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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NeuroExpresso Resource Report Resource Website 10+ mentions |
NeuroExpresso (RRID:SCR_015724) | data or information resource, database, software resource, web application | Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. | mouse brain, marker gene, tissue expression, microarray, gene expression, rna sequencing | NeuroDevNet ; CAMH ; NIMH MH077159; NIMH MH111099; NIGMS 719GM076990; NSERC Discovery Grant |
Freely available | https://github.com/oganm/neuroexpresso | SCR_015724 | 2026-09-12 12:58:29 | 26 | |||||||||
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SchizConnect Resource Report Resource Website 50+ mentions |
SchizConnect (RRID:SCR_015766) | data or information resource, database, disease-related portal, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 6,2026. Platform for mediation and integration of schizophrenia neuroimaging-related databases. It provides access to federated databases, novel mediation software, and large-scale data-sharing features. | schizophrenia, mediation, integration, neuroimaging, mental illness, brain disorder, FASEB list | Schizophrenia | NIMH 1U01MH097435 | PMID:26688837 | THIS RESOURCE IS NO LONGER IN SERVICE. | http://schizconnect.org | SCR_015766 | 2026-09-12 12:58:30 | 80 | |||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | data analysis software, data processing software, data visualization software, software application, software resource | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair ; NIMH U01 MH105979; NIMH U19 MH114830 |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-09-12 12:58:53 | 0 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | data processing software, image analysis software, image processing software, software application, software resource | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
National Science Foundation Graduate Research Fellowship Program ; NIDA DA018310; NIGMS T32 GM070421; NIMH U01 MH109062; Springborn Fellowship |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-09-12 12:58:53 | 1 | |||||||
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StimVision Resource Report Resource Website 1+ mentions |
StimVision (RRID:SCR_017457) | data processing software, data visualization software, software application, software resource | Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room. | Tractography, deep, brain, stimulation, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH R01 MH102238; NIMH R01 MH106173 |
PMID:28653482 | SCR_017457 | Stim Vision, StimVision | 2026-09-12 12:58:53 | 1 | ||||||||
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FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
California Research Alliance by BASF ; National Institutes of Health NRSA Trainee appointment ; NHGRI U01 HG007910; NIMH U01 MH105979 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-09-12 12:58:53 | 0 | ||||||
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JWatcher Resource Report Resource Website 50+ mentions |
JWatcher (RRID:SCR_017595) | data acquisition software, data analysis software, data analytics software, data processing software, software application, software resource | Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer. | Quantitative, analysis, behavior, theoretical, problem, action, scored, human, observer |
has parent organization: University of California at Los Angeles; California; USA has parent organization: Macquarie University; Sydney; Australia |
Australian Research Council ; Macquarie University ; NIMH R21 MH065226 |
Free, Available for download, Freely available | SCR_017595 | 2026-09-12 12:58:54 | 53 | |||||||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | data analysis software, data processing software, software application, software resource | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI F32CA165823; NCI K12 CA139160; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595; NIGMS U01 GM092691; NIGMS U01 GM61393; NIMH P50 MH094267; NIMH R01 MH090937; NIMH R01 MH101820; NIMH T32 MH020065 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-09-12 12:58:44 | 25 | |||||||||
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PAGODA Resource Report Resource Website |
PAGODA (RRID:SCR_017099) | data analysis software, data processing software, software application, software resource | Software tool for analyzing transcriptional heterogeneity to detect statistically significant ways in which measured cells can be classified. Used to resolve multiple, potentially overlapping aspects of transcriptional heterogeneity by testing gene sets for coordinated variability among measured cells. | heterogeneity, transcriptional, detect, statistically, cell, classified, overlapping, gene, set, coordinated, variability |
is related to: pagoda2 has parent organization: Harvard University; Cambridge; United States |
Ellison Medical Foundation ; NIA T32 AG00216; NIMH U01 MH098977; NINDS R01 NS084398; NSF DGE1144152; NSF NSF-14-532 |
PMID:26780092 | Free, Available for download, Freely available | http://hms-dbmi.github.io/scde/index.html | SCR_017099 | Pathway And Gene set OverDispersion Analysis, pagoda | 2026-09-12 12:58:48 | 0 | ||||||
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seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | data analysis software, data processing software, software application, software resource | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; G Harold and Leila Y. Mathers Foundation ; NIBIB T32 EB019940; NIDCD R01 DC009183; NIMH R25 MH062204; NINDS U19 NS10 4648; Simons Foundation Simons Collaboration for the Global Brain ; U.S. Department of Defense NDSEG Fellowship program |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-09-12 12:58:48 | 6 | ||||||||
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Common Cell Type Nomenclature Resource Report Resource Website 1+ mentions |
