chever , Deputy Director & Responsible for the 1st year Ludovic Galas , Deputy Director & PRIMACEN Director Programme website (French) Programme Brochure (English) MSc ADVANCED BIOMEDICAL IMAGING, London, UK 1 year course Imaging has contributed to some of the most significant advances in biomedicine and healthcare and this trend is accelerating. This MSc, taught by leading scientists and clinicians, will equip students from all science backgrounds with detailed knowledge of the advanced imaging techniques which provide new insights into cellular, molecular and functional processes, preparing them for a PhD or a career in industry. Student's skill sets Biomedical imaging Internship opportunities April to August Contact Daniel Stuckey , Course Director P. Stephen Patrick , Course Tutor Learn more MSc IMAGING ENGINEERING, Maastricht, Netherlands 120 ECTS, 2 years Maastricht University offers a 2-year English-taught MSc in Imaging Engineering that allows you to acquire top-level skills in this field. You will start by combining your understanding of instrumentation engineering with knowledge of molecular structures and processes. In semester 2 of your year 1, you choose a specialisation: Instrumentation Imaging engineering to create and optimise instrumentation Molecular imaging engineering to develop applications of imaging techniques in biochemistry Student's skill sets Molecular & Instrumentation Imaging Engineering Internship opportunities Short 4 week projects in June Thesis: 7-8 months (October to June) Contact fse-master@maastrichtuniversity.nl Learn more MSc IN BIOMEDICAL IMAGING, Turku, Finland 120 ECTS, 2 years The MSc Programme in Biomedical Imaging aims to train professionals to have a thorough understanding and practical skills in a wide range of imaging technologies, methods and applications. The two-year programme is jointly administered and run by the two universities in Turku, the University of Turku (part of biomedical sciences programme) and the Åbo Akademi University. The programme has been assembled on the true imaging strongholds of Turku and comprises a truly interdisciplinary array of prominent research groups and departments to share advanced imaging techniques in basic cell and molecular biology, disease characterization at the molecular level and in patient diagnostics. Student's skill sets Cellular and biomedical imaging Internship opportunities Inter", "headings": [ "Master’s programmes", "CELL BIOLOGY AND ADVANCED MICROSCOPY, Amsterdam, Netherlands 120 ECTS, 2 years", "Student's skill sets", "Internship opportunities", "Contact", "MASTER IN CELL IMAGING, Rouen, France 120 ECTS, 2 years", "Student's skill sets", "Internship opportunities", "Contact", "MSc ADVANCED BIOMEDICAL IMAGING, London, UK 1 year course", "Student's skill sets", "Internship opportunities", "Contact", "MSc IMAGING ENGINEERING, Maastricht, Netherlands 120 ECTS, 2 years", "Student's skill sets", "Internship opportunities", "Contact", "MSc IN BIOMEDICAL IMAGING, Turku, Finland 120 ECTS, 2 years", "Student's skill sets", "Internship opportunities", "Contact", "WORKING WITH INDUSTRY" ], "page_type": "training" }, { "id": "bb43378b", "url": "https://www.eurobioimaging.eu/our-partners/", "title": "Partners - Euro-BioImaging", "description": "Details on partner infrastructures, access to resources, and global collaboration contacts.", "documentation": "Partners Euro-BioImaging works closely with a number of partners in Europe and globally. We collaborate closely with the Life Science Research Infrastructures in the LS-RI Strategy Board and with all other European Research Infrastructure Consortia in the ERIC Forum . In addition, Euro-BioImaging has signed bilateral Collaboration Agreements with several European Life Science Research Infrastructures (RIs) with whom we have particularly close collaborations. Euro-BioImaging also has signed agreements and close working relationships with imaging facilities and networks around the globe and can facilitate collaboration with these. For more information on our global collaborations, find out more about Global BIoImaging. Below are short descriptions on the portfolio of our partners, including websites and contact details. Research Infrastructure Partners ELIXIR ELIXIR is a pan-European infrastructure that integrates national bioinformatics resources into a unified network, providing access to data, tools, compute resources, and expertise to support life-science research across Europe. EU-OPENSCREEN ERIC EU-OPENSCREEN is a European Research Infrastructure that provides open access to high-capacity screening platforms and a diverse compound collection for validating therapeutic targets and conducting studies in chemical biology across a range of systems. European Marine Biological Resource Centre The European Marine Biological Resource Centre (EMBRC) is a collaborative network of over 30 marine centres across 9 European countries, supporting research and innovation in marine biology by providing access to marine organisms and ecosystems. Instruct-ERIC Instruct-ERIC is a leading European research infrastructure offering comprehensive access to cutting-edge structural biology technologies, expertise, and training, aimed at understanding molecular mechanisms and advancing the field globally. International Partners Advanced BioImaging Support (ABiS) Advanced BioImaging Support (ABiS) is a Japanese infrastructure established by MEXT in 2016 to provide scientists with free access to advanced bioimaging resources and technical support, aiming to enhance life sciences research in Japan. India-Bioimaging India BioImaging, inspired by Euro-BioImaging, is a consortium established in 2012 providing Indian researchers with open access to imaging technologies, expertise, and training in biological sciences, aiming to enhance research capabilities beyond their home institutions. Institut Pasteur de Montevideo The Institut Pasteur de Montevideo is a non-profit foundation in Uruguay focused on advancing research in human biology, biomedicine, and molecular pathology, offering educational programs and working on discoveries and inventions to further scientific progress in these areas. Microscopy Australia Microscopy Australia offers a nationwide network of university-based microscopy facilities, providing open access to a wide range of instruments and expertise across multiple research disciplines, facilitated by their online tool, Techfi™. National Imaging Facility The National Imaging Facility (NIF) is an Australian collaborative network offering open access to state-of-the-art imaging technologies and expertise across molecular imaging, human imaging, and imaging for animals, plants, and materials, established in 2007 under the NCRIS program. SingaScope SingaScope is a Singapore-wide microscopy infrastructure network funded by the national research foundation, aiming to connect researchers with biological and biomedical microscopy resources across institutions, supported by an online database and app for easy access. The Canadian Network of Scientific Platforms The Canadian Network of Scientific Platforms (CNSP), established in 2017, is a nationwide network supporting multidisciplinary research infrastructure, with Canada BioImaging as its inaugural technology node, representing around 100 imaging facilities from 40 universities and institutions. Partner Communities COMULISglobe COMULISglobe - the international community for multimodal imaging across scales - aims to connect all who use multimodal, correlative imaging, expand their applications, and train researchers in their use. European Society for Molecular Imaging - ESMI The European Society for Molecular Imaging (ESMI) represents the scientific community involved in multidisciplinary molecular imaging science. Global BioImage Analysts’ Society - GloBIAS Global BioImage Analysts’ Society (GloBIAS) aims to be a worldwide association that brings together all those interested in bioimage analysis. QUAREP-LiMi QUAREP-LiMi - Quality Assessment and Reproducibility for Images and Instruments in Light Microscopy - aims provide a comprehensive set of community-agreed guidelines, protocols, automation procedures and other resources aimed at improving quality control. volumeEM - vEM The vEM community initiative aims to support all those practically involved in volume electron microsc", "headings": [ "Partners", "Research Infrastructure Partners", "ELIXIR", "EU-OPENSCREEN ERIC", "European Marine Biological Resource Centre", "Instruct-ERIC", "International Partners", "Advanced BioImaging Support (ABiS)", "India-Bioimaging", "Institut Pasteur de Montevideo", "Microscopy Australia", "National Imaging Facility", "SingaScope", "The Canadian Network of Scientific Platforms", "Partner Communities", "COMULISglobe", "European Society for Molecular Imaging - ESMI", "Global BioImage Analysts’ Society - GloBIAS", "QUAREP-LiMi", "volumeEM - vEM" ], "page_type": "homepage" }, { "id": "71450ac0", "url": "https://www.eurobioimaging.eu/data-services/user-services/", "title": "User services - Euro-BioImaging", "description": "Image Data Analysis services, access steps, Node connections, contact info.", "documentation": "User services Euro-BioImaging offers its users Image Data Analysis (IDA) as a Service through expert Bioimage Analysts at the Nodes. These services can be requested together with access to imaging instruments at a Node, or as a standalone analysis services for user image data irrespective of where it was acquired. In addition to directly supporting users with analysis of their data, many of our Bioimage Analysts are involved in developing and actively maintaining Open image analysis tools and libraries, which serve Euro-BioImaging users as well as the global scientific community. Our Nodes can provide users a variety of biological and biomedical image data analysis services including: Image denoising, registration, segmentation, tracking and many other image analysis procedures applied to a wide variety of image datasets Data workflows, bespoke analysis tools including implementation of machine learning methods Access to high performance computing and specialised software Euro-BioImaging does not provide access to medical image datasets . Nevertheless, we can attempt to connect you with certain institutions hosting our Nodes that might provide access to medical image data. Please consider that we are not liable for any negotiations you may ultimately engage in concerning this matter. If you wish to be contacted by these Institutions, please send a message to info@eurobioimaging.eu indicating information on the types of datasets you are looking for. Learn more: To access image data analysis services at any of our Nodes follow these simple steps: Click on Technologies tab on the Euro-BioImaging Access Portal. You will find \"Image Data and Image Analysis Services\" as part of our technology portfolio. Choose the desired service and proceed to submit a proposal ( requires log in ). Once we have your proposal we can provide you assistance in finding a suitable Node as well. Our Nodes make use of and contribute to the development of open tools and libraries for analysis and management of image data", "headings": [ "User services", "Euro-BioImaging does not provide access to medical image datasets. Nevertheless, we can attempt to connect you with certain institutions hosting our Nodes that might provide access to medical image data. Please consider that we are not liable for any negotiations you may ultimately engage in concerning this matter. If you wish to be contacted by these Institutions, please send a message to info@eurobioimaging.eu indicating information on the types of datasets you are looking for.", "Learn more:" ], "page_type": "services" }, { "id": "a0c9bd9e", "url": "https://www.eurobioimaging.eu/technologies/", "title": "Technologies - Euro-BioImaging", "description": "Access to advanced imaging tech: cryo-EM, light microscopy, multimodal imaging for research.", "documentation": "Technologies Overview Through the large number of included facilities, Euro-BioImaging can offer access to the full range of imaging technologies in the biological and biomedical imaging field. Our technology portfolio covers everything from the nano- to the tissue- and organism scale. We are constantly adding new technologies - making sure that the latest cutting-edge imaging technologies, such as MINFLUX and spatial transcriptomics, are available in open access to all researchers. You can browse our technologies here . Harnessing the imaging revolution The Euro-BioImaging technology portfolio ranges from light and electron microscopy on the biological imaging side to an expanding range of applications of biomedical imaging, from plant and ex-vivo imaging to animal and human imaging applications. Electron Microscopy Our Electron Microscopy portfolio covers cryo-EM techniques for in situ structural exploration, such as cryo-electron tomography (cryo-ET), as well as the full complement of volume EM techniques, such as FIB-SEM, Array Tomography and Serial Blockface SEM. Many of our facilities also specialise in correlative methods, Correlative X-ray Imaging and EM (CXEM) and Correlative Light and Electron Microscopy (CLEM). Left: Maximum intensity projection of Acantharia (plankton), plunge frozen and imaged with a high-end confocal microscope as part of a CLEM workflow. Green: Acantharia; red: chlorophyll of symbionts (microalgae). Credits: Anna Steyer/EMBL Light Microscopy In light microscopy, our Nodes offer everything from confocal microscopy up to single molecule location approaches and intravital imaging. Our light microscopy techniques allow for 3D live cell imaging, tracking, high content screening, and include a variety of functional imaging techniques to explore protein dynamics in living cells. Recently we have added a number of new and highly requested methods, such as MINFLUX, Single Particle tracking, Spatial transcriptomics, and Lattice Lightsheet microscopy to our portfolio. Right: Imaged with Lattice Lightsheet, in magenta membrane coated beads and in green virus like particles. Image courtesy of Steven Edwards, SciLifeLab. Multimodal in vivo animal and human imaging Left: 68Ga-DOTA-Siglec-9 PET/CT image of hands of a 49-y-old patient with early Rheumatoid Arthritis (Finnish Biomedical Imaging Node ) Our preclinical imaging Nodes provide access to all the relevant biomedical imaging technologies, from Magnetic Resonance Imaging to Ultrasound, Optical and PhotoAcoustic Imaging, up to the nuclear imaging technologies (PET, SPECT, CT and bimodal techniques) for animal studies with applications in preclinical research (e.g. evaluation of new therapeutics, assessment of new molecular probes and imaging markers) and in veterinary science. Expertise on protocols, sequences, probes and tracers is also provided where needed. Some of our Nodes also provide access to technologies for studies on human subjects. In this case support for subjects recruitment and ethics management is also provided. Use cases Model Systems Euro-BioImaging facilities also offer access and support with imaging a wide range of model systems and can advise how to get the best imaging results out of them, from Drosophila, zebrafish, mouse embryos and organoid systems to small rodents and even bigger animal models of the various pathologies. Here access to instruments is complemented by technical expertise of facility staff to support specialized sample and animal handling. Adaptive technologies to explore all facets of your sample And of course, we also provide access to adaptive and support technologies, such as laser-based microdissection, Feedback Microscopy, high-speed imaging, microscopes at high biosafety levels, and specialized sample preparation methods, such as Tissue Clearing and Expansion Microscopy. Euro-BioImaging can also support you if you want to explore the physical and chemical properties of your samples - through access to a