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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software application, software resource | 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 | Biotechnology and Biological Sciences Research Council ; Human Connectome Project ; Marie Skłodowska-Curie Individual Fellowship Grant ; McDonnell Center for Systems Neuroscience at Washington University ; Medical Research Council PhD Studentship UK ; MRC Career Development Fellowship UK ; Netherlands Organization for Scientific Research NWO Netherlands ; NIH ; NIMH 1U54MH091657; Sir Henry Dale Wellcome Trust Fellowship UK ; UK Biobank Resource ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust Collaborative Award UK ; Wellcome Trust grant UK ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-09-05 06:34:45 | 4 | ||||||||
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eddyqc Resource Report Resource Website |
eddyqc (RRID:SCR_024936) | data analysis software, data processing software, software application, software resource | 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 ; NIMH 1U01AG052564; NIMH 1U01MH109589; NIMH 1U54MH091657; UK Medical Research Council ; Wellcome-Trust Strategic Award |
PMID:30267859 | Free, Freely available | https://git.fmrib.ox.ac.uk/matteob/eddy_qc_release | SCR_024936 | 2026-09-05 06:34:45 | 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, | NHGRI R01 HG011883; NHGRI R01HG010773; NIGMS R01 GM126553; NIMH R01MH110531; NIMH R01MH116281; NSF ; Sloan Research Fellowship |
PMID:37770710 | Free, Available for download, Freely available | SCR_025023 | 2026-09-05 06:34:48 | 1 | ||||||||
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3D Developmental Mouse Brain Common Coordinate Framework Resource Report Resource Website 1+ mentions |
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) | atlas, data or information resource | Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain. | multimodal 3D atlases, developing mouse brain, mouse brain data, |
is related to: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative |
NIBIB R01EB031722; NIMH R01MH116176; NIMH RF1MH12460501; NINDS R01NS108407 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-09-05 06:35:01 | 2 | |||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | data analysis software, data processing software, software application, software resource | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | Gillings Innovation Laboratory in Statistical Genomics ; NCI R01 CA138255; NIEHS R01 ES015241; NIMH R01 MH090936; NSF ; US Environmental Protection Agency |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-09-05 06:35:00 | 75 | ||||||||
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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 | NeuroNex NSF ; NIMH RF1MH120034 |
Free, Freely available, | SCR_025464 | BEhavioral tAsk Description Language | 2026-09-05 06:34:59 | 1 | |||||||
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Genetic Tools Atlas Resource Report Resource Website 1+ mentions |
Genetic Tools Atlas (RRID:SCR_025643) | GTA | atlas, catalog, data or information resource, database | 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 |
NIMH 1RF1 MH114126; NIMH 1RF1 MH121274; NIMH 1UF1 MH128339; NIMH 1UG3 MH120095; Paul G. Allen Foundation n/a |
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 | 2026-09-05 06:35:03 | 9 | ||||||
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ezBIDS Resource Report Resource Website 1+ mentions |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | BRAIN CONNECTS ; Kavli Foundation ; NIBIB R01EB029272; NIBIB R01EB030896; NIMH R01MH133701; NINDS UM1NS132207; NSF ; Spanish Government ; Wellcome Trust |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-09-05 06:35:01 | 1 | |||||||
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DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | atlas, data or information resource, reference atlas | Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome. | Whole brain developmental map, neuronal circuit maturation, whole brain spatiotemporal mapping, circuit maturation, early postnatal development, mouse models of neurodevelopmental disorders, | Brain Research Foundation Seed Grant ; Human Frontier Science Program ; NIDCD DC014701; NIMH MH116673; NIMH RF1MH124605; NINDS NS115543; NINDS NS123710; Paul and Lilah Newton Brain Science Award ; Simons Center for the Social Brain Equipment Grant |
PMID:38260331 | Free, Freely available | DevATLAS | SCR_025718 | Developmental Activation Timing-based Longitudinal Acquisition System | 2026-09-05 06:35:05 | 0 | |||||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | data processing software, image processing software, software application, software resource, software toolkit | 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, | NCRR U24 RR021382; NIA R01AG008122; NIBIB R01EB006758; NIH Blueprint for Neuroscience Research ; NIMH F30 MH097312; NIMH MH091657; NIMH ROI MH60974; NINDS R01 NS052585; NINDS R01NS070963; NINDS R21NS072652 |
PMID:23668970 | Free, Available for download, Freely available | https://www.humanconnectome.org/software/hcp-mr-pipelines | SCR_026575 | Human Connectome Project Pipelines | 2026-09-05 06:35:26 | 36 | |||||||
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | software resource, software toolkit, source code | Software Python/Rust package for single-cell epigenomics analysis. | Single-cell epigenomics analysis, | NEI R01EY031663; NHGRI U01HG012059; NHGRI UM1HG011585; NIA R24AG073198; NIA R56AG069107; NIA U54AG079758; NIMH RF1MH128838; NIMH U01MH114828; NIMH U01MH121282; NIMH U19MH114831; NIMH UM1MH130994 |
PMID:38191932 | Free, Available for download, Freely available | SCR_026622 | 2026-09-05 06:35:27 | 4 | |||||||||
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neuropythy Resource Report Resource Website 1+ mentions |
