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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Automated Fiber Quantification in Python Resource Report Resource Website 10+ mentions |
Automated Fiber Quantification in Python (RRID:SCR_023366) | pyAFQ | software toolkit, software resource | Software package focused on automated delineation of major fiber tracts in individual human brains, and quantification of tissue properties within the tracts.Software for automated processing and analysis of diffusion MRI data. Automates tractometry. | Automates tractometry, automated delineation of major fiber tracts, individual human brains, quantification of tissue properties, tissue properties within fiber tracts, diffusion MRI data, | NIMH 1RF1MH121868; The BRAIN Initiative ; Gordon and Betty Moore Foundation ; Alfred P. Sloan Foundation ; NIBIB R01EB027585; NSF 1551330 |
PMID:35079748 | Free, Available for download, Freely available | SCR_023366 | 2026-02-12 09:47:37 | 12 | ||||||||
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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 | 2026-02-12 09:48:16 | 2 | |||||||
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ezBIDS Resource Report Resource Website |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/ |
SCR_025563 | ez Brain Imaging Data Structure | 2026-02-12 09:48:25 | 0 | |||||||
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Genetic Tools Atlas Resource Report Resource Website 1+ mentions |
Genetic Tools Atlas (RRID:SCR_025643) | GTA | data or information resource, database, atlas, catalog | 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 | 2026-02-12 09:48:26 | 6 | ||||||
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DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | data or information resource, reference atlas, 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 | 2026-02-12 09:48:27 | 0 | |||||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | software toolkit, software resource, software application, data processing software, image processing software | 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 | 2026-02-12 09:48:37 | 20 | |||||||
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | software toolkit, software resource, source code | 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 | 2026-02-12 09:48:26 | 3 | |||||||||
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Monkey Motion Resource Report Resource Website |
Monkey Motion (RRID:SCR_014285) | source code, software resource | A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation. | Magnetic resonance imaging, Neuroimaging, Macaca fascicularis, Operant conditioning, Reward | McDonnell Center for Systems Neuroscience at Washington University ; NINDS R01 NS044598; NIMH R21 MH081080; NIMH K24 MH087913 |
PMID:26798573 DOI:10.7759/cureus.397 |
Available for download | SCR_014285 | 2026-02-12 09:45:56 | 0 | |||||||||
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BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | source code, software resource | Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs. | OpenBehavior, automated behavioral detection, markerless pose tracking, detect frame by frame behavior, video time series, kinematic and postural statistics, |
is listed by: OpenBehavior is related to: SLEAP, LEAP and MotionMapper project works with: DeepLabCut |
NIMH K01MH116264; NIMH K08MH116125; Whitehall Foundation ; Simonsen Foundation ; NSF ; NIMH T32MH073526; Brain Research Foundation ; Brain and Behavior Research Foundation |
PMID:35997072 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/behaviordepot/ | SCR_023602 | 2026-02-12 09:47:57 | 1 | |||||||
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Autopatcher Resource Report Resource Website 1+ mentions |
Autopatcher (RRID:SCR_017464) | software application, software resource | Software tool for neuronal recording in intact brain. | Neuronal, recording, intact, brain, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH106027 | PMID:29297466 | Free, Available for download, Freely available | SCR_017464 | 2026-02-12 09:46:53 | 2 | ||||||||
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pyRayleighCuda Resource Report Resource Website |
pyRayleighCuda (RRID:SCR_017453) | software application, software resource | Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation. | Rayleigh-Sommerfeld, integral, acoustics, CUDA, graphics, processing, unit, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH109105 | Free, Freely available | SCR_017453 | 2026-02-12 09:47:09 | 0 | |||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) | data or information resource, atlas | Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform. | Anatomical labels, Allen Common Coordinate Framework, Franklin and Paxinos labels, MRI atlas, segment labels, transgenic mice, dorsal striatum, cortico-striatal connectivity data, mouse brain anatomical structure |
is used by: BICCN is related to: Allen Institute for Brain Science |
NIMH R01 MH116176; NINDS R01 NS10 8407; Pennsylvania Department of Health ; NIH Office of the Director R24 OD018559 |
PMID:31699990 | Free, Freely available | SCR_019267 | 2026-02-12 09:47:12 | 2 | ||||||||
