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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MassGeneral Institute for Neurodegenerative Disease Resource Report Resource Website 1+ mentions |
MassGeneral Institute for Neurodegenerative Disease (RRID:SCR_008746) | MIND | biomaterial supply resource, brain bank, material resource, tissue bank | An institute whose mission is to translate laboratory discoveries into prevention, treatment and cures for Alzheimer's, ALS, Huntington's, Parkinson's and other neurodegenerative diseases. MIND seeks to accelerate therapies that lessen the toll of disease on patients and families. Researchers of the institute collaborate, strategize, and share technology to find treatment for these diseases. As promising leads are developed in one area, they are tested in the other neurodegenerative disorders. | memory disorder, movement disorder, neuromuscular disease, alzheimer's disease, amyotrophic lateral sclerosis, huntington's disease, parkinson's disease, neurodegenerative disease, brain tissue, tissue, brain |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Harvard Medical School; Massachusetts; USA |
Memory disorder, Movement disorder, Neuromuscular Disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Parkinson's disease, Neurodegenerative disease, Aging | Available to the research community | nlx_144103 | http://www.massgeneral.org/mind/ | SCR_008746 | Massachusetts General Institute for Neurodegenerative Disease, Massachusetts General Hospital Institute for Neurodegenerative Disease | 2026-08-04 09:42:12 | 2 | |||||
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BrainPeps Resource Report Resource Website 1+ mentions |
BrainPeps (RRID:SCR_008851) | Brainpeps | storage service resource, data repository, service resource, database, data or information resource | Database of blood-brain barrier properties of peptides including structure, method, responses, physicochemical properties and related literature. The database is linked to a manuscript entitled Brainpeps: the blood-brain barrier peptide database, in which the BBB methods and responses are clarified and correlated to each other. Data may be submitted for addition to the database. | peptide, intravenous injection, efflux study, immortal cell line, brain slice, ultracentrifugation, bui method, capillary depletion, iam-hplc, indicator diffusion, bmec, shake flask, non-cerebral cell line, in vitro equilibrium dialysis, microdialysis, imaging techniques, quantitative autoradiography, antinociception, hplc, in situ brain perfusion, (co)-culture, mbua, ultrafiltration, cisternal puncture, bei method, gibbs adsorption isotherm, pampa, blood-brain barrier, brain, permeability, distribution, data set |
is listed by: 3DVC has parent organization: Ghent University; Ghent; Belgium |
Institute for the Promotion of Innovation through Science and Technology in Flanders IWT-Vlaanderen 73402 | PMID:22205159 | Acknowledgement requested, The community can contribute to this resource | nlx_149082 | SCR_008851 | Brain Peps | 2026-08-04 09:42:15 | 1 | |||||
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DOTS WM tract segmentation Resource Report Resource Website 100+ mentions |
DOTS WM tract segmentation (RRID:SCR_009459) | DOTS | segmentation software, data processing software, software resource, software application, image analysis software | A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance, diffusion tensor mr imaging, dti, fiber tract, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MIPAV: Medical Image Processing and Visualization is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
NIDA K25DA025356 | PMID:21718790 | Free | nlx_155605 | SCR_009459 | Diffusion-Oriented Tract Segmentation White Matter tract segmentation, Diffusion-Oriented Tract Segmentation | 2026-08-04 09:42:23 | 115 | |||||
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Baby Brain Toolkit Resource Report Resource Website |
Baby Brain Toolkit (RRID:SCR_009440) | BTK | data processing software, software resource, software application, image processing software, image analysis software, software toolkit | Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development. | computational neuroscience, magnetic resonance, fetus, brain, development, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | ERC | PMID:23036854 | CeCILL license, v2 | nlx_155584 | SCR_009440 | BTK : Baby Brain Toolkit | 2026-08-04 09:42:23 | 0 | |||||
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GingerALE Resource Report Resource Website 100+ mentions |
GingerALE (RRID:SCR_014921) | data processing software, data analysis software, algorithm resource, software resource, software application | Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions. | mri, brain, meta analysis, estimation, icbm2tal, conversion, software, coordinate, algorithm | has parent organization: brainmap.org | PMID:19172646 | Available for download | SCR_014921 | 2026-08-04 09:43:34 | 491 | |||||||||
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MultiXplore Resource Report Resource Website 1+ mentions |
MultiXplore (RRID:SCR_014814) | data processing software, software application, software resource, data analysis software | Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data. | gui, graphical user interface, cortical region, functional connectivity matrix, 3d, brain, grey matter, fiber bundle |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Western University; Ontario; Canada is a plug in for: 3D Slicer |
NSERC | Available for download | SCR_014814 | 2026-08-04 09:43:32 | 1 | |||||||||
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Automatic Tractography-based Parcellation Pipeline Resource Report Resource Website 1+ mentions |
Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) | ATPP | data processing software, software application, software resource, workflow software | Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). " | pipeline, integrated pipeline, tractography, brain, parcel, gui, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179 | Available for download | https://doi.org/10.5281/zenodo.239705, https://doi.org/10.5281/zenodo.239702 | https://github.com/haililihai/ATPP_CLI, https://github.com/haililihai/ATPP_GUI | SCR_014815 | Automatic Tractography-based Parcellation Pipeline (ATPP) | 2026-08-04 09:43:31 | 2 | |||||