neuropythy (RRID:SCR_027787) | software library, software resource, software toolkit, source code | Software neuroscience library for Python, intended to complement the existing nibabel library. Can automatic download data and interpret them into Python data structures. | Python, complement nibabel library, can automatic download data and interpret them into Python data structures, | NEI R00 EY022116; NEI R01 EY027401; NEI R01 EY027964; NIMH R01 MH111417 |
PMID:30520736 | Free, Available for download, Freely available | https://hub.docker.com/r/nben/neuropythy | SCR_027787 | 2026-09-05 06:35:58 | 4 | ||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | 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; NIGMS R01 GM078598; NIMH R01 MH101244 |
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 | 2026-09-05 06:35:57 | 0 | |||||||
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Reproducible Brain Charts Resource Report Resource Website |
Reproducible Brain Charts (RRID:SCR_027837) | data or information resource, data set | Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner. | Neuroimaging data, curated data, data resource, mapping brain development, mental health, | NIBIB R01EB022573; NIMH K08MH079364; NIMH P50MH109429; NIMH R01MH112847; NIMH R01MH113550; NIMH R01MH120482; NIMH R01MH123440; NIMH R01MH123550; NIMH R37MH125829; NIMH RF1MH121867; NINDS U24NS130411 |
PMID:40987284 | Free, Freely available | SCR_027837 | 2026-09-05 06:36:00 | 0 | |||||||||
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Baby Open Brains Resource Report Resource Website |
Baby Open Brains (RRID:SCR_027836) | data or information resource, data set | Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD. | MRI, image, dataset of infant brain segmentations, infant brain, brain segmentation, manually curated infant brain segmentations, | uses: OpenNeuro | Bill & Melinda Gates Foundation ; NIDA U01DA041148; NIDA U24DA055330; NIMH R01 MH104324; NIMH R01MH096773; NIMH R01MH125829; NIMH R37MH125829; NIMH U01 MH110274; NINDS T32 NS109604 |
PMID:40813378 | Free, Freely available, | SCR_027836 | , BOBs, Baby Open Brains (BOBs) Dataset | 2026-09-05 06:36:00 | 0 | |||||||
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tximeta Resource Report Resource Website 1+ mentions |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NCI P01 CA142538; NHGRI R01 HG009937; NHGRI U41 HG004059; NIEHS P30 ES010126; NIMH R01 MH118349 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | Tximeta | 2026-09-05 06:36:04 | 1 | ||||||||
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RDoC Resource Report Resource Website 100+ mentions |
RDoC (RRID:SCR_002244) | RDoC | data or information resource, knowledge environment, narrative resource, standard specification | NIMH Strategic Plan developing, for research purposes, new ways of classifying psychopathology based on dimensions of observable behavior and neurobiological measures. In brief, the effort is to define basic dimensions of functioning (such as fear circuitry or working memory) to be studied across multiple units of analysis, from genes to neural circuits to behaviors, cutting across disorders as traditionally defined. The intent is to translate rapid progress in basic neurobiological and behavioral research to an improved integrative understanding of psychopathology and the development of new and/or optimally matched treatments for mental disorders. The various domains of functioning, and their constituent elements, are being defined by an ongoing series of consensus workshops; input from the research community and other interested stakeholders is encouraged. | cognitive system, neural circuit, behavior, cognition, comorbidity, psychiatric diagnosis |
is related to: RDoCdb has parent organization: National Institute of Mental Health |
Mental disease | NIMH | PMID:24016027 PMID:23902986 PMID:22577302 PMID:21198381 PMID:20939653 PMID:20929969 PMID:20595427 |
Free, Freely available | nlx_155557 | SCR_002244 | Research Domain Criteria | 2026-09-05 06:24:45 | 167 | ||||
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Cognitive Paradigm Ontology Resource Report Resource Website 1+ mentions |
Cognitive Paradigm Ontology (RRID:SCR_002235) | CogPO | controlled vocabulary, data or information resource, ontology | Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response. | functional neuroimaging, owl, cognition, behavior |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: BioPortal is related to: Human Imaging Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA has parent organization: Mind Research Network |
NIMH 1R01MH084812-01A1 | Free, Freely available | nlx_155537 | http://www.nitrc.org/projects/cogpo | SCR_002235 | 2026-09-05 06:24:45 | 9 | ||||||
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OBART Resource Report Resource Website 1+ mentions |
OBART (RRID:SCR_001903) | OBART | atlas, data or information resource, software resource, web application | Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases. | atlas, brain, clinical, mapping, meta-analysis, neuroscience, visualization, label |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Architecture Project has parent organization: Boston University; Massachusetts; USA |
NIMH 5R01MH084802 | PMID:19787067 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10473 | http://www.nitrc.org/projects/obart | http://obart.brainarchitecture.org | SCR_001903 | The Online Brain Atlas Reconciliation Tool, Online Brain Atlas Reconciliation Tool | 2026-09-05 06:24:41 | 2 | |||
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NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH084358; NIMH R43 MH60507; NIMH R44 MH60507 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-09-05 06:24:24 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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