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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NeuralAct Resource Report Resource Website 10+ mentions |
NeuralAct (RRID:SCR_002066) | NeuralAct | software resource | Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo. | brain, imaging, electrocorticographic, eeg, meg, dot, matlab, cortex, visualization, neural activity | NIH ; NIBIB EB006356; NIBIB EB000856; United States army research office W911NF-08-1-0216; United States army research office W911NF-07-1-0415 |
PMID:25381641 | Free, Available for download, Freely available | SciRes_000162 | http://www.neuralgate.org/software | SCR_002066 | NeuralAct: A tool to visualize cortical activity on a 3D model of the cortex | 2026-02-14 02:00:18 | 13 | |||||
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SCORE Resource Report Resource Website 100+ mentions |
SCORE (RRID:SCR_014165) | data or information resource, experimental protocol, narrative resource | A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. | experiment protocol, method, different image algorithm, quantitative score |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NLM HHSN276201000584P; NIBIB 1R41 EB011796 |
SCR_014165 | 2026-02-14 02:02:38 | 458 | ||||||||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 10+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-02-14 02:02:58 | 47 | |||||||
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Computer Integrated Systems for Microscopy and Manipulation Resource Report Resource Website 1+ mentions |
Computer Integrated Systems for Microscopy and Manipulation (RRID:SCR_001413) | CISMM | training resource | Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies. | microscope, visual analytics, image analysis, biomedical, bioinstrumatics, scanning electron microscope, light microscope, microscopy | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Thrombosis, Lung disease, Cancer | NIBIB 5-P41-EB002025 | Freely Available | nlx_152648 | http://cismm.cs.unc.edu/ | SCR_001413 | UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation | 2026-02-14 02:00:00 | 8 | ||||
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Center for Biomedical OCT Research Resource Report Resource Website 1+ mentions |
Center for Biomedical OCT Research (RRID:SCR_001418) | CBORT | training resource | Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. | imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015903 | Free, Freely Available | nlx_152640 | SCR_001418 | Center for Biomedical OCT Research and Translation | 2026-02-14 02:00:03 | 2 | ||||||
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BioMEMS Resource Center Resource Report Resource Website 1+ mentions |
BioMEMS Resource Center (RRID:SCR_001417) | BMRC | training resource | Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments. | cell, tissue, microengineering, diagnostics, chip | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | NIBIB 5P41EB002503-12 | Free, Freely Available | nlx_152639 | SCR_001417 | Bio MicroElectroMechanical Systems (BioMEMS) Resource Center, Biomicroelectromechanical Systems (BioMEMS) Resource Center, BioMEMS, Bio MicroElectroMechanical Systems Resource Center | 2026-02-14 02:00:09 | 4 | ||||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | data or information resource, database, resource | An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-02-14 02:01:13 | 0 | ||||||
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Center for EPR Imaging in Vivo Physiology Resource Report Resource Website |
Center for EPR Imaging in Vivo Physiology (RRID:SCR_001410) | Center for EPR Imaging in Vivo Physiology | biomedical technology research center, training resource | Biomedical technology research center that develops instrumentation, analysis techniques, spin probes and spin traps, and methodologies for imaging physiologically relevant aspects of tissue fluids, including high-resolution oxygen maps, with very low frequency electron paramagnetic resonance imaging (EPRI). Novel bridges and high-access, low-field magnet/gradient systems have produced physiologically relevant measurements and accommodate a number of resonant structures. The Center is a consortium between the University of Chicago, the University of Denver, the University of Maryland and Novosibirsk Institute of Organic Chemistry (NIOC), Russia. | electron paramagnetic resonance, in vivo, spin probe | has parent organization: University of Chicago; Illinois; USA | Diseased, Healthy | NIBIB 4P41EB002034-17 | nlx_152632 | SCR_001410 | Center for Electron Paramagnetic Resonance (EPR) Imaging in Vivo Physiology, Center for Electron Paramagnetic Resonance Imaging in Vivo Physiology, Very Low Frequency ERP Imaging In Vivo Physiology | 2026-02-14 02:07:44 | 0 | ||||||