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BluePyOpt Resource Report Resource Website 10+ mentions |
BluePyOpt (RRID:SCR_014753) | simulation software, software application, software resource | An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms. | python, optimization, framework, library, brain, model parameter, neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | European Union FP7 604102 | Acknowledgement requested | http://www.nitrc.org/projects/bluepyopt/ | SCR_014753 | Blue Brain Python Optimization Library, Blue Brain Python Optimisation Library (BluePyOpt), Blue Brain Python Optimisation Library | 2026-08-04 09:43:31 | 27 | |||||||
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MRTool Resource Report Resource Website 1+ mentions |
MRTool (RRID:SCR_015956) | topical portal, portal, data or information resource | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-08-04 09:43:46 | 8 | |||||||||
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Marmoset Brain Connectivity Atlas Resource Report Resource Website 10+ mentions |
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) | storage service resource, data repository, service resource, atlas, database, data or information resource | Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex. | cortex, marmoset, monkey, cerebral, brain, architecture, primate |
has parent organization: Monash University; Melbourne; Australia has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland works with: Nencki-Monash template |
Australian Research Council DP140101968; Australian Research Council CE140100007; European Regional Development Fund ; NIDA R01 DA036400; NIMH R01 MH087988; International Neuroinformatics Coordinating Facility |
DOI:10.1038/s41467-020-14858-0 PMID:27099164 |
Free, Freely available | http://marmoset.braincircuits.org, http://analysis.marmosetbrain.org | SCR_015964 | Marmoset Monkey Cerebral Cortex Connectivity Atlas | 2026-08-04 09:43:47 | 26 | ||||||
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Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data processing software, source code, data analysis software, software resource, software application | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-08-04 09:43:48 | 149 | ||||||||
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NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-08-04 09:43:54 | 0 | ||||||||||
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Colour maps for brain imaging Resource Report Resource Website 1+ mentions |
Colour maps for brain imaging (RRID:SCR_016715) | data processing software, software resource, software application, image analysis software, data visualization software | Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging. | perceptually, uniform, color, map, brain, data, imaging |
is related to: MRIcron is related to: MATLAB has parent organization: University of Western Australia; Perth; Australia |
Free, Available for download, Freely available | SCR_016715 | Colour maps, brain_colours, colour maps, brain colours, Brain colours, colour maps for brain imaging, Colour maps for brain imaging | 2026-08-04 09:43:58 | 1 | |||||||||
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ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data processing software, software application, software resource, data analysis software | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; State of São Paulo Research Foundation ; Pew Latin American Fellowship ; Ciência sem Fronteiras Fellowship ; NAP eScience |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-08-04 09:43:58 | 0 | ||||
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MouseLight Project Resource Report Resource Website 1+ mentions |
MouseLight Project (RRID:SCR_016668) | data analysis service, portal, analysis service resource, web service, software resource, data access protocol, production service resource, service resource, database, data or information resource | Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain. | neuronal, reconstruction, connectomics, projectomics, brain, tissue, image, dataset, mouse, axonal, arbor, individual, neuron |
is related to: Allen Institute for Brain Science has parent organization: Janelia Research provides: MouseLight Neuron Browser |
Free, Freely available, Tutorial available, Acknowledgement required, Registration required | http://mouselight.janelia.org/ | SCR_016668 | MouseLight, The Mouse Light Project, Janelia MouseLight project, Mouse Light Project, Mouse Light, MouseLight Project | 2026-08-04 09:43:58 | 9 | ||||||||
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rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data processing software, software application, software resource, data analysis software | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-08-04 09:43:56 | 1 | |||||||||
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AFIDs Resource Report Resource Website 1+ mentions |
AFIDs (RRID:SCR_016623) | AFIDs | continuing medical education, data processing software, software resource, training resource, software application, image processing software, software toolkit | Open framework for evaluating correspondence between brain images and teaching neuroanatomy. | evaluate, correspondence, magnetic, images, human, brain, fiducial, placement, neuroanatomy | DOI:10.1002/hbm.24693 | Free, Available for download, Freely available | SCR_016623 | Anatomical Fiducials | 2026-08-04 09:43:57 | 2 | ||||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | portal, atlas, project portal, data or information resource | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-08-04 09:44:02 | 195 | ||||||||
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Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | storage service resource, data repository, data or information resource, service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-08-04 09:44:05 | 14 | |||||||
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MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases | SCR_017222 | MeshView for brain atlases | 2026-08-04 09:44:06 | 11 |
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