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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MNE software Resource Report Resource Website 100+ mentions |
MNE software (RRID:SCR_005972) | MNE | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. | Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MNE-BIDS is related to: MATLAB is related to: NumPy is related to: SciPy is related to: Matplotlib is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project is related to: NiBabel |
European Research Council (ERC) StG-263584; NCRR P41 RR014075; NIBIB P41 EB015896; NIBIB R01 EB009048; NIDCD F32DC012456; NSF 0958669; NSF 1042134 |
PMID:24161808 PMID:24431986 |
Free, Available for download, Freely available | nlx_151346 | https://sources.debian.org/src/python3-mne/, http://www.nitrc.org/projects/mne, http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html, https://github.com/mne-tools/, https://mne.tools/ | SCR_005972 | Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python | 2026-09-12 12:56:33 | 114 | ||||
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Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki Resource Report Resource Website 10+ mentions |
Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki (RRID:SCR_008046) | IMAG | group | Special interest group that brings together program officers who have a shared interest in applying modeling and analysis methods to biomedical systems. The meetings are formatted to facilitate an open discussion of what is currently being supported, and for planning future directions in these areas. At each meeting, time is allotted to hear focused presentations from one or two participants to discuss issues relating to modeling and analysis across the government agencies. Discussions also occur online, and participants are informed of talks, conferences and other activities of interest to the group. IMAG recognized that the modeling community is on the forefront of thinking across the biological continuum, rather than just focusing at one scale or level of resolution. In addition IMAG identified a strong desire among modelers to form multi-disciplinary partnerships across varied research communities. Overall Intent of IMAG through the MSM Consortium is: * To develop new methodologies that span across biological scales * To develop multiscale methodologies applicable to biomedical, biological and behavioral research * To develop methodologies within the local multidisciplinary team and within the larger Framework environment * To further promote multiscale modeling through model sharing This wiki contains information relevant to the IMAG (Interagency Modeling and Analysis Group) and the MSM (Multi-scale Modeling Consortium). | environment, analysis, behavioral, biological, biomedical, continuum, modeling, research, scale, system |
is listed by: 3DVC has parent organization: National Institute of Biomedical Imaging and Bioengineering |
NIBIB ; NIH Blueprint for Neuroscience Research |
nif-0000-10261 | SCR_008046 | IMAG wiki, MSM wiki | 2026-09-12 12:56:59 | 15 | |||||||
|
Charged Fluid Model for Brain Image Segmentation Resource Report Resource Website |
Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) | CFMBIS | data processing software, image analysis software, segmentation software, software application, software resource | A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats. | plugin, software, 2D image, brain image segmentation, brain MR image, image analysis, segementation |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
Available for educational and research purposes only | nif-0000-23325 | SCR_008281 | 2026-09-12 12:57:02 | 0 | |||||||
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MultiPhase-SEG Resource Report Resource Website |
MultiPhase-SEG (RRID:SCR_008275) | data processing software, image analysis software, segmentation software, software application, software resource | A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed. | segementation, visualization, 3D, software |
is related to: Laboratory of Neuro Imaging is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23319 | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 | SCR_008275 | 2026-09-12 12:57:02 | 0 | |||||||
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DualSurfaceMin Resource Report Resource Website |
DualSurfaceMin (RRID:SCR_008278) | DSM | data processing software, image processing software, software application, software resource | The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats. | software, image processing, optimization, deformable surface, surface extraction |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23322 | SCR_008278 | 2026-09-12 12:57:02 | 0 | |||||||
|
Sub-Volume Thresholding Analysis Resource Report Resource Website |
Sub-Volume Thresholding Analysis (RRID:SCR_008272) | SVT | data analysis software, data processing software, software application, software resource | Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software. | data processing, data analysis, functional magnetic resonance imaging, fMRI, software, brain, brain functional studies |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23314 | SCR_008272 | 2026-09-12 12:57:02 | 0 | |||||||
|
BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data processing software, data visualization software, image analysis software, software application, software resource | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-09-12 12:56:42 | 97 | |||||
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MRM NeAt (Neurological Atlas) Mouse Brain Database Resource Report Resource Website 1+ mentions |
MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) | MRM NeAt | atlas, data or information resource, database, image collection, reference atlas | Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data. | phenotype, mouse, brain, computational biology, in vivo, mouse brain atlas, magnetic resonance microscopy, mouse brain morphometry, image registration, in vitro, 3d brain atlas, adult mouse, male, c57bl/6j, autosegmentation, probabilistic atlas, t2 weighted protocol |
is related to: Mouse Brain Image Visualizer (MBIV) is related to: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery has parent organization: University of Florida; Florida; USA is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery |
National High Magnetic Field Laboratory ; NIBIB R01 EB 0023304; NCRR P41 RR16105; NIMH P50 MH58911 |
PMID:16165303 PMID:18958199 |
Registration required | nlx_59497 | http://brainatlas.mbi.ufl.edu | SCR_007053 | Magnetic Resonance Microimaging Neurological Atlas Mouse Brain Database, MRM Neurological Atlas Mouse Brain Database, C57BL/6J Mouse Atlas, Atlas of Adult C57BL/6J Mouse Brain, MRM NeAt Mouse Brain Database | 2026-09-12 12:56:49 | 8 | ||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | catalog, data or information resource, data repository, database, service resource, storage service resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-09-12 12:56:48 | 40 | ||||
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WFU PickAtlas Resource Report Resource Website 1000+ mentions |
WFU PickAtlas (RRID:SCR_007378) | PickAtlas | data processing software, image processing software, software application, software resource | A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | neuroanatomy, cytoarchitecture, fmri, matlab, brain, brain region, talairach daemon, analyze, atlas application, matlab, microsoft, magnetic resonance, posix/unix-like, win32 (ms windows), windows, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: SoftCite is related to: Talairach Daemon has parent organization: Wake Forest School of Medicine; North Carolina; USA |
NIBIB 1R03EB008670 | PMID:12880848 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00358 | SCR_007378 | WFU_PickAtlas | 2026-09-12 12:56:54 | 1276 | |||||
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Slicer3 Module Rician noise filter Resource Report Resource Website 1+ mentions |
Slicer3 Module Rician noise filter (RRID:SCR_009614) | Slicer3:Module:Rician Noise Removal | data processing software, image processing software, software application, software resource | Two Slicer3 modules removing rician noise in diffusion tensor MRI | c++, console (text based), linux, magnetic resonance, posix/unix-like, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 3D Slicer |
NIH Roadmap for Medical Research ; NIBIB U54 EB005149; NCRR 2-P41-RR12553-07 |
PMID:17354881 | GNU General Public License | nlx_155836 | http://www.nitrc.org/projects/dtiricianrem | SCR_009614 | 2026-09-12 12:57:14 | 1 | |||||
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LONI Brain Parser Resource Report Resource Website 1+ mentions |
LONI Brain Parser (RRID:SCR_009572) | Brain Parser | data processing software, image analysis software, segmentation software, software application, software resource | Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest. | analyze, anatomic, application, c++, console (text based), labeling, linux, microsoft, magnetic resonance, posix/unix-like, region of interest, segmentation, sh/bash, unix shell, windows, windows nt/2000, windows vista, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
GNU General Public License, LONI Software License | nlx_155783 | http://www.nitrc.org/projects/brainparser | SCR_009572 | BrainParser | 2026-09-12 12:57:13 | 3 | |||||
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Center for Integration of Medicine and Innovative Technology Resource Report Resource Website 1+ mentions |
Center for Integration of Medicine and Innovative Technology (RRID:SCR_003710) | CIMIT | consortium, data or information resource, funding resource, organization portal, portal | A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients. | device, procedure, diagnosis, healthcare, consortium, clinical, systems engineering, technology, patient care, translational research, medicine, science, engineering, innovation, consortium |
is listed by: Consortia-pedia has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Charles Stark Draper Laboratory |
United States Department of Defense ; Membership fees ; NIBIB |
nlx_157880 | SCR_003710 | Center for Integration of Medicine & Innovative Technology, Center for Integration of Medicine and Innovative Technology (CIMIT) | 2026-09-12 12:56:01 | 6 | |||||||
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Synapse Web Resource Report Resource Website 50+ mentions |
Synapse Web (RRID:SCR_003577) | atlas, data or information resource, image collection, narrative resource, training material | A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy. | electron microscopy, 3d reconstruction, neuroanatomy, astrocyte, axon, brain, cellular, dendrite, hippocampus, micrograph, microscopy, neurocytology, organelle, structure, synapse, tissue, ultrastructural, light microscopy, neuron, rat, experimental protocol, synapse structure |
is used by: NIF Data Federation has parent organization: University of Texas at Austin; Texas; USA |
The Human Brain Project ; NIDA R01 MH/DA 57351; NIMH R01 MH/DA 57351; NIBIB EB002170 |
Copyrighted, Acknowledgement required | nif-0000-00026 | SCR_003577 | SynapseWeb | 2026-09-12 12:56:00 | 73 | |||||||
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NUTMEG Resource Report Resource Website 10+ mentions |