range of methods such as MassSpec Imaging, Atomic Force Microscopy, and chemical imaging, such as µ-XRF and μ-PIXE. Left: Example of a centriol imaged with Structured Illumination Microscopy (SIM) after Expansion Microscopy sample preparation . Image courtesy of Ana Agostinho, SciLifeLab, Swedish NMI.", "headings": [ "Technologies", "Overview", "Harnessing the imaging revolution", "Electron Microscopy", "Light Microscopy", "Multimodal in vivo animal and human imaging", "Model Systems", "Adaptive technologies to explore all facets of your sample" ], "page_type": "homepage" }, { "id": "cad295ba", "url": "https://www.eurobioimaging.eu/evolve/", "title": "EVOLVE - Euro-BioImaging", "description": "Opportunities: job shadowing, training, mentoring; focus on Open Science data services.", "documentation": "EVOLVE The EVOLVE Project (Grant Agreement: 101130986) is a substantial advance in improving Euro-BioImaging’s operability, capacity, and impact. EVOLVE will profoundly enhance Euro-BioImaging as a Research Infrastructure, both internally and externally. Spanning over three and a half years, the EVOLVE project perfectly aligns with Euro-BioImaging’s Strategic Plan for 2024-2028. It will significantly strengthen our operation, administration, capacities for strategic partnering and capacity to facilitate innovation and excellent science. Furthermore, it will foster the family of Euro-BioImaging Nodes and Hub at the personal, institutional, national and European level. Opportunities for our Nodes Within the EVOLVE project, the Euro-BioImaging Hub team coordinates a number of opportunities for Euro-BioImaging Node staff to get to know each other, exchange their knowledge and experience and advance their careers. Learn more about these opportunities below. Job shadowing Training Mentoring Communication & Outreach Within the EVOLVE project, Euro-BioImaging ERIC will implement a sustainable strategy for external relations with policy makers, funders and industry, as well as boost its outreach and communication activities with partner communities and seek collaboration with new user communities for widening participation. In collaboration with our Nodes, we will support outreach activities with the general public. Partner communities Industry Citizens Open Science & Image data services By supporting and furthering the adoption of EU policy on Open Science, we aim to strengthen our ERIC and the European Research Area in the global image data landscape. Within the EVOLVE project, we will strengthen our research infrastructure by providing new data services and increase technical and coordination support, which is essential for our Nodes and users to stay at the brink of this fast-evolving field. Data services FAIR data Strengthening Euro-BioImaging ERIC The EVOLVE project will strengthen Euro-BioImaging operations, administration, capacities for strategic partnering and capacity to facilitate innovation and excellent science, as well as set-up the next generation of our user access web portal.  Furthermore, Euro-BioImaging Hub staff will reinforce their areas of competence and ability to work together for the benefit of the community. Sustainable Research Infrastructure During times of an energy crisis in Europe, Euro-BioImaging ERIC will launch activities to underpin European Commission sustainability plans, thus helping to shape a greener, more digital future for our infrastructure. This work is made possible by funding from the European Union as part of the EVOLVE project. This project is funded by the European Union. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.", "headings": [ "EVOLVE" ], "page_type": "homepage" }, { "id": "98dd78d0", "url": "https://www.eurobioimaging.eu/industry-board/ebib-members/", "title": "Euro-BioImaging Industry Board members", "description": "Membership offers access to imaging facilities, networking, and funding insights.", "documentation": "EBIB members Meet our Industry Board members EVIDENT JEOL Ltd. LEICA MICROSYSTEMS NIKON THERMO FISHER SCIENTIFIC ZEISS EXCELITAS PCO. GMBH HAMAMATSU IVIM Technology DENS SOLUTIONS FUJIFILM VISUALSONICS Life Imaging Services GmbH OXFORD INSTRUMENTS ANDOR PICOQUANT Proteintech TELIGHT TISSUE GNOSTICS TOKAI HIT How to become a member Interested to become a member? Board membership is open to all companies working in biological and (bio-)medical imaging field. Currently the Board members consist of a range of companies in the field of imaging, which are joined together by their recognition of the importance working closely with the open access infrastructure, Euro-BioImaging, to strengthening imaging research in Europe. By working as a single, professional entity the Board sets its own goals to proactively drive the interaction between the imaging industry, European researchers and the imaging facilities linked in Euro-BioImaging. A close relationship to Euro-BioImaging opens the door to current research trends and usage of imaging products, the organization of joint initiatives and common lobbying activities. Achieving this close interaction between industry and research communities boosts innovation in biomedical sciences, strengthens the position of companies which can accelerate new developments to the market and builds a foundation of sustainable industry interactions. The Industry Board runs a membership scheme to collect funding for the Board‘s activities and a dedicated Industry Board Coordinator who supports the Industry Board to achieve its objectives and organizes a series of activities to systematically strengthen and broaden the Board’s knowledge of imaging research and the two-way dialogue with its stakeholders. Membership benefits Examples of Industry Board activities and membership benefits include: Streamlined contact to the research infrastructure, Euro-BioImaging, and its 5,000 stakeholders Invitation to and participation in Euro-BioImaging stakeholder meetings Visibility amongst and interaction with national imaging communities Close links with Euro-BioImaging and its 33 Nodes of cutting-edge biological and biomedical imaging facilities Joint lobbying for imaging to national and European funders Direct information from Euro-BioImaging Nodes about their operation, management and use of technologies Feedback from users about their experience with technologies, interesting samples and information about new applications One-to-one networking opportunities with other imaging companies Industry-driven meetings and workshops to understand the needs of the imaging community Overview of the imaging-associated funding activities in Europe Insight into European research trends and culture changes More information on how to become a member Prospective members have the opportunity to attend one Board meeting as an observer. If you are interested in becoming a member of the Euro-BioImaging Industry Board, please contact the Industry Board Coordinator to set up a call. We can discuss how you and your company specifically could benefit from Industry Board membership. Download our flyer Download membership agreement", "headings": [ "EBIB members", "Meet our Industry Board members", "EVIDENT", "JEOL Ltd.", "LEICA MICROSYSTEMS", "NIKON", "THERMO FISHER SCIENTIFIC", "ZEISS", "EXCELITAS PCO. GMBH", "HAMAMATSU", "IVIM Technology", "DENS SOLUTIONS", "FUJIFILM VISUALSONICS", "Life Imaging Services GmbH", "OXFORD INSTRUMENTS ANDOR", "PICOQUANT", "Proteintech", "TELIGHT", "TISSUE GNOSTICS", "TOKAI HIT", "How to become a member" ], "page_type": "homepage" }, { "id": "f9b8978e", "url": "https://www.eurobioimaging.eu/scientific-ambassadors/", "title": "Scientific Ambassadors - Euro-BioImaging", "description": "Join as a Scientific Ambassador for training, networking, travel grants, and advocacy materials.", "documentation": "Scientific Ambassadors The Euro-BioImaging Scientific Ambassadors program aims to raise awareness about the services and opportunities provided by Euro-BioImaging. Our Scientific Ambassadors act as catalysts, connecting