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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-08-03 09:38:05 | 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 | 2026-08-03 09:38:19 | 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 | organization portal, laboratory portal, portal, atlas, data or information resource | 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 | 2026-08-03 09:38:48 | 3 | |||||||
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eddyqc Resource Report Resource Website |
eddyqc (RRID:SCR_024936) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:38:28 | 0 | |||||||
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BEADL:BEhavioral tAsk Description Language Resource Report Resource Website 1+ mentions |
BEADL:BEhavioral tAsk Description Language (RRID:SCR_025464) | BEADL | narrative resource, data or information 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 | 2026-08-03 09:38:46 | 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) | data or information resource, atlas | 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 |
NIMH RF1MH12460501; NINDS R01NS108407; NIMH R01MH116176; NIBIB R01EB031722 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-08-03 09:39:10 | 2 | |||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-03 09:39:10 | 69 | ||||||||
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ezBIDS Resource Report Resource Website |
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, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-08-03 09:38:49 | 0 | |||||||
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Genetic Tools Atlas Resource Report Resource Website 1+ mentions |
Genetic Tools Atlas (RRID:SCR_025643) | GTA | data or information resource, catalog, atlas, 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 |
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 | 2026-08-03 09:39:11 | 6 | ||||||
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DevATLAS Resource Report Resource Website |
DevATLAS (RRID:SCR_025718) | data or information resource, reference atlas, 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, | Human Frontier Science Program ; Brain Research Foundation Seed Grant ; Simons Center for the Social Brain Equipment Grant ; Paul and Lilah Newton Brain Science Award ; NIMH RF1MH124605; NIDCD DC014701; NINDS NS123710; NINDS NS115543; NIMH MH116673 |
PMID:38260331 | Free, Freely available | DevATLAS | SCR_025718 | Developmental Activation Timing-based Longitudinal Acquisition System | 2026-08-03 09:39:11 | 0 | |||||||
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HCP Pipelines Resource Report Resource Website 10+ mentions |
HCP Pipelines (RRID:SCR_026575) | image processing software, software toolkit, software application, data 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 | 2026-08-03 09:38:58 | 20 | |||||||
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SnapATAC2 Resource Report Resource Website 1+ mentions |
SnapATAC2 (RRID:SCR_026622) | software toolkit, software resource, source code | 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 | 2026-08-03 09:38:58 | 3 | |||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software resource, software application, 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; 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 | 2026-08-03 09:39:33 | 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, | NIMH R01MH120482; NIMH R37MH125829; NIBIB R01EB022573; NIMH R01MH112847; NIMH R01MH113550; NIMH RF1MH121867; NIMH R01MH123550; NINDS U24NS130411; NIMH P50MH109429; NIMH R01MH123440; NIMH K08MH079364 |
PMID:40987284 | Free, Freely available | SCR_027837 | 2026-08-03 09:39:34 | 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 ; NIMH R01 MH104324; NIMH U01 MH110274; NINDS T32 NS109604; NIDA U01DA041148; NIDA U24DA055330; NIMH R01MH096773; NIMH R01MH125829; NIMH R37MH125829 |
PMID:40813378 | Free, Freely available, | SCR_027836 | , BOBs, Baby Open Brains (BOBs) Dataset | 2026-08-03 09:39:19 | 0 | |||||||
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neuropythy Resource Report Resource Website |
neuropythy (RRID:SCR_027787) | software library, software toolkit, software resource, 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; 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 | 2026-08-03 09:39:14 | 0 | ||||||||
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NIMH Image Library Resource Report Resource Website 1+ mentions |
NIMH Image Library (RRID:SCR_005588) | NIMH Image Library | image collection, data or information resource | Database of photographs and illustrations of general biomedical research and research tools, mental health specific research, and treatment related images that are available, copyright free, to the public at no cost. Many images are available in low, medium, and high resolutions. Formats include jpg, gif, and png. NIMH images may not be used to state or imply the endorsement by NIMH or by an NIMH employee of a commercial product, service, or activity, or use in any other manner that might mislead. No fee is charged for using the images. However, credit must be given to the National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services unless otherwise instructed to give credit to the photographer or other source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | database, biomedical, mental health, treatment, brain, research, imaging, genetics, research lab, tool, therapy, medical care | has parent organization: National Institute of Mental Health | NIMH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_146221 | SCR_005588 | National Institute of Mental Health Image Library | 2026-08-01 12:02:56 | 3 | ||||||
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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 | 2026-08-01 12:05:02 | 3 | |||||||||
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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 | 2026-08-01 12:04:46 | 107 | |||||||
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OSA Resource Report Resource Website 1+ mentions |
OSA (RRID:SCR_002016) | OSA | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on. | gene, genetic, genomic, c++, unix, solaris, linux |
is listed by: Genetic Analysis Software has parent organization: Duke University; North Carolina; USA |
NIMH R01 MH59528 | PMID:18473393 PMID:15185403 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154504 | http://wwwchg.duhs.duke.edu/software/osa.html | SCR_002016 | Ordered Subset Analysis, OSA Program, Ordered Subset Analysis Program | 2026-08-01 12:10:44 | 1 |
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