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Laser Microbeam and Medical Program Resource Report Resource Website 1+ mentions |
Laser Microbeam and Medical Program (RRID:SCR_001409) | LAMMP | biomedical technology research center, training resource | Biomedical technology research center dedicated to the use of lasers and optics in biology and medicine with activities in technological research and development, collaborative research, service, training, and dissemination. One of the primary goals of LAMMP is to facilitate translational research by rapidly moving basic science and technology discoveries from blackboard to benchtop to bedside. This is accomplished by combining state of the art optical technologies with specialized resource facilities for cell and tissue engineering, histopathology, pre-clinical animal models, and clinical care. The resource center has been organized into 3 cores: * Microscopy and Microbeam Technologies (MMT) for high-resolution functional imaging and manipulation of living cells and tissues * Medical Translational Technologies (MTT) for non- and minimally-invasive monitoring, treating, and imaging pre-clinical animal models and human subjects, and * Virtual Photonics Technologies (VPT) for developing computational models and methods that advance the performance of biophotonic technologies, and enhance the information content derived from optical measurements. LAMMP cores contain complementary technologies that are capable of quantitatively characterizing, imaging, and perturbing structure and biochemical function in cells and tissues with scalable resolution and depth sensitivity ranging from micrometers to centimeters. | laser, optics, biology, medicine, imaging, microscopy, microbeam, photonics, computational model, cell, tissue | has parent organization: University of California at Irvine; California; USA | NIBIB P41EB015890 | Free, Freely Available | nlx_152631 | http://lammp.bli.uci.edu/ | SCR_001409 | 2026-02-14 02:07:18 | 4 | ||||||
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Pittsburgh NMR Center for Biomedical Research Resource Report Resource Website |
Pittsburgh NMR Center for Biomedical Research (RRID:SCR_001408) | Pittsburgh NMR Center for Biomedical Research | biomedical technology research center, training resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Biomedical Technology Research Center that develops methodologies for the acquisition of morphological, biochemical, cellular, and functional information in living animals using nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS). Novel techniques utilizing multidimensional MR imaging, magnetic resonance microscopy (MRM), and multinuclear in vivo spectroscopy are being applied to a wide range of problems in the biomedical sciences. | mri, magnetic resonance spectroscopy, imaging, in vivo, nuclear magnetic resonance imaging, magnetic resonance microscopy, multinuclear | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIBIB P41 EB001977 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152651 | SCR_001408 | 2026-02-14 02:07:48 | 0 | |||||||
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Hyperpolarized MRI Technology Resource Center Resource Report Resource Website |
Hyperpolarized MRI Technology Resource Center (RRID:SCR_001405) | Hyperpolarized MRI Technology Resource Center | biomedical technology research center, training resource | Biomedical technology research center developing, investigating, and disseminating new hyperpolarized MR techniques, new 13C agents and specialized analysis open-source software for data reconstruction and interpretation. The Technology Research & Development projects will leverage the extensive DNP facilities and experience of the project leaders to develop improved, robust hyperpolarized MRI methods. These technology developments will be driven by Collaborative Projects led by outstanding clinical and basic scientists who aim to use hyperpolarized 13C MRI to accomplish the scientific goals of their funded research. These technical developments will also be disseminated to the Service Project investigators for extramural feedback and then widely to the scientific community via a dedicated website and onsite training. This center will provide state-of-the-art training in this new metabolic imaging field and sponsor a yearly symposium focused on hyperpolarized MR technology development. | mri, hyperpolarized, dynamic nuclear polarization, imaging, carbon-13 | has parent organization: University of California at San Francisco; California; USA | NIBIB P41EB013598 | Free, Freely Available | nlx_152628 | SCR_001405 | UCSF Hyperpolarized MRI Technology Resource Center | 2026-02-14 02:07:44 | 0 | ||||||