with like-minded individuals who share a common goal to impact in their communities. By effectively communicating the services offered by Euro-BioImaging, our Scientific Ambassadors play a crucial role in expanding the reach of Euro-BioImaging. Through their advocacy and engagement, Scientific Ambassadors help foster a greater understanding of Euro-BioImaging services, making imaging technologies more accessible for researchers and creating opportunities for collaboration, scientific advancement, and innovation in bioimaging. Meet our Scientific Ambassadors Why you should become a Scientific Ambassador You should become a Scientific Ambassador if you believe in the Euro-BioImaging mission of providing open access to imaging expertise and want to help spread the word about this fabulous opportunity to other researchers. But being a Scientific Ambassador can also contribute to your personal and career development. As a Euro-BioImaging Scientific Ambassador, you can expect a range of valuable offerings and support throughout your journey: Welcome pack : Upon joining the program, you will receive a special welcome pack containing branded items such as a t-shirt, stickers, bag, pen, notebook, etc. These items not only serve as a token of appreciation but also allow you to represent Euro-BioImaging proudly. Training by Euro-BioImaging staff : Euro-BioImaging is committed to equipping its Scientific Ambassadors with the necessary knowledge and skills to excel in their roles. You will receive training directly from the experienced staff at Euro-BioImaging, ensuring you understand the organisation, its mission, and the scientific principles it operates on. Presentation and teaching materials : To support your advocacy efforts, Euro-BioImaging will provide you with materials that you can use for presentations, teaching, or workshops. These resources will help you effectively communicate the benefits and opportunities offered by Euro-BioImaging to your community and beyond. Recognition on the Euro-BioImaging website : Your role as a Scientific Ambassador will be acknowledged and highlighted on the Euro-BioImaging website and social media. Your activities and achievements will be showcased, demonstrating your impact and serving as an inspiration for others. Networking opportunities : As a Euro-BioImaging Scientific Ambassador, you will have the chance to network with professionals from Euro-BioImaging and other ambassadors. This networking provides a platform for collaboration, knowledge sharing, and building meaningful connections within the scientific community. Travel grants: With support from the EVOLVE project , you’ll have the chance to pitch for potential travel funding opportunities to attend events in which you can present Euro-BioImaging. The maximum limit is 1,500 Euros per person. Personalised support and guidance : The Euro-BioImaging team will provide personalised support and guidance throughout your ambassadorial journey. Whether you have questions, need assistance organising events, or require advice on engaging your community, the Euro-BioImaging team will help you every step of the way. Growth opportunities : Euro-BioImaging is committed to supporting your personal and professional growth. If you have a particular area of interest within bioimaging, the organisation will provide resources, connections, and opportunities to develop your expertise further and expand your knowledge. Increased visibility : As a Euro-BioImaging Scientific Ambassador, you will gain increased visibility for yourself and your community. Your active involvement and contributions to the program will be recognised and celebrated. Euro-BioImaging will actively promote and highlight your activities through various communication channels, including social media platforms and newsletters. This visibility showcases the impactful work you do as an ambassador, inspiring others to engage with Euro-BioImaging and its services. How it works The Euro-BioImaging Scientific Ambassadors program follows a structured process consisting of three distinct phases that unroll over one year in close collaboration with Euro-BioImaging Hub team staff. Onboarding phase During the onboarding phase, which lasts  approximately one month , you will be introduced to Euro-BioImaging along with other selected Euro-BioImaging Scientific Ambassadors. This phase aims to foster a sense of community and provides you with a comprehensive understanding of Euro-BioImaging's mission, services, and opportunities . You will have the chance to explore different aspects of Euro-BioImaging and identify which areas are most interesting to you and where you would like to develop your knowledge further. Running phase Once the onboarding phase is complete, the ", "headings": [ "Scientific Ambassadors", "Why you should become a Scientific Ambassador", "How it works", "Onboarding phase", "Running phase", "Offboarding", "What are the requirements?", "Must have:", "Nice to have:", "Who cannot apply:", "What can you expect from the program?", "Time Commitment", "How to apply?", "How does the selection work?" ], "page_type": "homepage" }, { "id": "352d7b66", "url": "https://www.eurobioimaging.eu/how-to-access/", "title": "How to access - Euro-BioImaging", "description": "Access procedures, expert consultations, proposal requests, and contact info for imaging services.", "documentation": "How to access Access Portal Euro-BioImaging services are available for everyone! Independent of your area of research, whether you work in academia or industry, your career stage, level of expertise with the needed technology or where you work.  Here’s an overview of the path to access to Euro-BioImaging services. The User Access Process Initial Consult You can use the information on the Euro-BioImaging web portal to select technologies and Nodes that meet your needs. If you are not sure what technology is right for your research question or which of our Nodes would provide the best support for your research area, the expert Euro-BioImaging staff are available to provide support and consultation. Access Proposal Request After the technologies and Nodes are selected, you can submit an access proposal request . Scientific Advice Applications receive scientific advice from external experts to support project development. If your project is not requesting funding and has already undergone scientific review - e.g. as part of a funded project, through a PhD committee, Node access evaluation committee or similar -  the proposal can be fast-tracked to the technical check. Technical Advice The selected Node confirms the technical feasibility of the planned work or supports the applicant in developing a feasible plan for use of the requested technology. Service Provision Once the access proposal request is granted, the Node contacts the users regarding practicalities for the access, such as planning the visit. Contact us at info@eurobioimaging.eu for support and consultation A successful Euro-BioImaging access request unlocks the power of imaging technologies and provides the expertise that users need to apply state-of-the-art imaging equipment to their project and analyze their results. Read about what our users have been able to achieve with access to imaging technologies through Euro-BioImaging here .", "headings": [ "How to access", "The User Access Process", "Initial Consult", "Access Proposal Request", "Scientific Advice", "Technical Advice", "Service Provision" ], "page_type": "access" }, { "id": "3cb9f1e9", "url": "https://www.eurobioimaging.eu/validation/", "title": "Technology validation at Euro-BioImaging Nodes", "description": "Validation services, 240+ imaging facilities, EP PerMed funding up to €80,000.", "documentation": "Technology validation Technology developers can collaborate with Euro-BioImaging to validate new imaging technologies across various Technology Readiness Levels (TRLs). This collaboration is designed to ensure that innovations are effectively integrated