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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Monkey Motion Resource Report Resource Website |
Monkey Motion (RRID:SCR_014285) | software resource, source code | 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 | 2026-02-13 10:57:15 | 0 | |||||||||
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BehaviorDEPOT Resource Report Resource Website 1+ mentions |
BehaviorDEPOT (RRID:SCR_023602) | software resource, source code | 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 | 2026-02-13 10:59:01 | 1 | |||||||
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TADA-A Resource Report Resource Website |
TADA-A (RRID:SCR_024538) | software resource, source code | Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies. | mapping risk genes, de novo mutations, whole genome sequencing, | NIMH R01MH110531; Simons Foundation |
PMID:29754769 | Free, Available for download, Freely available | SCR_024538 | TADA-Annotations | 2026-02-13 10:59:15 | 0 | ||||||||
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Early Postnatal Developmental Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Early Postnatal Developmental Mouse Brain Atlas (RRID:SCR_024725) | epDevAtlas | portal, laboratory portal, data or information resource, atlas, organization portal | Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology. | 3D atlases, early postnatally developing mouse brain, mapped cell type density growth charts, Allen Mouse Reference Atlas Ontology, |
uses: Allen Mouse Reference Atlas Ontology uses: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative Cell Atlas Network |
NIMH RF1MH12460501; NINDS R01NS108407 |
DOI:10.1101/2023.11.24.568585 | Free, Freely available | SCR_024725 | 2026-02-13 10:59:18 | 3 | |||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software resource, software application | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-02-13 10:59:20 | 2 | ||||||||
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eddyqc Resource Report Resource Website |
eddyqc (RRID:SCR_024936) | data analysis software, software resource, data processing software, software application | Software tool allows to assess dMRI data both at single subject and group levels.Calculates average SNR across all voxels within brain mask to give summary measure of overall quality of dataset. Used to generate single subject and study wise reports and databases. | assess dMRI data, voxels within brain mask, summary measure of overall data quality, generate single subject and study wise reports, | is a plug in for: FSL | European Research Council ; UK Medical Research Council ; Wellcome-Trust Strategic Award ; NIMH 1U01MH109589; NIMH 1U01AG052564; NIMH 1U54MH091657 |
PMID:30267859 | Free, Freely available | https://git.fmrib.ox.ac.uk/matteob/eddy_qc_release | SCR_024936 | 2026-02-13 10:59:24 | 0 | |||||||
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Guided Sparse Factor Analysis Resource Report Resource Website 1+ mentions |
Guided Sparse Factor Analysis (RRID:SCR_025023) | GSFA | software resource, software toolkit | Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data. | sparse factor analysis, differential gene expression, discovery simultaneously, single cell CRISPR screening data, | NIMH R01MH110531; NHGRI R01HG010773; NIMH R01MH116281; NIGMS R01 GM126553; NHGRI R01 HG011883; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-02-13 10:59:21 | 1 | ||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | data analysis software, software resource, data processing software, software application | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | NIMH R01 MH090936; NIEHS R01 ES015241; US Environmental Protection Agency ; NCI R01 CA138255; NSF ; Gillings Innovation Laboratory in Statistical Genomics |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-02-13 10:59:28 | 69 | ||||||||
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BEADL:BEhavioral tAsk Description Language Resource Report Resource Website 1+ mentions |
BEADL:BEhavioral tAsk Description Language (RRID:SCR_025464) | BEADL | data or information resource, narrative resource, standard specification | Universal framework for describing behavioral tasks. Language to abstract and standardize behavioral task descriptions on two layers. Graphical layer specifies elements to describe behavioral tasks as state machine in formal flow diagram and how task controlling system interacts with subject. This graphical layer has been designed to be easy to understand while retaining all aspects of behavioral task. The second layer is corresponding, XML-based description of task. This layer forms rigid, yet extensible foundation of BEADL and hides hardware implementation related details form graphical representation.BEADL-specific extension for Neurodata Without Borders data standard defines how behavioral outcomes of task are stored in NWB including corresponding BEADL task description. | Language to abstract and standardize behavioral task descriptions, two layers, graphical layer specifies elements, describe behavioral tasks as state machine, formal flow diagram, behavioral task | is related to: Neurodata Without Borders | NIMH RF1MH120034; NeuroNex NSF |
Free, Freely available, | SCR_025464 | BEhavioral tAsk Description Language | 2026-02-13 10:59:27 | 1 | |||||||
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Genetic Tools Atlas Resource Report Resource Website 1+ mentions |