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Medical Information Mart for Intensive Care-III Resource Report Resource Website 100+ mentions |
Medical Information Mart for Intensive Care-III (RRID:SCR_017384) | MIMIC-III, MIMIC 3 | data or information resource, database | Collection of comprising deidentified health related data associated with patients who stayed in critical care units of Beth Israel Deaconess Medical Center between 2001 and 2012. Database includes information such as demographics, vital sign measurements made at bedside (~1 data point per hour), laboratory test results, procedures, medications, caregiver notes, imaging reports, and mortality (both in and out of hospital). | deidentified, health-related data, Beth Israel Deaconess Medical Center, , FASEB list | NIBIB | Freely Available, Free, Available for Download | https://physionet.org/users/help/data-sharing/ | SCR_017384 | , MIMIC-III, MIMIC 3, 3, MIMIC, Medical Information Mart for Intensive Care, Medical Information Mart for Intensive Care-III | 2026-02-14 02:06:31 | 174 | |||||||
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MRI Studio Resource Report Resource Website 100+ mentions |
MRI Studio (RRID:SCR_001398) | software application, data visualization software, image processing software, data processing software, software resource, image analysis software | An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration | tensor calculation, color mapping, fiber tracking, 3d visualization, dti, image registration, mri, diffusion mr fiber tracking, microsoft, c++, analyze |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion Tensor Imaging ToolKit has parent organization: Johns Hopkins University; Maryland; USA works with: UManitoba - JHU Functionally Defined Human White Matter Atlas |
NCRR ; Biomedical Informatics Research Network ; NIBIB |
Free, Freely Available | nif-0000-00291 | http://www.nitrc.org/projects/mri_studio | SCR_001398 | dtiStudio, DTI Studio | 2026-02-15 09:18:05 | 165 | ||||||
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PNEUMA Resource Report Resource Website 1+ mentions |
PNEUMA (RRID:SCR_001391) | PNEUMA | software application, simulation software, software toolkit, software resource | A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer. | matlab, simulate, autoregulation, cardiovascular system, respiratory system, sleep-wake state, physiological intervention, pharmacological intervention, drug, breathing, heart rate, blood pressure, respiration, glucose, insulin, fatty acid, regulation, autonomic nervous system, chemoreflex, ventilation, circulation, cardiorespiratory, metabolic control system, circadian, regulation, epinephrine | has parent organization: Biomedical Simulations Resource | NIBIB P41-EB001978; NCRR P41-RR01861 |
PMID:17271149 | Free, Freely Available | nlx_152572 | SCR_001391 | 2026-02-15 09:18:05 | 3 | ||||||
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Center for Gamma Ray Imaging Resource Report Resource Website |
Center for Gamma Ray Imaging (RRID:SCR_001384) | Center for Gamma-Ray Imaging | service resource, instrument manufacture, material service resource, production service resource | Biomedical technology resource center that develops new gamma-ray imaging instruments and techniques that yield substantially improved spatial and temporal resolutions. The Center makes its imagers and expertise available to a wide community of biomedical and clinical researchers through collaborative and service-oriented interactions. The collaborative research applies these new imaging tools to basic research in functional genomics, proteomics, cancer, cardiovascular disease and cognitive neuroscience, and to clinical research in tumor detection and other selected topics. There are five core research projects: * Detector technology research and development * Reconstruction algorithms and system modeling * Data acquisition, signal processing, and system development * Image-quality assessment and system optimization * Techniques for molecular imaging | spect, ct, imaging, clinical, gamma-ray, imaging instrument, basic research, functional genomics, cardiovascular disease, cognitive neuroscience, breast cancer, tumor detection, proteomics, cancer | has parent organization: University of Arizona; Arizona; USA | NIBIB EB002035-14 | nlx_152567 | SCR_001384 | 2026-02-15 09:18:05 | 0 | ||||||||
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National ESCA and Surface Analysis Center for Biomedical Problems Resource Report Resource Website 1+ mentions |