into life sciences research, enhancing the overall impact on health and disease understanding. Whether it is validation of a new technological concept or imaging application, beta-testing of a new prototype, validation of a technology for service-readiness or testing and demonstrating a new product with a wide user base, Euro-BioImaging can support technology developers in putting their concepts and innovation through rigorous validation. Explore our facilities Micro-PIXE setup at the Jožef Stefan Institute, Ljubljana Credit: SiMBION. There are several pathways open to developers: 1. Validation services Gain access to almost 240 imaging facilities across Europe and a large network of imaging and image analysis experts. Our facilities are selected in a rigorous application process for Scientific and technical excellence European and national significance Technology maintenance and updates Access and service package Quality assurance User training Each facility can link you to their specific surrounding research ecosystem, e.g. software developers and image analysts, clinical researchers, service providers with a large number of technology users or other technology developers that match your technical or geographic requirements. Contact us to find the right validation partner for you! Note on medical image data : Euro-BioImaging does not provide access to medical image datasets. Nevertheless, we can attempt to assist you in getting in touch with certain institutions hosting our Nodes that might provide access to medical image data. Please consider that we are not liable for any negotiations you may ultimately engage in relation to this matter. If you wish to be contacted by these Institutions, please send us a message indicating information on the types of datasets you are looking for to carry out your validation. Fast Track Call European Partnership for Personalized Medicine The EP PerMed Fast Track Validation Programme has been established to address a critical bottleneck in the development of PM solutions: the validation phase. The programme provides a structured, accelerated pathway for PM innovators to validate their solutions and supports start-ups and small teams to identify and access validation resources and guidance. Euro-BioImaging can provide technology validation in the field of imaging technology, image data analysis and AI-driven image data tools by partnering with applicants as validation centers. EP PerMed provides financial support to successful applicants of up to €80.000,- for their validation project. Please visit the website for more information: https://www.eppermed.eu/funding-projects/calls/fast-track-call . There are currently no open calls, but please revisit the website for future opportunities. Status: May 2025. Roberta Ranieri and Faba Neuman validating screening results. Image credit: Euro-BioImaging. Validation use case 1 For the validation of hit compounds out of a screening campaign for potential drugs for acute myeloid leukemia (AML), Roberta Ranieri accessed advanced imaging technology at the Advanced Light Microscopy Facility at the EMBL Node of Euro-BioImaging to further characterize their effect on cellular disease models. Besides obtaining valuable data for further lead optimization, the collaboration with screening experts also helped the researcher to improve their strategies for drug screening and image analysis. Read more . Validation use case 2 Accessing innovative MALDI Mass Spectrometry Imaging (MSI) technology at the M4I Institute of the Euro-BioImaging Facility of Multi Modal Imaging AMMI Maastricht Node significantly enhanced the impact of the ProstOmics project, by giving the researcher and ERC-grantee Dr. Maria K. Anderson access to the cutting-edge, highly sensitive MALDI-2 MSI instrument that was required to map cholesterol and other sterols in prostate tissue. Working with Euro-BioImaging generated otherwise inaccessible data that deepened the understanding of cholesterol's role in prostate cancer, marking a significant advancement in biomarker validation for this aggressive cancer form. Read more . Maria K. Anderson in front of the MALDI-2 MSI in Maastricht. Image credit: Euro-BioImaging. 2. Expert Consultation Technology developers can engage in fully confidential consultations with Euro-BioImaging's technology experts. These consultations facilitate knowledge exchange, allowing developers to refine their technologies based on feedback from leading imaging specialists. 3. Collaborative Projects Euro-BioImaging encourages partnerships for technology and methods development. Developers can collaborate on national or European funded programs , leveraging Euro-BioImaging's extensive network to identify suitab", "headings": [ "Technology validation", "1. Validation services", "Fast Track Call European Partnership for Personalized Medicine", "Validation use case 1", "Validation use case 2", "2. Expert Consultation", "3. Collaborative Projects", "4. Suggesting a new technology for our portfolio" ], "page_type": "nodes" }, { "id": "794e897b", "url": "https://www.eurobioimaging.eu/data-services/fair-image-data/", "title": "FAIR image data - Euro-BioImaging", "description": "FAIR data training, resources, 1-on-1 guidance, contact fairdata@eurobioimaging.eu.", "documentation": "FAIR image data As a result of the digital revolution, scientific data must be created with longevity in mind more than ever before. FAIR data increase the value of scientific data by enabling it to be more easily incorporated into a variety of different research projects. The FAIR principles thus facilitate and accelerate knowledge generation and scientific progress, improve research transparency, and foster collaboration within the scientific community. FAIR principles Q&A What does FAIR actually stand for? According to the FAIR principles (1), scientific data is of the highest value if it is: Findable : Data and associated Metadata should be easy to find and discover for both humans and computers by a standard identification mechanism Accessible : (Meta)data are available and obtainable by their identifier using a standardized communication protocol; even if the data itself is restricted, the metadata is visible Interoperable : Data needs to be integratable with other data and into applications or workflows for analysis, processing and storage by the use of shared and broadly applicable language Reusable : To optimize the data for reuse, the data and metadata should be richly described by accurate and relevant attributes. What are the challenges for BioImage data? Biological imaging methods present special challenges in regards to FAIR, as they likely generate large volumes (up to several TB) of often complex and multidimensional data in various (proprietary) file formats that must be properly handled, processed and stored. Supporting FAIR image data The FAIRification process often begins by recognizing the value of FAIR data and subsequently making adjustments in data acquisition, processing and management where appropriate. Euro-BioImaging promotes and facilitates the adoption of FAIR practices relevant to image data which get implemented at our Nodes and the Hub. To this end, we offer resources, training and 1-on-1 guidance to FAIRify your data in all stages of the data lifecycle – from project planning to data deposition and reuse. We also work closely with dedicated image data repositories making important connections between the resources and the users. Contact: fairdata@eurobioimaging.eu FAIR training We have launched the ' Euro-BioImaging's Guide to FAIR BioImage Data ' series of events, which aims to introduce the FAIR principles in the context of bioimaging and provide you with simple yet effective steps for a smooth start to your FAIR journey. View all events The \"Webinar on Data Management of Preclinical Image Datasets\" showcases the tools developed to improve the discoverability, access, interoperability, and reusability of preclinical image