Common Cell Type Nomenclature (RRID:SCR_021124) | controlled vocabulary, data or information resource, narrative resource, standard specification | Framework for creating brain cell type nomenclature, and include examples using published datasets. System allows designation of cell types with or without hierarchical organization. Nomenclature convention initially applied to brain cells and types, is intended to encompass existing naming strategies used in publications across diverse research teams. Allows tracking of many different taxonomies, including those from different organ systems or across diverse areas of bioscience. | Allen Cell Type Nomenclature CCN, Allen Brain Map, Common Cell Type Nomenclature, CCN, creating brain cell type nomenclature, hierarchical organization, nomenclature convention, naming strategies, taxonomies tracking |
is related to: Allen Brain Atlas is related to: Brain Data Standards Ontology is related to: Cell Type Knowledge Explorer has parent organization: Allen Institute |
Allen Institute ; NIMH U01 MH114812; NIMH U19 MH114830 |
PMID:33372656 | Free, Available for download, Freely available | https://github.com/AllenInstitute/nomenclature, https://github.com/AllenInstitute/CCN | SCR_021124 | Allen Cell Type Common Cell type Nomenclature, Allen Brain Map Cell Type Nomenclature CCN | 2026-09-12 12:59:51 | 3 | ||||||
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Marmoset Brain Connectivity Atlas Resource Report Resource Website 10+ mentions |
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) | atlas, data or information resource, data repository, database, service resource, storage service 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 CE140100007; Australian Research Council DP140101968; European Regional Development Fund ; International Neuroinformatics Coordinating Facility ; NIDA R01 DA036400; NIMH R01 MH087988 |
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 | 2026-09-12 12:58:33 | 26 | ||||||
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inBio Map Resource Report Resource Website 10+ mentions |
inBio Map (RRID:SCR_016147) | data or information resource, data processing software, data visualization software, database, software application, software resource | Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research. | ppi, protein, visualization | Broad Institute of MIT and Harvard ; Lundbeck Foundation ; Massachusetts General Hospital ; NICHD P01 HD068250; NIMH R01 MH109903; Novo Nordisk Foundation NNF14CC0001 |
PMID:27892958 | Freely available, Free, Available for download | SCR_016147 | inBio | 2026-09-12 12:58:35 | 23 | ||||||||
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fMRIPrep Resource Report Resource Website 1000+ mentions |
fMRIPrep (RRID:SCR_016216) | data processing software, image processing software, software application, software resource | Software tool as robust preprocessing pipeline for functional MRI.Used for preprocessing of diverse fMRI data. | Processing data, fmri, neuroimaging, coregistration, normalization, unwarping, noise, component, extraction, segmentation, skullstripping |
uses: Nipype has parent organization: Poldracklab Portal works with: NiPoppy |
Laura and John Arnold Fundation ; NIDCR UL1 DE019580; NIMH PL1 MH083271; NIMH RL1 DA024853; NIMH RL1 MH083268; NIMH RL1 MH083269; NIMH RL1 MH083270; NINDS PL1 NS062410; NLM RL1 LM009833 |
PMID:30532080 PMID:32514178 |
Free, Available for download, Freely available | https://zenodo.org/record/1219187#.WuDlO4jwZPY | SCR_016216 | fMRIPrep, FMRI PREP | 2026-09-12 12:58:36 | 1457 | ||||||
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Primate Data Exchange Resource Report Resource Website 10+ mentions |
Primate Data Exchange (RRID:SCR_016435) | PRIME-DE | consortium, data or information resource, database, organization portal, portal | Open resource for nonhuman primate imaging.Used for aggregation independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI).Consortium and data collection for the neuroimaging community to map the non-human primate connectome. Anatomical, functional, and diffusion MRI datasets openly shared via the International Neuroimaging Data sharing Initiative (INDI). | nonhuman, primate, neuroimaging, magnetic, resonance, imaging, dataset, share | is affiliated with: 1000 Functional Connectomes Project | Joseph P. Healy ; NIMH P50 MH109429; NIMH R01 MH111439; the BRAIN Initiative ; the Max Planck Society ; the Sylvio O. Conte Center “Neurobiology and Dynamics of Active Sensing” |
DOI:10.1016/j.neuron.2018.08.039 | Restricted | SCR_016621 | SCR_016435 | PRIME-DE:PRIMate Data Exchange | 2026-09-12 12:58:39 | 16 | |||||
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BAMS Cells Resource Report Resource Website 10+ mentions |
BAMS Cells (RRID:SCR_003531) | BAMS Cells, BAMS Cell | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein. | neuroanatomy, cell, neuron, neural circuitry, brain |
is used by: NIF Data Federation has parent organization: Brain Architecture Management System |
NIBIB ; NIMH ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-90175 | http://brancusi.usc.edu/bkms/ | SCR_003531 | Brain Architecture Management System Cells | 2026-09-12 01:01:29 | 11 | |||||
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Language Map Experiment Management System Resource Report Resource Website |
Language Map Experiment Management System (RRID:SCR_004562) | Language Map EMS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An experiment management system for researchers studying language organization in the brain. Data from thirteen patients are available as a public demo. Language Map EMS | fmri, 3d models, anatomy, cortex, data managementas of 2006/11 data from 110 patients in repository., imaging, mri, segmentation, volume | has parent organization: University of Washington; Seattle; USA | Aging | NIMH ; NIDCD ; NIA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00065 | SCR_004562 | UW Integrated Brain Project Language Map Experiment Management System | 2026-09-12 01:01:32 | 0 | |||||