National ESCA and Surface Analysis Center for Biomedical Problems (RRID:SCR_001430) | NESAC/BIO | biomedical technology research center, training resource, service resource, production service resource, material analysis service, access service resource, biomaterial analysis service, analysis service resource | Biomedical technology research center that provides state-of-the-art surface analysis expertise, instrumentation, experimental protocols, and data analysis methods to address surface-related biomedical problems. NESAC/BIO develops and applies surface science methodologies that produce a full understanding of the surface composition, structure, spatial distribution, and orientation of biomaterials and adsorbed biomolecules. The NESAC/BIO program identifies areas where surface science must evolve to keep pace with the growth in biochemical knowledge and biomaterial fabrication technology, and develops instrumentation, experimental protocols, and data analysis methods to achieve this evolution. NESAC/BIO provides state-of-the-art surface analysis tools to researchers in the biomedical community. You can gain access to the NESAC/BIO facilities in one of the following ways: * Collaborative: Propose a project to collaborate on with NESAC/BIO. The project should be rewarding for both groups, and the results should reflect the utility of surface analysis for biomedical research * Service: Ask NESAC/BIO to analyze your biomaterial specimens. The spectra obtained from the analyses will be interpreted for you. * Training: Visit the University of Washington to receive training in surface analysis and personally run experiments for your individual research projects. These experiments should have a high probability for yielding useful information and should not involve the development of new ESCA techniques or methodologies. | surface, composition, structure, spatial distribution, orientation, biomaterial, biomolecule, surface science, biochemical, biomaterial fabrication, surface analysis | has parent organization: University of Washington; Seattle; USA | NIBIB 5P41RR001296-11 | Free, Freely Available | nlx_152654 | SCR_001430 | NESAC/BIO - National ESCA and Surface Analysis Center for Biomedical Problems | 2026-02-15 09:18:06 | 1 | ||||||
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Farsight Toolkit Resource Report Resource Website 1+ mentions |
Farsight Toolkit (RRID:SCR_001728) | FARSIGHT | software application, image processing software, data processing software, software resource, image analysis software, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. | editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image | has parent organization: University of Houston; Texas; USA | NIBIB R01-EB005157; NSF EEC-9986821; NIBIB R01EB005157 |
PMID:24808857 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10227 | SCR_001728 | FARSIGHTWiki | 2026-02-15 09:18:10 | 2 | |||||
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Atlas3D Resource Report Resource Website 10+ mentions |
Atlas3D (RRID:SCR_001808) | software application, data visualization software, data processing software, software resource, atlas, data or information resource | A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images. | analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oslo; Oslo; Norway |
Research Council of Norway ; NIH ; NIBIB R01-EB00790; NCRR U24-RR021382 |
Free, Freely available | nif-0000-10373 | http://www.nitrc.org/projects/incf_atlas3d | SCR_001808 | Neural Systems and Graphics Computing Laboratory: Atlas3D Software, NeSys Atlas3D | 2026-02-15 09:18:11 | 17 | ||||||
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Reproducible Brain Charts Resource Report Resource Website |
Reproducible Brain Charts (RRID:SCR_027837) | data or information resource, data set | Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner. | Neuroimaging data, curated data, data resource, mapping brain development, mental health, | NIMH R01MH120482; NIMH R37MH125829; NIBIB R01EB022573; NIMH R01MH112847; NIMH R01MH113550; NIMH RF1MH121867; NIMH R01MH123550; NINDS U24NS130411; NIMH P50MH109429; NIMH R01MH123440; NIMH K08MH079364 |
PMID:40987284 | Free, Freely available | SCR_027837 | 2026-02-14 02:09:32 | 0 | |||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | source code, data analysis service, software resource, data set, data access protocol, web service, service resource, storage service resource, data repository, production service resource, data or information resource, image repository, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01; |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me http://www.nitrc.org/projects/ocp/ |
SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-02-15 09:18:39 | 7 |
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