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neuropythy Resource Report Resource Website |
neuropythy (RRID:SCR_027787) | software toolkit, software library, software resource, source code | 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 | 2026-02-12 09:48:58 | 0 | ||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | source code, software application, 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 | 2026-02-12 09:48:42 | 0 | |||||||
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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 | 2026-02-07 02:08:43 | 107 | |||||||
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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 | 2026-02-07 02:14:05 | 2723 | ||||||
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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 | 2026-02-07 02:09:00 | 3 | |||||||||
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National NeuroAIDS Tissue Consortium Resource Report Resource Website 10+ mentions |
National NeuroAIDS Tissue Consortium (RRID:SCR_007323) | NNTC | biomaterial supply resource, tissue bank, material resource, brain bank | Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators. | human immunodeficiency virus, nervous tissue, cerebral spinal fluid, blood, tissue, brain, neuromedical data, neuropsychiatric data, tissue, plasma, peripheral blood mononuclear cell, serum, urine, spinal cord, nervous tissue, pituitary gland, trigeminal ganglia, dorsal root ganglion, peripheral nerve, lymph node, liver, spleen, adipose tissue, bone marrow, muscle, hair, heart, thymus, kidney, lung, eye, brain, ante-mortem, post-mortem, normal, subsyndromic, minor cognitive motor disorder, hiv - associated dementia, cytomegalovirus encephalitis, neurological impairment, traumatic brain injury, neurocognitive disease, frozen, fixed, aids, one mind tbi, asymptomatic neurocognitive impairment, minor cognitive disorder, gene array, snp |
is listed by: One Mind Biospecimen Bank Listing is related to: Manhattan HIV Brain Bank is related to: CHARTER - CNS HIV Antiretroviral Therapy Effects Research |
Human immunodeficiency virus, Neurocognitive disease, Normal, Subsyndromic, Minor Cognitive Motor Disorder, HIV - Associated Dementia, Cytomegalovirus Encephalitis, Neurological impairment, Infectious disease | NIMH ; NINDS ; NIH Blueprint for Neuroscience Research |
Public: The NNTC encourages external researchers to submit tissue requests for ancillary studies. | nif-0000-00193 | SCR_007323 | nntc.org, nntc | 2026-02-11 10:57:34 | 11 | |||||
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Brain Research Institute Biobank Resources Resource Report Resource Website |
Brain Research Institute Biobank Resources (RRID:SCR_008756) | biomaterial supply resource, tissue bank, material resource, brain bank | Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal. | postmortem, brain, coronal, brain tissue, cerebral spinal fluid, blood, cerebral spinal fluid cell, cell-free cerebral spinal fluid, serum, plasma, buffy coat, frozen, formalin fixed, paraformaldehyde-fixed, paraffin-embedded, neurological disease, alzheimer's disease, amyotrophic lateral sclerosis, depressive disorder, suicide, epilepsy, huntington's disease, multiple sclerosis, parkinson's disease, progressive supranuclear palsy, schizophrenia, stroke, cerebrovascular accident, fronto-temporal dementia, neurologically normal, coronal section, control, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Brain Research Institute |
Neurological disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Depressive Disorder, Suicide, Epilepsy, Huntington's disease, Multiple Sclerosis, Parkinson's disease, Progressive Supranuclear Palsy, Schizophrenia, Stroke, Cerebrovascular Accident, Fronto-temporal dementia, Aging | NINDS ; NIMH ; National MS Society ; United States Department of Veterans Affairs ; Veterans Affairs West Los Angeles Healthcare Center ; NIA |
Public, Available to the research community | nlx_143996 | http://www.bri.ucla.edu/bri_research/research_resources.asp | SCR_008756 | Brain Research Institute Research Resources, Brain Research Institute Biobanks, BRI Research Resources, BRI Biobanks, BRI Biobank Resources | 2026-02-11 10:57:56 | 0 | |||||
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NIH NeuroBioBank Resource Report Resource Website 100+ mentions |
NIH NeuroBioBank (RRID:SCR_003131) | NBB | biomaterial supply resource, tissue bank, material resource, brain bank | National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor. | human post-mortem brain tissue, human brain, brain tissue, tissue, adult, child, brain donation, human post-mortem brain tissue and related biospecimens, |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is listed by: One Mind Biospecimen Bank Listing has parent organization: National Institutes of Health |
Brain disorder, Autism spectrum disorder, Autism, Major Depressive Disorder, Schizophrenia, Multiple Sclerosis, Epilepsy, Traumatic brain injury | NIMH ; NINDS ; NICHD ; NIA ; NIDA |
PMID:29496155 | Free, Freely available | nlx_156783 | SCR_003131 | NeuroBioBank, National Institutes of Health NeuroBioBank | 2026-02-11 10:56:36 | 177 |
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