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SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-09-12 01:01:36 | 740 | |||||
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NIMH Psychoactive Drug Screening Program Resource Report Resource Website 50+ mentions |
NIMH Psychoactive Drug Screening Program (RRID:SCR_005630) | PDSD, NIMH PDSP | analysis service resource, material analysis service, production service resource, service resource | This service provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters. Bryan Roth MD, PhD (University of North Carolina Chapel Hill) will perform pharmacological and functional screening of novel compounds as a contractor to NIMH. Screening of compounds is provided to qualified academic investigators at no cost. * Assays using for a large number of cloned human or rodent cDNAs for CNS receptors, channels and transporters. For a list of current receptors/transporters go to:clones.html * Ki determinations * Functional assays to determine effects on second messenger systems, channel activity and transporter function * Cloned receptors are also available at no cost to qualified investigators. * Assays are now available for bioavailability predictions (CaCo2, MDR-1) and cardiovascular toxicity predictions (HERG, 5-HT2B) Who is eligible * Academic investigators involved in basic or clinical research relevant to mental health. * Projects from research and development areas in small businesses relevant to mental and behavioral science. * Areas of interest to NIMH include the design and development of new chemical entities and small molecules as research tools, probes, targeted drug delivery systems, and PET ligands for brain imaging. * Research areas of interest are described in the Division of Basic and Clinical Neuroscience Research webpage, http://www.nimh.nih.gov/about/organization/dnbbs/index.shtml. | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | NIMH contract HHSN-271-2008-00025-C | nlx_146244 | SCR_005630 | National Institute of Mental Health Psychoactive Drug Screening Program | 2026-09-12 01:01:38 | 77 | ||||||||
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NIMH Toxicological Screens of Novel Ligands Resource Report Resource Website |
NIMH Toxicological Screens of Novel Ligands (RRID:SCR_005631) | Toxicological Evaluation of Novel Ligands | analysis service resource, material analysis service, production service resource, service resource | The purpose of the NIMH Toxicological Evaluation of Novel Ligands Program is to accelerate the discovery, development, and application of novel ligands for PET, SPECT, and MRI imaging in humans by providing toxicology and safety assessment of promising, target-selective compounds. The program will also provide limited assessment of novel psychoactive agents for clinical research and as potential therapeutics. Toxicology and safety data generated by the program will be used to support an Investigational New Drug (IND) application to the Food and Drug Administration (FDA), or for Radioactive Drug Research Committee (RDRC) evaluation of a compound for human studies. The contract will evaluate toxicity and safety of compounds submitted for testing which may include, but are not limited to, novel chemical entities, structural analogs of compounds with an IND, or analogs of FDA-approved drugs. The services available under this program fall under four general phases: (1) analytical, (2) pharmacokinetics, (3) preliminary safety, and (4) IND-directed toxicity including safety pharmacology. What is available A broad range of tasks are available for assessing the safety and/or pharmacokinetics of each ligand. Specific capabilities available to investigators include: * Validation of the analytical methods for quantitating drug concentrations in dosing solutions, biological fluids, and tissues, as required. Determination of plasma drug levels in animals administered the agent under study, and calculation of pharmacokinetic parameters derived from these data. * Determination of bioavailability of the drug after different routes of administration, including oral, intravenous (i.v.), subcutaneous (s.c.), intramuscular (i.m.), or intraperitoneal (i.p.), as needed. Calculation of the pharmacokinetic parameters from the derived data. * In vitro evaluation of hepatotoxicity in human and animal liver cells. * Preclinical acute toxicity evaluations on lead compounds, evaluating clinical observations, body weights, clinical pathology, histopathology, and plasma drug levels in rodents and non-rodent species. Other toxicology endpoints may be selected if needed. * Subacute and subchronic toxicity evaluations in rodents and large animal species, evaluating clinical observations, body weights, clinical pathology, and histopathology. * Genotoxicity assessments using a battery of appropriate assays. Since these preclinical studies are needed to demonstrate to the FDA that a candidate medication or imaging agent is understood well enough for designing appropriate clinical treatment regimens, most of the work to be conducted to achieve these objectives must be performed and the resulting data analyzed and reported in strict compliance with the FDA''s GLP regulations for nonclinical laboratory studies (21 CFR 58). These data must be obtained by carefully planned and skillfully executed methods that are specific, accurate, and precise. The applicable portions of the accumulated safety data will be included in documents submitted to the FDA in support of regulatory applications. Who is eligible Academic investigators involved in basic or clinical research relevant to mental health. Research areas are described on the NIMH website. | ligand, toxicology, pet, spect, mri, imaging, safety | has parent organization: Stanford Research Institute International | NIMH | nlx_146245 | SCR_005631 | Toxicological Evaluation of Novel Ligands Program, NIMH Toxicological Screens of Novel Ligands Program | 2026-09-12 01:01:38 | 0 |
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