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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HBP: Healthy Brain Project Resource Report Resource Website |
HBP: Healthy Brain Project (RRID:SCR_013137) | HBP | data or information resource, disease-related portal, portal, research forum portal, topical portal | Research forum portal to address brain status by acquiring comprehensive, multimodal data from healthy humans across the lifespan to characterize brain status, assess its change over time, and associate composite descriptors of brain status. Specifically, the measurements are acquired noninvasively by existing neuroimaging technologies (structural MRI, functional MRI, magnetic resonance spectroscopy, diffusion MRI, and magnetoencephalography); in addition, genetic, cognitive, language, and lifestyle data are acquired. Goals: * Derive the Brain Health Index- An integrative assessment of brain status derived from multimodal measurements of brain structure, function, and chemistry. * Continue acquiring data to construct the first-ever databank on brain, cognitive, language and genetic measurements for healthy people across the lifespan. * Provide a novel and unique dataset by which to: characterize brain status, assess its change over time, and associate it with genetic makeup, cognitive function, and language abilities. * Forecast future brain health and disease based on current measurements and guide physicians towards new interventions and evaluate interventions as they develop. * Extend to siblings and other family members to further assess the genetic influences and inheritability. | cognition, language, genetic, cognitive, brain, structure, function, longitudinal, multimodal, neuroimaging, adult human, late adult human, neurological exam, neuropsychological exam, cognitive assessment, structured interview, questionnaire, mental health status, structural mri, fmri, mr spectroscopy, diffusion mri, meg, dna, genetic assessment, montreal cognitive assessment, 3ms, mmse, language assessment, lifestyle, controlled oral word association test | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Aging, Healthy | nlx_153925 | SCR_013137 | Healthy Brain Project, Minnesota Women Healthy Brain Project, Women Healthy Brain Project, Minnesota Healthy Brain Project | 2026-08-29 11:27:34 | 0 | |||||||
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BECA Resource Report Resource Website 1+ mentions |
BECA (RRID:SCR_015846) | BECA | data processing software, data visualization software, image analysis software, software application, software resource | Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version. | visual exploration, brain, neuroscience, network, genetic determinant, fmri, neuroimaging, genome | has parent organization: Indiana University School of Medicine; Indiana; USA | NIA P30 AG10133; NIA R01 AG19771; NIA RC2 AG036535; NIA U01 AG024904; NIBIB R01 EB022574; NLM R01 LM011360; NSF IIS-1117335 |
PMID:27171688 | Free, Available for download | SCR_015846 | Brain Explorer for Connectome Analysis (BECA), BECA - Brain Explorer for Connectome Analysis | 2026-08-29 11:25:02 | 5 | ||||||
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BICCN Resource Report Resource Website 100+ mentions |
BICCN (RRID:SCR_015820) | BICCN | consortium, data or information resource, organization portal, portal | Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains. | cell census, neuroscience, brain, brain initiative cell census network, whole mouse brain, |
uses: QuickNII uses: HistoloZee uses: CellLocator uses: Semi-Manual Alignment to Reference Templates uses: LoomPy uses: Cytosplore Viewer uses: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) uses: Blue Brain Cell Atlas uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Hippocampome.org uses: Neuron Phenotype Ontology uses: Brain Image Library uses: Distributed Archives for Neurophysiology Data Integration uses: NeuroMorpho.Org uses: Azimuth uses: Brain Observatory Storage Service and Database (BossDB) uses: Optimus Pipeline uses: scATAC Pipeline uses: Smart-seq2 Single Nucleus Multi Sample Pipeline uses: CEMBA MethylC Seq Pipeline uses: Brain Architecture Project uses: Single Cell Portal uses: MorphoHub uses: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas uses: Mouse Connectome Project uses: Allen Mouse Brain Reference Atlas uses: Allen Mouse Brain Common Coordinate Framework uses: Allen Human Reference Atlas, 3D, 2020 uses: NeMO Analytics uses: ANTS - Advanced Normalization ToolS uses: CloudReg uses: Brainome portal uses: CATlas uses: MetaNeighbor uses: Cell Annotation Platform uses: cellxgene uses: Neuroglancer uses: Vaa3D uses: QuickNII and VisuAlign uses: Hi5App uses: CloudVolume uses: neuroXiv uses: Brain Data Standards Ontology uses: Pittsburgh Supercomputing Center uses: Molecular Biosensor and Imaging Center uses: Generative Diffeomorphic Mapping uses: NIH NeuroBioBank uses: NeMOarchive lists: ccf_streamlines is related to: Mouse Connectome Project is related to: BarensLab Mini-Atlas is related to: Cumulus is related to: Pegasus is related to: Cirrocumulus is related to: Gene functional conservation across cell types and