datasets, consequently providing a solid step towards the adoption of the FAIR principles of our imaging community. Learn more FAIR resources Data deposition recipe in FAIRcookbook One of the critical aspects of data sharing is data deposition, which is often not as straightforward as it needs to be for rapid data exchange. We have therefore created a step-by-step process for depositing bioimage data in the BioImage Archive. Read the recipe Image repository decision tree For guidance in the selection of appropriate repositories, we have created an overview of available repositories for different types of image data, including their scope and requirements. This decision tree guides you through questions about your data and directs you to the correct repository. Follow the tree Research data management plan template Euro-BioImaging strongly encourages its users to prepare a Data Management Plan (DMP). To assist with this, we have developed a comprehensive template with tailored questions for bioimaging research projects, available as a fillable PDF. Check out the DMP Catalogue of FAIR image data resources We have compiled a Fairsharing catalogue of FAIR, public image data resources including repositories, policies and standards that Euro-BioImaging recommends and supports. View the catalogue Publication on FAIR image data ecosystem To capture the current position of the imaging community in its journey towards FAIR data and ongoing initiatives we have written the article 'Building a FAIR image data ecosystem for microscopy communities ' in the journal Histochemistry and Cell Biology (HCB). Read the article Tool and workflow development Euro-BioImaging provides technical support by developing tools and workflows for preclinical data and for working with the next-generation file format OME-Zarr, which facilitate FAIR image data management and analysis. Explore the tools Selected BioImage Data repositories Open BioImage Data (contact: fairdata@eurobioimaging.eu ) The BioImage Archive : an image deposition database for all microscopy data (from organism to molecular scale) associated with a publication. It adopts the recommended metadata for biological images‘ ( REMBI ) (2)scheme to define metadata, which improves the FAIRness of the data by enhancing interope", "headings": [ "FAIR image data", "FAIR principles Q&A", "Supporting FAIR image data", "FAIR training", "FAIR resources", "Data deposition recipe in FAIRcookbook", "Image repository decision tree", "Research data management plan template", "Catalogue of FAIR image data resources", "Publication on FAIR image data ecosystem", "Tool and workflow development", "Selected BioImage Data repositories", "Open BioImage Data (contact: fairdata@eurobioimaging.eu)", "Pre-clinical BioImage Data (contact: preclinicaldata@eurobioimaging.eu)", "Further reading:", "FAIR News", "Euro-BioImaging at TiM2025: Sharing Knowledge and Celebrating Open Data", "AI4Life Community Event Celebrating AI Innovation in Life Sciences held in Helsinki", "Towards Global Image Data Sharing", "FAIR Image Analysis: Insights from BioHackathon Europe 2024", "Join us for the Euro-BioImaging Image Data Community Days 2025", "Celebrating 3 years of BY-COVID project", "The Triangle of Interoperability: Metadata, Ontology and Vocabulary", "Becoming part of the Global Image Data Ecosystem", "Great success of Euro-BioImaging’s Guide to FAIR BioImage Data 2024" ], "page_type": "homepage" }, { "id": "7cc0db67", "url": "https://www.eurobioimaging.eu/news/agroservs-4th-call-for-access-is-open/", "title": "AgroSERV’s 4th call for access is open - Euro-BioImaging", "description": "Funding for agroecology projects; apply by Oct 15, 2025; contact agroservprojects@eurobioimaging.eu.", "documentation": "AgroSERV’s 4th call for access is open Published June 20, 2025 AgroServ is a transdisciplinary initiative supported by the European Union through the Horizon Europe program and will continue until 2027. It supports the research community by funding interdisciplinary agroecology research projects aimed at building sustainable and resilient agri-food systems. These projects focus on areas like plant biology, water, soil, and microorganisms. Euro-BioImaging is a partner in the AgroServ consortium, which includes 12 other research infrastructures and partners across 23 countries. As part of this project, nine Euro-BioImaging Nodes currently offer access to their expertise and services. Fourth open call for access After a successful first, second and third calls for access, we are pleased to announce that AgroSER V has launched the Fourth Open Call for projects (Pre-proposals deadline : July 31st , 2025 , Full Proposals deadline : October 15th, 2025 ). Selected projects will receive funding for free access to integrated research infrastructure services & expertise. Users are invited to check the catalogue of services and engage with the facility managers at the infrastructures to prepare the proposals. Get funding for imaging technologies, services & expertise to enhance your project We invite all researchers from various sectors, including academia, industry, and practitioners, to explore AgroServ’s extensive Catalogue of Services to enhance their agroecology research projects using imaging and image data services. Services offered by Euro-BioImaging Nodes are marked with the Euro-BioImaging logo for easy identification. However, we also encourage you to explore the complete array of expertise and services provided by our project partners. This rich resource pool may inspire you to design experiments that use services from multiple research infrastructures, increasing your chances of securing funding by applying to more than one. If you have an idea for a plant research project that involves services from Euro-BioImaging and at least one other project partner, we strongly encourage you to apply for funding in this Second Open Call. If you need help in selecting the right combination of services for your research or in navigating the application process, we will be happy to advise and support you. You can contact us at agroservprojects@eurobioimaging.eu . How the application process works ? Access is granted on the basis of scientific excellence through the submission of a research project proposal. According to the AgroSERV eligibility criteria , applicants have to request to use at least 2 different services from 2 different Research Infrastructures within the AgroSERV services portfolio. Applicants are also required to engage with the facility staff to elaborate the project's scientific and technical aspects before submitting the proposal. The approval from the facility staff is mandatory before submission . We encourage you to check the AgroSERV catalogue of services for more information about all available services: Euro-BioImaging services: Click here All Services: Click here Once you have identified the services you are interested in, submit your expression of interest using the Euro-BioImaging Pre-proposal form . You can also reach out to us at agroservprojects@eurobioimaging.eu if you have difficulties identifying the service(s) best for your research topic. The Euro-BioImaging team will then reach out to you and provide you with the necessary information and support, and put you in touch with the facility staff at our Nodes who will provide support in developing the technical aspects of your proposal. Researchers are eligible to apply for Euro-BioImaging services from Nodes within AgroSERV, including those located in their country. The transnationality requirement is waived for ERIC service providers. Key dates & deadlines 1st Step : Pre-proposals (internal expression of interest) - Deadline : 31st of July 2025. 