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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Neuron Phenotype Ontology Resource Report Resource Website 1+ mentions |
Neuron Phenotype Ontology (RRID:SCR_017403) | NPO | controlled vocabulary, data or information resource, ontology | An ontology for describing the complex phenotypes of neurons. | Cell, type, phenotype, neuron, ontology |
is used by: BICCN is provided by: NIFSTD |
NIMH U24 MH114827; BRAIN Initiative |
Free, Freely available | SCR_017403 | 2026-07-28 09:44:33 | 2 | ||||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | service resource, data or information resource, storage service resource, data repository | Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets. | archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, |
is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: DataCite is listed by: re3data.org is related to: BRAIN Initiative is related to: Allen Institute for Brain Science works with: CBI BrAinPI is organization facet of: BRAIN Initiative Cell Atlas Network |
BRAIN Initiative ; NIMH R24 MH114793 |
PMID:38187527 | Free, Available for download, Freely available | DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 | https://doi.org/10.17616/R31NJN9G, https://doi.org/10.17616/r31NJN9G, https://doi.org/10.35077/, https://dx.doi.org/10.35077/, https://doi.org/10.17616/R31NJN9G | SCR_017272 | Brain Image Library | 2026-07-28 09:44:28 | 16 | ||||
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Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | service resource, data or information resource, data repository, database, image, storage service resource, 3d spatial image | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-07-28 09:44:32 | 27 | |||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | service resource, data or information resource, software resource, production service resource, analysis service resource, portal | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; NIDCD R01 DC013817; NIMH R24 MH114815; Hearing Health Foundation (Hearing Restoration Project) |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-07-28 09:44:30 | 76 | |||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | software application, data analysis software, software resource, data processing software, network analysis software | Methods for reconstructing transcriptional regulatory networks. | Reconstructing, transcriptional, regulatory, network, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH114788 | Free, Available for download, Freely available | SCR_017458 | 2026-07-28 09:44:36 | 0 | |||||||||
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SenseLab Resource Report Resource Website 10+ mentions |
SenseLab (RRID:SCR_007276) | SenseLab | data or information resource, organization portal, database, portal | The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data. | neuron, model, olfactory system, brain, disease, neuronal, olfactory |
is related to: Neuroscience Information Framework is related to: International Neuroinformatics Coordinating Facility has parent organization: Yale University; Connecticut; USA is parent organization of: SimToolDB |
Aging | Human Brain Project ; Multidisciplinary University Research Initiative ; NIMH ; NIA ; NICD ; NINDS ; NIDCD RO1 DC 009977 |
nif-0000-00017 | SCR_007276 | SenseLab Project, The SenseLab Project | 2026-07-28 09:41:44 | 41 | ||||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | data or information resource, atlas, reference atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-07-28 09:44:37 | 3 | |||||||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | software application, software resource, data processing software, image processing software, software toolkit | Software package as set of tools, primarily shell scripts, for processing multi-modal, high-quality MRI images for the Human Connectome Project. Minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space. | Minimal preprocessing pipelines, Human Connectome Project, MRI images processing, MRI images, | NIMH MH091657; NIH Blueprint for Neuroscience Research ; NIMH F30 MH097312; NIMH ROI MH60974; NCRR U24 RR021382; NIBIB R01EB006758; NIA R01AG008122; NINDS R01 NS052585; NINDS R21NS072652; NINDS R01NS070963 |
PMID:23668970 | Free, Available for download, Freely available | https://www.humanconnectome.org/software/hcp-mr-pipelines | SCR_026575 | Human Connectome Project Pipelines | 2026-07-28 09:46:42 | 20 | |||||||
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | source code, software toolkit, software resource | Software Python/Rust package for single-cell epigenomics analysis. | Single-cell epigenomics analysis, | NHGRI U01HG012059; NHGRI UM1HG011585; NIMH RF1MH128838; NIMH UM1MH130994; NIA R24AG073198; NIMH U01MH114828; NIA R56AG069107; NIA U54AG079758; NIMH U01MH121282; NIMH U19MH114831; NEI R01EY031663 |
PMID:38191932 | Free, Available for download, Freely available | SCR_026622 | 2026-07-28 09:46:43 | 3 | |||||||||
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neuropythy Resource Report Resource Website |
neuropythy (RRID:SCR_027787) | software resource, source code, software toolkit, software library | Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures. | Python, complement nibabel library, can automatic download data and interpret them into Python data structures, | NEI R00 EY022116; NIMH R01 MH111417; NEI R01 EY027964; NEI R01 EY027401 |
PMID:30520736 | Free, Available for download, Freely available | https://hub.docker.com/r/nben/neuropythy | SCR_027787 | 2026-07-28 09:47:04 | 0 | ||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, source code, software resource | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIMH R01 MH101244; NIGMS R01 GM078598 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | Cancer Bayesian SElection estimation | 2026-07-28 09:47:16 | 0 | |||||||
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tximeta Resource Report Resource Website |
tximeta (RRID:SCR_028005) | software toolkit, software resource | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NHGRI R01 HG009937; NIMH R01 MH118349; NCI P01 CA142538; NIEHS P30 ES010126; NHGRI U41 HG004059 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | Tximeta | 2026-07-28 09:47:06 | 0 | ||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | software application, software resource, data analysis software, data processing software | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | NIMH R01 MH090936; NIEHS R01 ES015241; US Environmental Protection Agency ; NCI R01 CA138255; NSF ; Gillings Innovation Laboratory in Statistical Genomics |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-07-28 09:46:22 | 69 | ||||||||
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3D Developmental Mouse Brain Common Coordinate Framework Resource Report Resource Website 1+ mentions |
