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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Synapse Web
 
Resource Report
Resource Website
50+ mentions
Synapse Web (RRID:SCR_003577) image collection, narrative resource, atlas, data or information 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 2026-08-03 09:32:28 69
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 organization portal, portal, funding resource, consortium, data or information resource 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) 2026-08-03 09:32:31 5
NITRC-IR
 
Resource Report
Resource Website
1+ mentions
NITRC-IR (RRID:SCR_004162) NITRC IR data repository, image database, data or information resource, database, image repository, catalog, storage service resource, service resource Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data. database, neuroimaging, magnetic resonance, mri, image collection, nifti, dicom uses: XNAT Central
is used by: NIF Data Federation
lists: 1000 Functional Connectomes Project
lists: studyforrest.org
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: 1000 Functional Connectomes Project
is related to: NITRC Enhanced Services
has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC)
Bipolar Disorder, Schizophrenia, Parkinson's disease, ADHD NINDS R44 NS074540;
NIBIB U24 EB023398
PMID:26044860 Free, Available for download, Freely available nlx_18447, SCR_015623 SCR_004162 NeuroImaging Tools and Resources Collaboratory Image Repository, NITRC Image Repository 2026-08-03 09:32:37 8
MNE software
 
Resource Report
Resource Website
50+ mentions
MNE software (RRID:SCR_005972) MNE software toolkit, software application, data processing software, data analysis software, software resource, data visualization software 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
NIBIB R01 EB009048;
NIBIB P41 EB015896;
NCRR P41 RR014075;
NIDCD F32DC012456;
NSF 0958669;
NSF 1042134;
European Research Council (ERC) StG-263584
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 2026-08-03 09:32:50 97
BrainSuite
 
Resource Report
Resource Website
50+ mentions
BrainSuite (RRID:SCR_006623) BrainSuite software application, data processing software, image analysis software, software resource, data visualization software 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 2026-08-03 09:33:06 93
neurodata
 
Resource Report
Resource Website
50+ mentions
neurodata (RRID:SCR_014264) data repository, portal, data or information resource, service resource, storage service resource, image repository, software resource, project portal Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs. neuroscience, neuroimage, graph explorer, data repository, johns hopkins university, BRAIN Initiative, FASEB list is related to: Open Connectome Project
has parent organization: Johns Hopkins University; Maryland; USA
NSF 1707298;
NIDA R01 DA036400;
NIBIB R01 EB016411;
NIH Office of the Director R01 OD19123;
NSF ACI-1261715;
NSF OCI-1040114;
DARPA
Free, Freely available https://neurodata.io/tools/ SCR_014264 2026-08-03 09:35:39 93
NetPyNE
 
Resource Report
Resource Website
10+ mentions
NetPyNE (RRID:SCR_014758) network analysis software, software application, data processing software, data analysis software, software resource Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. Simulation, analysis, neuronal, network, NEURON, simulator, BRAIN Initiative uses: Python Programming Language
is recommended by: BRAIN Initiative
works with: NEURON
NIBIB EB022903 DOI:10.7554/eLife.44494.001 Free, Available for download, Freely available http://www.neurosimlab.org/netpyne/overview.html SCR_014758 Network development Python package for NEURON 2026-08-03 09:35:50 26
Group ICA Of EEG Toolbox
 
Resource Report
Resource Website
1+ mentions
Group ICA Of EEG Toolbox (RRID:SCR_002478) EEGIFT software toolkit, software application, data processing software, data analysis software, software resource Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher. matlab, eeg, independent component analysis, magnetic resonance, algorithm is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Group ICA of fMRI Toolbox
has parent organization: MIALAB - Medical Image Analysis Lab
NIH ;
NIBIB 1R01EB000840
PMID:21747835 Available for download nlx_155861 http://www.nitrc.org/projects/gift SCR_002478 Group ICA Of EEG Toolbox (EEGIFT) 2026-08-03 09:31:42 5
NUTMEG
 
Resource Report
Resource Website
10+ mentions
NUTMEG (RRID:SCR_002748) NUTMEG software application, data processing software, 1d time-series analysis software, data analysis software, signal processing software, image analysis software, 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 2026-08-03 09:31:59 29
MGED Ontology
 
Resource Report
Resource Website
1+ mentions
MGED Ontology (RRID:SCR_004484) MO controlled vocabulary, data or information resource, ontology An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. microarray, biomaterial, treatment, mage, owl is listed by: BioPortal
is related to: MIAME
is related to: MIAME
is related to: RNA Abundance Database
has parent organization: Functional Genomics Data Society
has parent organization: SourceForge
NIBIB ;
NHGRI P41HG003619
PMID:16428806 nlx_47223 http://purl.bioontology.org/ontology/MO SCR_004484 Microarray and Gene Expression Data Ontology 2026-08-03 09:32:34 1
Laplace Beltrami Filter on QuadEdge Meshes
 
Resource Report
Resource Website
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) data acquisition software, software resource, software application, data processing software A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. data acquisition software, filter, laplace beltrami, surface harmonic is used by: Insight Segmentation and Registration Toolkit
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
NIBIB R01-EB008171-01A1;
NCRR P41-RR015241
Available to the research community SCR_014133 Laplace-Beltrami Filter on QuadEdge Meshes 2026-08-03 09:35:23 0
NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering
 