2nd Step : Full Proposals - Deadline : 15th of October 2025. Eligible costs Selected users obtain full support to perform the proposed experiments including : Free access for eligible user groups to research facilities Support for travel and accommodation On-site logistic support by the infrastructure staff Access to knowledge and know-how at the research infrastructures necessary to complete the proposed experimental work Participating Euro-BioImaging Nodes More news from Euro-BioImaging June 30, 2025 Deuterium Metabolic Imaging to measure hepatic fructose metabolism Chronic intake of high amounts of fructose has been linked to the development of metabolic disorders caused by the almost complete clearance of fructose… June 30, 2025 VISITING THE PRIME NODE With the occasion of the Board meeting which took place in Amsterdam last May, the Med-Hub section Director Linda Chaabane and the Med-Hub Head… June 24, 2025 EU Project CANDLE starts building National Cancer Data Nodes The EU-funded project ", "headings": [ "AgroSERV’s 4th call for access is open", "Fourth open call for access", "Get funding for imaging technologies, services & expertise to enhance your project", "How the application process works ?", "Key dates & deadlines", "Eligible costs", "More news from Euro-BioImaging", "Deuterium Metabolic Imaging to measure hepatic fructose metabolism", "VISITING THE PRIME NODE", "EU Project CANDLE starts building National Cancer Data Nodes" ], "page_type": "access" }, { "id": "5a24f1ad", "url": "https://www.eurobioimaging.eu/technologies/new-technologies-pcs/", "title": "New technologies - Euro-BioImaging", "description": "Details on showcasing, proof-of-concept, and new imaging technologies access.", "documentation": "New technologies Innovation in imaging technologies in life sciences is continuous, fast and exciting. To remain at the technological forefront, Euro-BioImaging has established a workflow to ensure that new technologies are continuously integrated into our portfolio. The expert imaging facility staff at the Euro-BioImaging Nodes are developing many new imaging methods and are making the latest developments available in open access. On the right, Nicolas D'Ascenzo of our NEUROMED DIMP Node, proudly shows off the portable PET machine he is developing to study plant growth in the field. Suggest a new imaging technology Whether you are a technology developer, provider, or Euro-BioImaging user, use this simple form to inform us of a new imaging technology. The technology may be either completely new, or new to Euro-BioImaging. After you have made a suggestion for a new technology, the workflow for its inclusion into the Euro-BioImaging portfolio is: The technology is Showcased by a person or group to demonstrate the user need, its relevance to the scientific community and user access feasibility. (Not all suggestions lead to Showcasing.) After successful showcasing, a Proof-of-Concept study is arranged to confirm that the new technology can be offered as an open access service via Euro-BioImaging. After a successful Proof-of-Concept, the technology is accepted into the Euro-BioImaging portfolio and becomes available to everyone. To Euro-BioImaging Nodes: If you wish to add more technologies from the Euro-BioImaging portfolio to your Node, use this simple form . See below for more information and current technologies in Showcasing and Proof-of-Concept studies. Showcasing new imaging technologies Any technology developer/provider/imaging facility at a public research institution/university which is offering a new technology to external users can perform a Showcasing - it is not limited to Euro-BioImaging Nodes. In fact, Showcasing can also be a stepping-stone for becoming a Euro-BioImaging Node. Euro-BioImaging does not coordinate Showcasing, but facilities are invited to inform us of ongoing Showcasing. Afterwards, a simple report needs to be sent to us, if the new technology is to proceed towards becoming a Euro-BioImaging technology. If you are about to start Showcasing, please tell us about it , so we can advertise your Showcasing. If you are a user and interested in a technology being Showcased, tell us about it . This will help us in making it a Euro-BioImaging technology. If you have completed Showcasing, please send us a simple report . Currently ongoing/completed Showcases Soft X-ray Tomography (showcasing successfully concluded March 2023) EPR imaging Laser Speckle Contrast Imaging (Please see below for a list of technologies that have already moved from Showcasing to Proof-of-Concept studies.) Proof-of-Concept studies A new technology with user need and a functional access model demonstrated by the Showcasing process is included in the next available round of Proof-of-Concept studies (PCS). At this point, access to the technology is possible via Technologies on our Web Portal, just like for any other technology. Technologies undergoing Proof-of-Concept studies are marked with a star (*) in the technology listing and the Proof-of-Concept study has a defined time frame, after which the user demand and user and provider experience is reviewed by our Scientific Advisory Board to evaluate the Proof-of-Concept study. If the Proof-of-Concept studies are successful, the technology is then included into the Euro-BioImaging portfolio permanently. Visit our Proof-of-Concept page to learn more about the new technologies Euro-BioImaging offers. If you are a Node wishing to offer a technology for a proof-of-concept study, please let us know by sending an email to info@eurobioimaging.eu . Technology highlights January 17, 2024 EDX Imaging: Electron Microscopy beyond the grey-scale Electron Microscopy holds the key to understanding the ultrastructure of biological systems, but finding what you are looking for in the high resolution EM… January 3, 2024 Cryo-ET: Imagination is the limit Studying macromolecular complexes in their native environment in a cell is a real challenge, but new methods and technology advances are allowing scientists to… November 20, 2023 TeraHertz Imaging: Portable plant imaging Working on plant biology? Want to detect leaf water stress or assess the quality of dry fruits like chestnuts and hazelnuts? TeraHertz Imaging could… March 23, 2023 CXEM: Finding a needle in a haystack Correlative X-ray imaging and electron microscopy (CXEM) is the combination of X-ray imaging and electron microscopy. It is a correlative approach that makes it… March 16, 2023 MINFLUX: A light microscopy technique that closes the gap on structural biology MINFLUX is a super-resolution approach developed by Nobel prize laureate Stefan Hell in 2016. Two Euro-BioImaging Nodes are currently offering MINFLUX in open access… Mar", "headings": [ "New technologies", "Technology highlights", "EDX Imaging: Electron Microscopy beyond the grey-scale", "Cryo-ET: Imagination is the limit", "TeraHertz Imaging: Portable plant imaging", "CXEM: Finding a needle in a haystack", "MINFLUX: A light microscopy technique that closes the gap on structural biology", "MINFLUX: Super fast, super-resolution microscopy", "Laser Microdissection: Extract specific regions from your sample", "A powerful high speed, low phototoxicity microscopy method to achieve super-resolved images", "Spatial Transcriptomics – For understanding tissue architecture" ], "page_type": "homepage" }, { "id": "bf0d07e1", "url": "https://www.eurobioimaging.eu/industry-board/ebib-activities/", "title": "Euro-BioImaging Industry Board activities", "description": "Tech Exchange webinars, Board meetings, industry events, and new member announcements.", "documentation": "EBIB activities EBIB activities No scheduled events All events Tech Exchange In March 2021, the Euro-BioImaging Industry Board launched the Tech Exchange webinar series for companies in the imaging field that provides an opportunity for imaging facilities and users in the Euro-BioImaging network to learn about new technologies and imaging products and exchange on technical questions. Please check out the dedicated page for upcoming episodes and how to take part. Euro-BioImaging Industry Board Meetings The Industry Board meets 3-4 times a year to discuss the strategic planning for the upcoming months and identify new areas of engagement for its members. At least one of