Genetic Tools Atlas (RRID:SCR_025643) | GTA | data or information resource, atlas, database, 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 | 2026-02-13 10:59:30 | 6 | ||||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | data processing software, software toolkit, software application, image processing software, software resource | 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 | 2026-02-13 10:59:43 | 20 | |||||||
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | software resource, source code, software toolkit | 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 | 2026-02-13 10:59:42 | 3 | |||||||||
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neuropythy Resource Report Resource Website |
neuropythy (RRID:SCR_027787) | software resource, source code, software library, software toolkit | 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 | 2026-02-13 10:59:58 | 0 | ||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software resource, source code, software application | 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 | 2026-02-13 10:59:51 | 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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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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NKI-RS Multiband Imaging Test-Retest Pilot Dataset Resource Report Resource Website 1+ mentions |
NKI-RS Multiband Imaging Test-Retest Pilot Dataset (RRID:SCR_010460) | NKI-RS Multiband Test-Retest Pilot Dataset | data or information resource, data set | A test-retest dataset to assess the reliability of multiband resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) scans prior to launch of the Enhanced Nathan Kline Institute - Rockland Sample (NKI-RS). The dataset is primarily composed of individuals from the initial NKI-RS - for these individuals psychiatric assessment information is available and included (participants were not excluded due to history of illness. In addition to R-fMRI and DTI, they included: 1) simple visual checkerboard stimulation fMRI scans to allow for assessment of traditional fMRI data quality metrics (e.g., contrast-to-noise ratio), 2) breath holding data to enable assessment of regional differences in vascular responsiveness, and 3) eye movement calibration scans to enable the assessment of eye-movement related artifacts which may be particularly troublesome for multiband sequences since several slices are acquired simultaneously. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, psychiatric assessment |
is related to: NKI/Rockland Sample is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Creative Commons Attribution-NonCommercial License | nlx_157648 | SCR_010460 | Enhanced Nathan Kline Institute-Rockland Sample Multiband Imaging Test-Retest Pilot Dataset, Enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) Multiband Imaging Test-Retest Pilot Dataset | 2026-02-11 10:58:13 | 1 | |||||
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NKI-RS Enhanced Sample Resource Report Resource Website 50+ mentions |
NKI-RS Enhanced Sample (RRID:SCR_010461) | Enhanced NKI-RS | data or information resource, data set | Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, lifespan, physiological assessment, psychological assessment, genetic |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: Mind Research Network - COINS is related to: NIMH Repository and Genomics Resources has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Public, Data Usage Agreement | nlx_157649 | SCR_010461 | Enhanced Nathan Kline Institute - Rockland Sample | 2026-02-11 10:58:20 | 97 | |||||
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Brain RNA-Seq Resource Report Resource Website 100+ mentions |
Brain RNA-Seq (RRID:SCR_013736) | data or information resource, database | Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list | has parent organization: Stanford University; Stanford; California | NIMH R01MH09955501; NINDS R01NS08170301; NIGMS T32GM007365 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | Barres Brain RNA-Seq | 2026-02-11 10:58:49 | 109 | |||||
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BALSA Resource Report Resource Website 1+ mentions |
BALSA (RRID:SCR_022960) | BALSA | data or information resource, database | Database for hosting and sharing neuroimaging and neuroanatomical datasets for human and primate species. Includes 1) curated, user created Study datasets, extensively analyzed neuroimaging data associated with published figures/manuscripts, 2) Reference datasets mapped to brain atlas surfaces and volumes in human and nonhuman primates for use as general resources (e.g., published cortical parcellations), and 3) ConnectomeDB powered by BALSA for distributing HCP-Young Adult and related HCP-style processed imaging and phenotypic datasets. Datasets in BALSA may include PMID and/or DOI that links them directly to relevant publications. | Brain Analysis Library, spatial maps and atlases, hosting and sharing neuroimaging and neuroanatomical datasets, human and primate species, neuroimaging data associated with published figures, datasets mapped to brain atlas, Human Connectome Project, HCP |
is used by: BRAIN Initiative Cell Atlas Network is related to: Human Connectome Coordination Facility is related to: Connectome Workbench |
NIMH MH060974; NIMH R01MH060974 |
PMID:27074495 | Free, Freely available | r3d100013646 | https://balsa.wustl.edu/about https://doi.org/10.17616/R31NJN0U |
SCR_022960 | Brain Analysis Library of Spatial maps and Atlases | 2026-02-11 11:00:33 | 2 |
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