species is related to: BRAIN Initiative Cell Atlas Network is related to: ATAC Pipeline is related to: Slide-seq Pipeline is related to: Brain Knowledge Platform has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science provides: mBrainAligner provides: BICCN Cell Registry provides: Cell Type Knowledge Explorer provides: Epiviz has organization facet: BICCN Anatomy and Morphology Project has organization facet: Cell Type Knowledge Explorer has organization facet: mBrainAligner has organization facet: Terra has organization facet: Allen Brain Cell Atlas has organization facet: Multiome Pipeline has organization facet: Allen Software Development Kit has organization facet: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain has organization facet: Allen Brain Map BICCN Data Catalog has organization facet: snm3C Pipeline has organization facet: Paired-Tag Pipeline has organization facet: BuildIndices has organization facet: MapMyCells |
NIMH U19 MH114821; NIMH U19 MH114830; NIMH U19 MH114831 |
PMID:37390046 | Restricted | SCR_017266 | SCR_015820 | BICCN 2.0, BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Census Network (BICCN) | 2026-08-29 11:25:06 | 234 | |||||
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UK Brain Expression Consortium Resource Report Resource Website 1+ mentions |
UK Brain Expression Consortium (RRID:SCR_015889) | UKBEC | consortium, data or information resource, organization portal, portal | Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | is parent organization of: Braineac | SCR_015889 | 2026-08-29 11:25:07 | 3 | ||||||||||
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ABCDreport Resource Report Resource Website |
ABCDreport (RRID:SCR_016030) | data analysis software, data processing software, software application, software resource | Software application as a simple system to review study progress. Used in ABCD study. | system, simple, review, study, progress, development, adolescence, brain, cognitive, report | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016030 | 2026-08-29 11:25:28 | 0 | |||||||||
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IMAGEN Resource Report Resource Website 100+ mentions |
IMAGEN (RRID:SCR_016045) | consortium, data or information resource, organization portal, portal, project portal | Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | adolescence, teen, mental, health, study, brain, development, neurological, prevention, therapy, disorder, psychology | European Commission ; German Federal Ministry of Research & Education (BMBF) ; Medical Research Council ; National Institute for Health Research UK ; National Institute for Health Research US ; National Institute on Drug Abuse ; Swedish Research Council (Vetenskapsrådet) |
PMID:21102431 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016045 | IMAGEN Consortium, IMAGEN Project, IMAGEN Study | 2026-08-29 11:25:05 | 158 | ||||||||
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NeuroImage Field-of-View Normalization Tool Resource Report Resource Website 1+ mentions |
NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) | data or information resource, portal, topical portal | FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets. | normalization, fov, field, view, filed of view, brain, mri, magnetic, resonance, neuroimaging, imaging, atlas | DOI:10.1007/s12021-018-9359-z | Free, Available for download | SCR_015957 | Normalize FOV, normalizefov | 2026-08-29 11:25:25 | 4 | |||||||||
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DEAP - Data Exploration and Analysis Portal Resource Report Resource Website 10+ mentions |
DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) | DEAP | data access protocol, software resource, web service | Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States. | data, exploration, analysis, portal, brain, development, child, health, United, States, long, term, study | is related to: ABCD Study | Free, Available for download | SCR_016158 | DEAP: Data Exploration and Analysis Portal | 2026-08-29 11:25:08 | 18 | ||||||||
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NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | data or information resource, data repository, database, service resource, storage service resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
BRAIN Initiative ; NIMH MH114788 |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-08-29 11:25:32 | 126 | ||||||
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iELVis Resource Report Resource Website 10+ mentions |
iELVis (RRID:SCR_016109) | data processing software, data visualization software, software application, software resource | Software toolkit consisting of MATLAB and Bash scripts for intracranial electrode localization/visualization. It maps electrodes to various anatomical and functional atlases, and overlays electrode data over functional neuroimaging data. Software for intracranial electrode localization and visualization. | electrode, stimulus, visualization, brain, neuroimaging, intracranial, localization, anatomy, functional, BRAIN Initiative | is recommended by: BRAIN Initiative | Natural Sciences and Engineering Research Council of Canada RGPIN-2014-04465; Page and Otto Marx Jr. Foundation ; Swiss National Science Foundation P300P3_148388; Swiss National Science Foundation PBGEP3_139829 |
