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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Brain Test Resource Report Resource Website |
Brain Test (RRID:SCR_006212) | Brain Test | data or information resource, portal, topical portal | A portal of online studies that encourage community participation to tackle the most challenging problems in neuropsychiatry, including attention-deficit / hyperactivity disorder, schizophrenia, and bipolar disorder. Our approach is to engage the community and try to recruit tens of thousands of people to spend an hour of their time on our site. You folks will provide data in both brain tests and questionnaires, as well as DNA, and in return, we will provide some information about your brain and behavior. You will also be entered to win amazon.com gift cards. While large collaborative efforts were made in genetics in order to discover the secrets of the human genome, there are still many mysteries about the behaviors that are seen in complex neuropsychiatric syndromes and the underlying biology that gives rise to these behaviors. We know that it will require studying tens of thousands of people to begin to answer these questions. Having you, the public, as a research partner is the only way to achieve that kind of investment. This site will try to reach that goal, by combining high-throughput behavioral assessment using questionnaires and game-like cognitive tests. You provide the data and then we will provide information and feedback about why you should help us achieve our goals and how it benefits everyone in the world. We believe that through this online study, we can better understand memory and attention behaviors in the general population and their genetic basis, which will in turn allow us to better characterize how these behaviors go awry in people who suffer from mental illness. In the end, we hope this will provide better, more personalized treatment options, and ultimately prevention of these widespread and extremely debilitating brain diseases. We will use the data we collect to try to identify the genetic basis for memory and impulse control, for example. If we can achieve this goal, maybe we can then do more targeted research to understand how the biology goes awry in people who have problems with cognition, including memory and impulse control, like those diagnosed with ADHD, Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorders. By participating in our research, you can learn about mental illness and health and help researchers tackle these complex problems. We can''t do it without your help. | neuropsychiatry, brain, behavior, behavioral assessment, questionnaire, cognitive test, crowdsourcing, online study, memory, attention, brain disease, gene, exercise, genetics, mental disease, mental health, research project, research | has parent organization: University of California at Los Angeles; California; USA | Attention deficit-hyperactivity disorder, Schizophrenia, Bipolar Disorder, Mental disease, Normal, Autism Spectrum Disorder | NIMH ; NARSAD |
nlx_151777 | SCR_006212 | Brain Test project | 2026-09-05 06:25:49 | 0 | ||||||
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Genes Cognition and Psychosis Program Resource Report Resource Website 1+ mentions |
Genes Cognition and Psychosis Program (RRID:SCR_006292) | GCAP | data or information resource, disease-related portal, portal, topical portal | Schizophrenia related portal that aims to solve the mystery of genetic predisposition to psychosis, develop new methods for early diagnosis and prevention, and discover new treatments that will cure people suffering from it. Our objectives are to fully characterize: # neurobiological mechanisms related to susceptibility genes for schizophrenia and related clinical disorders; # genetic variation in aspects of cognition and emotionality associated with schizophrenia; and # small molecular targets for novel therapies. A unique feature of this Program is that its diverse scientific resources will be focused on a highly specific scientific agenda, that is to acquire the critical biological information about the susceptibility genes associated with schizophrenia and related illnesses. Our mission and goal, to understand the basic mechanisms of serious mental illness, has again guided us into new areas of research and to new insights. We have found evidence of new genes implicated in the cause of schizophrenia and involved in brain functions related to cognition and emotion and we have begun to explore how genes interact with each other and with the environment to individualize risk for these conditions. We are working now with over 20 genes related to schizophrenia. One of the key developments in our research over the past year has been the emergence of some targets for the development of novel therapeutics. We have discovered a new schizophrenia susceptibility gene, KCNH2, which represents the first clear target for the development of novel treatments. Just in this past year, for example, we published the first extensive statistical analysis of how schizophrenia genes may vary in their risk effects based on different genetic background (Nicodemus et al Hum Gen 2006), the first studies of schizophrenia genes interacting in effecting gene expression in brain (Lipska et al Hum Mol Genetics 2006a, Lipska et al Hum Mol Gen 2006 b); the first evidence that the mechanism of genetic association of NRG1 with schizophrenia involves a novel isoform of the gene in human brain (Law et al PNAS 2006), and the first evidence that MAOA may be linked to mood and impulse control because it effects critical mood regulatory neural networks (Meyer-Lindenberg et al PNAS 2006). | gene, genetic variation, cognition, emotion, therapeutics, treatment, drug development, brain function, psychosis, drug |