Resource Report
Resource Website
1+ mentions
NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) software application, data processing software, segmentation software, image analysis software, software resource A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet. matlab gui, pet image, region of interest, 2d, 3d, segmentation, affinity propagation clustering Howard Hughes Medical Institute ;
Center for Infectious Disease Imaging ;
NIAID Intramural research program ;
NIBIB ;
NIH Directors New Innovator Award OD006492;
NIAD R01AI079590;
NIAID R01A1035272
Available to the research community http://www.nitrc.org/projects/ap_seg_2013_nih SCR_014151 2026-08-03 09:35:36 1
Slicer3 Module Rician noise filter
 
Resource Report
Resource Website
1+ mentions
Slicer3 Module Rician noise filter (RRID:SCR_009614) Slicer3:Module:Rician Noise Removal image processing software, software resource, software application, data processing software 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 2026-08-03 09:34:25 1
LONI Brain Parser
 
Resource Report
Resource Website
1+ mentions
LONI Brain Parser (RRID:SCR_009572) Brain Parser software application, data processing software, segmentation software, image analysis software, 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 2026-08-03 09:34:24 3
OpenElectrophy
 
Resource Report
Resource Website
10+ mentions
OpenElectrophy (RRID:SCR_000819) OpenElectrophy software resource, data processing software, software application, data analysis software Software Python module for electrophysiology data analysis. neurophysiology, electrophysiology, python, intracellular, extracellular, data sharing, analysis sharing, neural signal, spike, oscillation, mysql, eeg, meg, electrocorticography uses: Neo
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
has parent organization: NeuralEnsemble
NIBIB 5R24EB029173 PMID:19521545 THIS RESOURCE IS NO LONGER IN SERVICE nlx_151873 http://www.nitrc.org/projects/openelectrophy, https://sources.debian.org/src/openelectrophy/ SCR_000819 2026-08-03 09:31:09 10
Insight Segmentation and Registration Toolkit
 
Resource Report
Resource Website
50+ mentions
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) ITK topical portal, data or information resource, software resource, portal Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk uses: Laplace Beltrami Filter on QuadEdge Meshes
uses: VTK
is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
is used by: Displacement Field Viewer
is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Vaa3D
is related to: elastix
is related to: VMTK in 3D Slicer
is related to: NA-MIC Kit
is related to: SimpleITK
NIBIB EB006733;
NIBIB EB008374;
NIBIB EB009634;
NCRR P41RR013218
Free, Available for download, Freely available nif-0000-00319 http://www.nitrc.org/projects/insighttoolkit SCR_001149 Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit 2026-08-03 09:31:17 83
Diffusion Tensor Imaging ToolKit
 
Resource Report
Resource Website
10+ mentions
Diffusion Tensor Imaging ToolKit (RRID:SCR_001642) DTI-TK software toolkit, software application, data processing software, image analysis software, software resource A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation dti, visualization, segmentation, resampling, smoothing, warping, registration, spatial normalization, atlas construction, analysis, atlas application, intersubject, image-to-template, analyze, nifti-1, macos, linux is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Diffusion MRI of Traumatic Brain Injury
is related to: Camino
is related to: MRI Studio
has parent organization: University of Pennsylvania; Philadelphia; USA
has parent organization: SourceForge
NIBIB 1R03EB009321-01 Free, Available for download, Freely available nlx_153914 http://www.nitrc.org/projects/dtitk SCR_001642 2026-08-03 09:31:30 22
Brainstorm
 
Resource Report
Resource Website
500+ mentions
Brainstorm (RRID:SCR_001761) Brainstorm software application, data processing software, data analysis software, software resource, data visualization software Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: OpenMEEG
is related to: Open MEG Archive
is related to: MATLAB
has parent organization: University of Southern California; Los Angeles; USA
NIBIB R01 EB002010;
NIBIB R01 EB009048;
NIBIB R01 EB000473;
NIBIB R01 EB026299;
CNRS ;
McGill University
PMID:21584256 Free, Available for download, Freely available nif-0000-10267 http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 SCR_001761 brainstorm3 2026-08-03 09:31:33 558
ITK-SNAP
 
Resource Report
Resource Website
1000+ mentions
ITK-SNAP (RRID:SCR_002010) software application, data processing software, segmentation software, image analysis software, 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 2026-08-03 09:31:36 2629
Group ICA of fMRI Toolbox
 
Resource Report
Resource Website
1000+ mentions
Group ICA of fMRI Toolbox (RRID:SCR_001953) GIFT software toolkit, software application, data processing software, image analysis software, software resource Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki. independent component analysis, matlab, magnetic resonance, fmri, algorithm is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Group ICA Of EEG Toolbox
has parent organization: MIALAB - Medical Image Analysis Lab
NIBIB 1R01EB000840 PMID:18165105 Free, Available for download, Freely available SCR_024416, nif-0000-00309 http://www.nitrc.org/projects/gift http://mialab.mrn.org/software/gift/ SCR_001953 Group ICA Of fMRI Toolbox (GIFT) 2026-08-03 09:31:39 1411

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