NUTMEG (RRID:SCR_002748) | NUTMEG | 1d time-series analysis software, data analysis software, data processing software, image analysis software, signal processing software, software application, software resource, time-series analysis software | Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms. | MEG, EEG, analysis, reconstructing, neural, activation, overlaying, structural, MR, image, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at San Francisco; California; USA |
NIBIB EB022717; NIDCD F31 DC006762; NIDCD R01 DC004855 |
PMID:16012626 | nif-0000-24052 | http://www.nitrc.org/projects/nutmeg, | http://www.radiology.ucsf.edu/research/labs/biomagnetic-imaging/nutmeg | SCR_002748 | Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography | 2026-09-12 12:55:45 | 31 | ||||
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EONS Resource Report Resource Website 10+ mentions |
EONS (RRID:SCR_002979) | EONS | simulation software, software application, software resource | Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux. | synapse, geometry, distribution hypothesis, 2d, synaptic modeling, synaptic, modeling, neuron, nervous system, presynaptic, postsynaptic, electromicrograph, animation, simulation, calcium channel, synaptic cleft, excitatory postsynaptic potential, potassium channel, computational neuroscience, java, macos, microsoft, windows, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Simulations Resource |
NIBIB P41-EB001978 | PMID:17946227 | Free, Available for download, Freely available | nif-0000-00504 | http://www.nitrc.org/projects/eons, http://synapticmodeling.com/ | http://www.synaptic-modeling.com | SCR_002979 | Elementary Objects of the Nervous System, EONS-The integrated synaptic modeling platform, EONS (Elementary Objects of the Nervous System) | 2026-09-12 12:55:49 | 12 | |||
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XNAT - The Extensible Neuroimaging Archive Toolkit Resource Report Resource Website 50+ mentions |
XNAT - The Extensible Neuroimaging Archive Toolkit (RRID:SCR_003048) | XNAT | data management software, data processing software, software application, software resource, source code | Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data. | analyze, client application, collaboration, data archive, data management, data sharing, data store, informatics, metadata, middleware, middleware engine, neuroinformatics, open source, productivity task, quality control, sharing, software platform, user interface, workflow, xml schema, neuroimaging, mri, processing, image, clinical, dicom, anonymization, clinical assessment, application, ct, database application, eeg, meg, ecog, java, magnetic resonance, nifti-1, os independent, pet, spect, platform, web environment, FASEB list |
is used by: studyforrest.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MIRIAD is related to: pyxnat is related to: XNAT Extras is related to: XNAT Central is related to: NUNDA is related to: CardioVascular Research Grid (CVRG) is related to: ConnectomeDB is related to: NA-MIC Kit has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIBIB R01 EB009352; NIBIB U54 EB005149 |
PMID:17426351 | Free, Available for download, Freely available | nif-0000-00531 | http://www.nitrc.org/projects/xnat, https://sources.debian.org/src/xnat/ | SCR_003048 | Extensible Neuroimaging Archive Toolkit, Extensible Neuroimaging Archive Toolkit (XNAT) | 2026-09-12 12:55:50 | 66 | ||||
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BioImage Suite Resource Report Resource Website 50+ mentions |
BioImage Suite (RRID:SCR_002986) | data processing software, data visualization software, image analysis software, image processing software, software application, software resource | Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM. | Analysis, multimodal, multispecies, neuroimaging, data, DTI, fMRI, processing, visualization, registration, surface, editing, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: 3D Slicer has parent organization: Yale University; Connecticut; USA |
NIBIB R01 EB006494; NIBIB R03 EB012969; NIMH MH114805 |
PMID:21249532 | Free, Available for download, Freely available | nif-0000-30179 | https://sources.debian.org/src/bioimagesuite/, http://www.nitrc.org/projects/bioimagesuite, https://medicine.yale.edu/bioimaging/suite/ | http://bioimagesuite.yale.edu/index.aspx | SCR_002986 | Bioimagesuite Web | 2026-09-12 12:55:49 | 65 | ||||
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IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | data processing software, image analysis software, image processing software, software application, software resource, source code | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-09-12 12:55:55 | 1685 | ||||
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ITK-SNAP Resource Report Resource Website 1000+ mentions |
ITK-SNAP (RRID:SCR_002010) | data processing software, image analysis software, segmentation software, software application, software resource | Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). | medical, image, segmentation, delineating, anatomical, structure, region, MRI, CT, 3D image, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: neurodebian is related to: AHEAD is related to: LiverSegm is related to: Waxholm Space Atlas of the Sprague Dawley Rat Brain is related to: Waxholm Space has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB014346 | PMID:29946897 | Free, Available for download, Freely available | nif-0000-00317 | https://github.com/google/neuroglancer, https://opensource.google.com/projects/neuroglancer | SCR_002010 | 2026-09-12 12:55:35 | 2647 |
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