is related to: NIMH Intramural Research Program Clinical Brain Disorders Branch has parent organization: NIMH Division of Intramural Research Programs |
Schizophrenia, Mental illness, Psychiatric disorder | NIMH | nlx_151948 | SCR_006292 | 2026-09-05 06:25:50 | 1 | |||||||
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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 | 2026-09-05 06:29:34 | 3 | ||||||
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ARGON Resource Report Resource Website 1+ mentions |
ARGON (RRID:SCR_021635) | simulation software, software application, software resource | Software tool as fast simulator of genetic data that samples from Discrete Time Wright Fisher process backwards in time. Used to simulate long chromosomes and large samples under DTWF, with computational time comparable to recent coalescent simulators. | DTWF, genetic data simulator, discrete time Wright Fisher, process backwards in time, large samples simulation, long chromosomes simulation, discrete time Wright Fisher, coalescent simulation | has parent organization: University of Oxford; Oxford; United Kingdom | NIMH R01 MH101244 | PMID:27312410 | Free, Available for download, Freely available | https://github.com/pierpal/ARGON | SCR_021635 | 2026-09-05 06:29:43 | 1 | |||||||
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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 | 2026-09-05 06:28:13 | 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 | 2026-09-05 06:28:18 | 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 | 2026-09-05 06:28:18 | 6 | ||||||||
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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 | 2026-09-05 06:28:24 | 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 | 2026-09-05 06:28:24 | 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 | 2026-09-05 06:28:24 | 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 | 2026-09-05 06:28:24 | 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 | 2026-09-05 06:28:26 | 53 | |||||||||
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MNE-BIDS Resource Report Resource Website 1+ mentions |
MNE-BIDS (RRID:SCR_018766) | MNE-BIDS | data analysis software, data management software, data processing software, software application, software resource, software toolkit | Software Python package to link Brain Imaging Data Structure and MNE-Python software for analyzing neurophysiology data with goal to make analyses faster to code, more robust to errors, and easily shareable with colleagues. Provides programmable interface for BIDS datasets in electrophysiology with MNE-Python. Used for organizing electrophysiological data into BIDS format and facilitating their analysis. | Data structure, brain imaging, Minimum Norm current Estimates, M/EEG data, neurophysiology data analysis, BIDS dataset, electrophysiology, BIDS format organization |
is related to: MNE software works with: Brain Imaging Data Structure (BIDs) |
Academy of Finland ; Bezos Family Foundation ; Google Summer of Code 2019 ; NIMH R24 MH114705; NINDS R01 NS10 4585; Simms Mann Foundation |
DOI:10.21105/joss.01896 | Free, Available for download, Freely available | https://mne.tools/mne-bids/stable/index.html | SCR_018766 | Minimum Norm current Estimates - Brain Imaging Data Structure | 2026-09-05 06:28:42 | 5 | |||||
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Minian Resource Report Resource Website 1+ mentions |
Minian (RRID:SCR_022601) | data analysis software, data processing software, software application, software resource, software toolkit | Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output. | Miniscope, analysis pipeline, calcium imaging, mouse, Visualization, OpenBehavior |
is listed by: OpenBehavior has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIA F32AG067640; NIBIB R01EB028166; NIDA R21 DA049568; NIMH DP2MH122399; NIMH R01MH120162; NINDS R01 NS116357; NINDS R03 NS111493; NINDS U01NS094286; NSF 1700408; NSF 1926800; NSF 2046583 |
PMID:35642786 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/minian/ | SCR_022601 | 2026-09-05 06:30:15 | 6 | |||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, image processing software, software application, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; Multidisciplinary University Research Initiative Army Research Office ; NIAID R01AI130303; NIGMS F31GM116517; NIGMS P41GM10371; NIH Office of the Director DP2OD006514; NIMH P50MH09427; NIMH R01MH110932; NINDS R01NS076467; NINDS R01NS095367; NINDS U01NS090449; NSF NSF-1707316 |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-09-05 06:30:18 | 0 | ||||||||
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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 | 2026-09-05 06:27:58 | 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 | 2026-09-05 06:27:59 | 80 | |||||||
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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 | 2026-09-05 06:28:01 | 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 | 2026-09-05 06:28:04 | 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 | 2026-09-05 06:28:05 | 1457 |
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