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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MPIDB Resource Report Resource Website 1+ mentions |
MPIDB (RRID:SCR_001898) | MPIDB | data or information resource, database | Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included. | 3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiology |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Database of Interacting Proteins (DIP) is related to: BIND is related to: MINT is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry has parent organization: J. Craig Venter Institute |
J. Craig Venter Institute ; Indgen Life Technologies ; NIH ; NIMH R01GM79710 |
PMID:18556668 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010673, nif-0000-10467 | http://jcvi.org/mpidb/ | SCR_001898 | The Microbial Protein Interaction Database, Microbial Protein Interaction Database | 2026-08-03 09:31:28 | 5 | ||||
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Chronux Resource Report Resource Website 500+ mentions |
Chronux (RRID:SCR_005547) | Chronux | software resource, data processing software, software application, data analysis software | Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data. | fmri, brain mapping, brain, matlab |
is related to: Zebra Finch Song Learning Consortium has parent organization: Cold Spring Harbor Laboratory |
NIMH | Open-source. Please cite. | nif-0000-00082 | SCR_005547 | Chronux Analysis Software | 2026-08-03 09:32:42 | 535 | ||||||
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NIMH Brain Tissue Collection Resource Report Resource Website 1+ mentions |
NIMH Brain Tissue Collection (RRID:SCR_008726) | NIMH Brain Bank | tissue bank, biomaterial supply resource, material resource, brain bank | A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development. | schizophrenia, bipolar disorder, depressive disorder, anxiety disorder, substance abuse, healthy, neurological disorder, mental disease, suicide, tourette's syndrome, dementia, brain development, brain, brain tissue, tissue, post-mortem, normal control, ClinicalTrials.gov Identifier: NCT00001260 |
is listed by: One Mind Biospecimen Bank Listing has parent organization: NIMH Intramural Research Program Clinical Brain Disorders Branch |
Schizophrenia, Bipolar Disorder, Depressiive Disorder, Anxiety Disorder, Drug Abuse, Healthy, Neurological disorder, Mental disease, Suicide, Tourette's Syndrome, Dementia, Normal control, Aging | NIMH | Samples available to investigators approved by an NIMH Oversight Committee, Molecular and genetic data available to the scientific community | nlx_143684 | http://cbdb.nimh.nih.gov/neuropath.htm | SCR_008726 | 2026-08-03 09:33:55 | 1 | |||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | image processing software, software toolkit, software application, data processing software, image analysis software, software resource | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-08-03 09:32:11 | 27070 | ||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | software resource, data processing software, software application, data analysis software | 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 K12 CA139160; NCI F32CA165823; NIMH T32 MH020065; NIMH R01 MH101820; NIMH R01 MH090937; NIGMS U01 GM61393; NIMH P50 MH094267; NIGMS U01 GM092691; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-08-03 09:36:35 | 23 | |||||||||
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PAGODA Resource Report Resource Website |
PAGODA (RRID:SCR_017099) | software resource, data processing software, software application, data analysis software | 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 ; NSF NSF-14-532; NSF DGE1144152; NIMH U01 MH098977; NINDS R01 NS084398; NIA T32 AG00216 |
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 | 2026-08-03 09:36:31 | 0 | ||||||
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seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | software resource, data processing software, software application, data analysis software | 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; | Simons Foundation Simons Collaboration for the Global Brain ; NIDCD R01 DC009183; G Harold and Leila Y. Mathers Foundation ; U.S. Department of Defense NDSEG Fellowship program ; Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; NIBIB T32 EB019940; NINDS U19 NS10 4648; NIMH R25 MH062204 |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-08-03 09:36:59 | 5 | ||||||||
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FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | software application, data processing software, data analysis software, software resource, data visualization software | 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 |
National Institutes of Health NRSA Trainee appointment ; California Research Alliance by BASF ; NIMH U01 MH105979; NHGRI U01 HG007910 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-08-03 09:37:03 | 0 | ||||||
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JWatcher Resource Report Resource Website 10+ mentions |
JWatcher (RRID:SCR_017595) | data acquisition software, software application, data processing software, data analysis software, data analytics software, 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 |
NIMH R21 MH065226; Australian Research Council ; Macquarie University |
Free, Available for download, Freely available | SCR_017595 | 2026-08-03 09:37:05 | 49 | |||||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | software application, data processing software, data analysis software, software resource, data visualization software | 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 | NIMH U19 MH114830; NIMH U01 MH105979; Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-08-03 09:36:38 | 0 | ||||||||
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microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | image processing software, software application, data processing software, image analysis software, 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 |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-08-03 09:36:38 | 1 | |||||||
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StimVision Resource Report Resource Website 1+ mentions |
StimVision (RRID:SCR_017457) | software resource, data visualization software, software application, data processing software | 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 | 2026-08-03 09:36:51 | 1 | ||||||||
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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 |
NIMH ; NINDS ; NIBIB |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-90175 | http://brancusi.usc.edu/bkms/ | SCR_003531 | Brain Architecture Management System Cells | 2026-08-03 09:32:16 | 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 | 2026-08-03 09:32:36 | 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 | 2026-08-03 09:32:50 | 740 | |||||
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Minian Resource Report Resource Website 1+ mentions |
Minian (RRID:SCR_022601) | software toolkit, software application, data processing software, data analysis software, software resource | 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 |
NIMH DP2MH122399; NIMH R01MH120162; NIBIB R01EB028166; NSF 1926800; NSF 2046583; NINDS U01NS094286; NSF 1700408; NIA F32AG067640; NINDS R03 NS111493; NIDA R21 DA049568; NINDS R01 NS116357 |
PMID:35642786 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/minian/ | SCR_022601 | 2026-08-03 09:37:44 | 4 | |||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | image processing software, software resource, software application, data processing software | 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 ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-08-03 09:38:13 | 0 | ||||||||
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TrumpetPlots Resource Report Resource Website 1+ mentions |
TrumpetPlots (RRID:SCR_023742) | software toolkit, software application, data processing software, 3d visualization software, software resource, data visualization software | Software R package to visualize relationship between allele frequency and effect size in genetic association studies. | genetic association studies, visualization of genetic association studies, allele frequency, effect size, genetics, | NIMH R01 MH122866; Brain and Behavior Research Foundation ; Icahn School of Medicine at Mount Sinai |
DOI:10.1101/2023.04.21.23288923 | Free, Available for downlaod, Freely available | https://juditgg.shinyapps.io/shinytrumpets/ | SCR_023742 | 2026-08-03 09:38:30 | 1 | ||||||||
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Allen Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Allen Brain Cell Atlas (RRID:SCR_024440) | expression atlas, data or information resource, atlas | Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression. | visualizing multimodal single cell data across mammalian brain, explore and analyze multiple whole brain datasets, identify cell types in brain, brain regions defined by gene expression, |
has parent organization: Allen Institute is organization facet of: BICCN |
NIMH MH130919 | Free, Freely available | SCR_024440 | Allen Brain Cell (ABC) Atlas, The Allen Brain Cell Atlas, ABC Atlas | 2026-08-03 09:38:41 | 42 | ||||||||
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MNE-BIDS Resource Report Resource Website 1+ mentions |
MNE-BIDS (RRID:SCR_018766) | MNE-BIDS | data management software, software toolkit, software application, data processing software, data analysis software, software resource | 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 ; NINDS R01 NS10 4585; NIMH R24 MH114705; Bezos Family Foundation ; Simms Mann Foundation ; Google Summer of Code 2019 |
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 | 2026-08-03 09:37:19 | 3 |
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