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) | data or information resource, atlas | Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain. | multimodal 3D atlases, developing mouse brain, mouse brain data, |
is related to: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative |
NIMH RF1MH12460501; NINDS R01NS108407; NIMH R01MH116176; NIBIB R01EB031722 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-07-28 09:46:24 | 2 | |||||||
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Genetic Tools Atlas Resource Report Resource Website 1+ mentions |
Genetic Tools Atlas (RRID:SCR_025643) | GTA | catalog, database, atlas, data or information resource | Searchable catalog of enhancer-adeno-associated viruses (AAVs) that have been developed and tested at the Allen Institute for Brain Science. We present a suite of enhancer AAVs that can provide access to specific cell types when delivered to the whole brain. Multiple epigenomic and transcriptomic datasets were interrogated to reveal candidate enhancers that are selectively accessible in particular cell populations. Enhancer AAVs were constructed and screened for desirable expression and a sizeable subset of enhancer AAVs were subjected to further characterization by single cell transcriptomics and/or brain-wide expression imaging in mouse. In the GTA, we present a large toolkit for selective gene expression in cell types of interest. Genetic Tools Atlas is part of the growing Brain Knowledge Platform. | enhancer-adeno-associated viruses, enhancer AAVs, mouse transgenes, epifluorescence imaging, serial two-photon tomography, sc/snRNA-seq, genetic tools, |
is related to: Neuroglancer is related to: Addgene has parent organization: Allen Institute |
Paul G. Allen Foundation n/a; NIMH 1UF1 MH128339; NIMH 1UG3 MH120095; NIMH 1RF1 MH114126; NIMH 1RF1 MH121274 |
Free, Freely available | https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/summary, https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens | SCR_025643 | Allen Genetic Tools Atlas | 2026-07-28 09:46:26 | 6 | ||||||
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DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | data or information resource, atlas, reference atlas | Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome. | Whole brain developmental map, neuronal circuit maturation, whole brain spatiotemporal mapping, circuit maturation, early postnatal development, mouse models of neurodevelopmental disorders, | Human Frontier Science Program ; Brain Research Foundation Seed Grant ; Simons Center for the Social Brain Equipment Grant ; Paul and Lilah Newton Brain Science Award ; NIMH RF1MH124605; NIDCD DC014701; NINDS NS123710; NINDS NS115543; NIMH MH116673 |
PMID:38260331 | Free, Freely available | DevATLAS | SCR_025718 | Developmental Activation Timing-based Longitudinal Acquisition System | 2026-07-28 09:46:27 | 0 | |||||||
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NIMH Image Library Resource Report Resource Website 1+ mentions |
NIMH Image Library (RRID:SCR_005588) | NIMH Image Library | image collection, data or information resource | Database of photographs and illustrations of general biomedical research and research tools, mental health specific research, and treatment related images that are available, copyright free, to the public at no cost. Many images are available in low, medium, and high resolutions. Formats include jpg, gif, and png. NIMH images may not be used to state or imply the endorsement by NIMH or by an NIMH employee of a commercial product, service, or activity, or use in any other manner that might mislead. No fee is charged for using the images. However, credit must be given to the National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services unless otherwise instructed to give credit to the photographer or other source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, biomedical, mental health, treatment, brain, research, imaging, genetics, research lab, tool, therapy, medical care | has parent organization: National Institute of Mental Health | NIMH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_146221 | SCR_005588 | National Institute of Mental Health Image Library | 2026-07-25 12:06:06 | 3 | ||||||
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SPM Anatomy Toolbox Resource Report Resource Website 100+ mentions |
SPM Anatomy Toolbox (RRID:SCR_013273) | SPM Anatomy Toolbox | software resource | A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space. | human, brain, imaging, functional magnetic resonance imaging, structure, mapping, atlas, pet, neuroimaging | is related to: SPM | NIMH ; NINDS ; NIBIB ; DFG KFO-112; DFG Schn 362/13-2 |
PMID:15850749 | nif-0000-10477 | SCR_013273 | 2026-07-25 12:07:51 | 107 | |||||||
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NUNDA Resource Report Resource Website 1+ mentions |
NUNDA (RRID:SCR_013664) | NUNDA | A resource for managing study data collected by the Northwestern University neuroimaging community. It includes a secure database, automated pipelines for processing managed data, and tools for exploring and accessing the data. Access to data in the NUNDA is restricted to users authorized by the specific study's investigators. The NUNDA is hosted by the Neuroimaging & Applied Computational Anatomy Lab, and it is modeled after the Washington University's Central Neuroimaging Data Archive (CNDA). The NUNDA is powered by XNAT, an open source software package for managing neuroimaging and related data. | MRI, imaging, |
is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Northwestern University; Illinois; USA |
NIMH 1R01 MH0848803; NIMH 1U01 MH097435-01A1; NIDCD P50 DC012283-01A1 |
SCR_013664 | The Northwestern University Neuroimaging Data Archive | 2026-07-25 12:07:58 | 3 | |||||||||
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Patient-Reported Outcomes Measurement Information System Resource Report Resource Website 1000+ mentions |
Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) | PROMIS | assessment test provider, material resource | Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children. | adult, child, assessment, clinical, anger, pain, fatigue, physical function, depression, anxiety, social function, patient reported outcome, health, measure |
is recommended by: National Library of Medicine has parent organization: University of Washington; Seattle; USA |
NCCIH ; NCI ; NHLBI ; NIA ; NIAMS ; NIDA ; NIDCD ; NIDDK ; NIMH ; NINDS ; NINR ; OD |
nlx_143881 | http://www.healthmeasures.net/index.php?option=com_content&view=category&layout=blog&id=71&Itemid=817 | SCR_004718 | PROMIS, Patient Reported Outcomes Measurement Information System | 2026-07-25 12:12:31 | 2881 |
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