these meetings is an in-person event including opportunities to meet the Euro-BioImaging Nodes, often combined with a technical workshop. Companies interested in joining the Board can participate in a Board meeting as observers. Please contact the Coordinator for more information about upcoming meetings. Past events organized and supported by the Industry Board 25th & 26th March 2025 - Euro-BioImaging Academia-Industry Day and FLIM workshop (EMBL, Heidelberg) 17th April 2024 – ' Imaging services for Discovery and Translational Research ' (Torino, Italy) 20th April 2023 – 'BioImaging and the European Open Science Cloud' (EMBL, Heidelberg) 13th October 2022 – ' Smart Microscopy Workshop ' (EMBL, Heidelberg) 27th October 2021 – ' Nodes & Industry meeting ' (virtual) 7/8th November 2018 – Industry Board Image Data workshop (EMBL, Heidelberg) EBIB news June 2, 2025 Proteintech joins Euro-BioImaging Industry Board Euro-BioImaging is pleased to welcome Proteintech as the newest member of the Euro-BioImaging Industry Board (EBIB). A global leader in antibody and reagent production,… February 3, 2025 JEOL Ltd. joins the Euro-BioImaging Industry Board Euro-BioImaging is pleased to announce the addition of JEOL Ltd. to its Industry Board. JEOL Ltd. is a leading global manufacturer of electron… January 28, 2025 PicoQuant joins Euro-BioImaging industry internship programme PicoQuant, a leading optoelectronics company based in Berlin, has joined the Euro-BioImaging industry internship programme for Master’s students in Biomedical Imaging (BIMA) at… See all news", "headings": [ "EBIB activities", "EBIB activities", "Tech Exchange", "Euro-BioImaging Industry Board Meetings", "Past events organized and supported by the Industry Board", "EBIB news", "Proteintech joins Euro-BioImaging Industry Board", "JEOL Ltd. joins the Euro-BioImaging Industry Board", "PicoQuant joins Euro-BioImaging industry internship programme" ], "page_type": "homepage" }, { "id": "265320da", "url": "https://www.eurobioimaging.eu/our-partners/gbi/", "title": "Global BioImaging - Euro-BioImaging", "description": "Global BioImaging offers international workshops, training, and support for imaging facilities.", "documentation": "Global BioImaging An international network Global BioImaging is an international network of imaging infrastructures and communities, which was founded in 2015 supported by a EU-funded international collaboration award. It started as a project built on three collaboration frameworks between the nascent Euro-BioImaging infrastructure on one hand and Microscopy Australia, the National Imaging Facility Australia, and India BioImaging. Since these early days, Global BioImaging has grown to a large international network, currently comprising 13 imaging networks and infrastructures, representing more than 60 countries. It is funded by CZI and runs the Wellcome Trust funded Imaging4All program. Global BioImaging Network Euro-BioImaging and Global BioImaging Euro-BioImaging is not just one of founding members of Global BioImaging but actively contributes as a partner in the network to Global BioImaging's diverse activities. Euro-BioImaging Bio-Hub Director Dr. Antje Kepple r is also the Coordinator of Global BioImaging. Connecting the world Recognizing that scientific, technical and data challenges are universal and not restricted by geographical boundaries, Global BioImaging brings together imaging facility managers and technical staff, scientists and science policy officers from around the globe, to join forces and build capacity internationally. It provides a unique opportunity for international discussion and cooperation to tackle the practical challenges as well as the strategic questions linked to operating open access infrastructures for cutting edge imaging technologies in the life sciences. Annual international workshops to learn from leaders around the globe in infrastructure operation and management, research policies and technology trends. The Exchange of Experience meeting 2024 is taking place 29-31 October 2024 in Okazaki, Japan. More information and registration here . Focused meetings and working groups to discuss specific subjects and build international collaborations. Working group topics include - among others - Impact of Imaging Infrastructure, Image Data Management, Biomedical Imaging, Career Paths for Imaging Core Facility staff. Training to support the professional development of managerial and technical imaging facility staff. Trainings are available as in-person events , as well as via the Virtual Training Platform . Job Shadowing programs to allow imaging facility staff to learn from their peers around the world. Learn more here . Imaging4All initiative, backed by Wellcome Trust and led by Global BioImaging, will provide support for researchers from low/middle income countries to access imaging technologies and imaging training around the world. International recommendations on important topics for imaging core facilities. Recent recommendations include: Charting a course for success: International recommendations for Imaging Scientist Careers in core facilities Organizing training courses for core facility staff Added value of imaging core facilities Measuring imaging core facility impact", "headings": [ "Global BioImaging", "An international network", "Euro-BioImaging and Global BioImaging", "Connecting the world" ], "page_type": "homepage" }, { "id": "fd91e441", "url": "https://www.eurobioimaging.eu/our-partners/research-infrastructures/", "title": "Research infrastructures - Euro-BioImaging", "description": "Access to biobanks, imaging, ELIXIR, EU-OPENSCREEN, Instruct-ERIC services and collaborations.", "documentation": "Research infrastructures Euro-BioImaging is part of an ecosystem of many research infrastructure consortia in Europe that offers a wide range of services for life science applications - and also in other scientific domains. The Life Science Research Infrastructure services range from mouse models and drug compound libraries to biobanks, from imaging and structural biology to marine and microbial samples. Here’s an overview of our partner research infrastructures, some of which you may have heard of before. Within this ecosystem, Euro-BioImaging has signed bilateral Collaboration Agreements with several European Life Science Research Infrastructures (RIs) with whom we have particularly close collaborations. These partner research infrastructures are listed below. Research Infrastructures ELIXIR ELIXIR is a pan-European infrastructure that integrates national bioinformatics resources into a unified network, providing access to data, tools, compute resources, and expertise to support life-science research across Europe. EU-OPENSCREEN ERIC EU-OPENSCREEN is a European Research Infrastructure that provides open access to high-capacity screening platforms and a diverse compound collection for validating therapeutic targets and conducting studies in chemical biology across a range of systems. European Marine Biological Resource Centre The European Marine Biological Resource Centre (EMBRC) is a collaborative network of over 30 marine centres across 9 European countries, supporting research and innovation in marine biology by providing access to marine organisms and ecosystems. Instruct-ERIC Instruct-ERIC is a leading European research infrastructure offering comprehensive access to cutting-edge structural biology technologies, expertise, and training, aimed at understanding molecular mechanisms and advancing the field globally. A new, promising collaborative agreement among top-class life science research infrastructures was made official during the International Conference on Research Infrastructures (ICRI 2022) in Brno, Czech Republic, on October 21, 2022. This trilateral Memorandum of Understanding between Instruct-ERIC, EU-OPENSCREEN ERIC and Euro-BioImaging ERIC is designed to benefit the life science research community. 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