PMID:28192130 | Open source, Free, Available for download | https://github.com/iELVis/iELVis | SCR_016109 | iELVis (intracranial electrode visualization), Intracranial ELectrode VISualization | 2026-08-29 11:25:31 | 47 | ||||||
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International Initiative for Traumatic Brain Injury Research Resource Report Resource Website 1+ mentions |
International Initiative for Traumatic Brain Injury Research (RRID:SCR_016237) | InTBIR | access service resource, service resource | Project whose goal is to improve health care and lessen the global burden of TBI through the discovery of causal relationships between treatments and clinically meaningful outcomes. InTBIR seeks to encourage well-designed, hypothesis-driven studies that include the collection of high quality data followed by rigorous statistical analysis. | tbi, traumatic, brain, injury, neurology, neuroscience, neuroanatomy, medical, clinical, research, nih |
has parent organization: European Commission has parent organization: Canadian Institutes of Health Research |
SCR_016237 | International Initiative for Traumatic Brain Injury Research (InTBIR) | 2026-08-29 11:25:35 | 4 | |||||||||
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Nighres Resource Report Resource Website 1+ mentions |
Nighres (RRID:SCR_016287) | data processing software, image analysis software, software application, software resource, software toolkit | Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend. | neuroimaging, python, high-resolution, MRI, ultra-high, field, laminar, brain | Free, Available for download, Runs on Linux | http://nighres.readthedocs.io/en/latest/ | https://github.com/juhuntenburg/laminar_python | SCR_016287 | nighres | 2026-08-29 11:25:37 | 3 | ||||||||
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Virtual Digital Brain Resource Report Resource Website |
Virtual Digital Brain (RRID:SCR_016265) | VDB | software resource | Virtual resource for neuroscience. | brain, neuroscience, neuroimaging, cerebral | Free for academic use | SCR_016265 | 2026-08-29 11:25:09 | 0 | ||||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-08-29 11:25:40 | 1 | ||||||
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Canadian Open Neuroscience Platform Resource Report Resource Website 10+ mentions |
Canadian Open Neuroscience Platform (RRID:SCR_016433) | CONP | data or information resource, data repository, organization portal, portal, service resource, storage service resource | Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers. | interactive, network, brain, research, interdisciplinary, student, training, international, partnership, clinical, translation, open, publishing, Canada |
is related to: Brain Canada is related to: Health Canada |
Open source | r3d100013461 | https://github.com/CONP-PCNO/conp-portal, https://doi.org/10.17616/R31NJMVP | SCR_016433 | CONP:Canadian Open Neuroscience Platform | 2026-08-29 11:25:14 | 11 | ||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | User Friendly Functional Connectivity | 2026-08-29 11:25:49 | 1 | |||||||
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nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | data analysis software, data processing software, software application, software resource | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | nonparametric Granger Geweke Causality | 2026-08-29 11:25:48 | 2 | |||||||
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Computational Anatomy Toolbox for SPM Resource Report Resource Website 500+ mentions |
Computational Anatomy Toolbox for SPM (RRID:SCR_019184) | CAT | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry. | MRI, neuroimaging, brain, voxel based morphometry, surface based morphometry, deformation based morphometry, label based morphometry, region based morphometry | works with: SPM | Free, Available for download, Freely available | SCR_019184 | CAT12 | 2026-08-29 11:26:18 | 581 | ||||||||
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NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource, topical portal | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | Neuroscience Multi-Omic Analytics | 2026-08-29 11:25:59 | 16 | ||||||||
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BICCN Cell Registry Resource Report Resource Website 10+ mentions |
BICCN Cell Registry (RRID:SCR_017267) | data or information resource | Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols. | data, dataset, brain, initiative, cell, registry |
is related to: BRAIN Cell Data Center is related to: BRAIN Cell Data Center has parent organization: Allen Institute for Brain Science is provided by: BICCN |
NIH | Free, Freely available, Available for download | http://www.brainimagelibrary.org/download.html, https://nemoarchive.org/resources/data-download.php | SCR_017267 | BRAIN Initiative Cell Census Network Cell Registry, BICCN Cell Registry | 2026-08-29 11:25:32 | 13 |
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