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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Roadmap Epigenomics Project Resource Report Resource Website 100+ mentions |
Roadmap Epigenomics Project (RRID:SCR_008924) | Roadmap Epigenomics Project | organization portal, project portal, consortium, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data. | epigenomics, genome, genetic variation, gene regulation, genomics, stem cell, primary cell, tissue, blood, lung, heart, gastrointestinal tract, brain, embryonic stem cell, fetus, adult, cell, epigenome, methylome, chip-seq, rna, breast, muscle, connective, gastrointestinal, genitourinary, fat, hematopoietic stem cell, thymus, spleen, placenta, kidney, adrenal, induced pluripotent stem cell, skin, angular gyrus, anterior caudate, cingulate gyrus, hippocampus, inferior temporal lobe, mid frontal lobe, substantia nigra, dna methylation, histone modification, chromatin, rna transcript, dna, methylation, histone, data set |
is used by: NIF Data Federation is used by: VizHub is used by: Integrated Data Annotation is listed by: 3DVC is listed by: OMICtools is related to: NCBI Epigenomics is related to: Gene Expression Omnibus is related to: Spark is related to: Deep Blue Epigenomic Data Server has parent organization: NIH Common Fund is parent organization of: Human Epigenome Atlas is parent organization of: WashU Epigenome Browser is parent organization of: VizHub |
PMID:22690667 PMID:20944595 PMID:20944597 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151644, OMICS_01564 | SCR_008924 | Epigenomics Program, Common Fund Epigenomics, NIH Roadmap Epigenomics Program, NIH Roadmap Epigenomics Project, Common Fund Epigenomics Program, NIH Common Fund Epigenomics, NIH Common Fund Epigenomics Program, Common Fund Roadmap Epigenomics Program | 2026-02-16 09:47:18 | 310 | ||||||
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DOTS WM tract segmentation Resource Report Resource Website 100+ mentions |
DOTS WM tract segmentation (RRID:SCR_009459) | DOTS | software application, data processing software, image analysis software, software resource, segmentation software | A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance, diffusion tensor mr imaging, dti, fiber tract, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MIPAV: Medical Image Processing and Visualization is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
NIDA K25DA025356 | PMID:21718790 | Free | nlx_155605 | SCR_009459 | Diffusion-Oriented Tract Segmentation White Matter tract segmentation, Diffusion-Oriented Tract Segmentation | 2026-02-16 09:47:24 | 115 | |||||
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genes2mind Resource Report Resource Website 1+ mentions |
genes2mind (RRID:SCR_008872) | genes2mind | data analysis service, analysis service resource, database, production service resource, service resource, data or information resource | genes2mind is a tool for rapid exploratory analysis of psychotropic drug-induced gene expression in the brain. We present here an open resource containing comparison of effects of various classes of psychotropic drugs on transcriptional alterations of ~20,000 genes in the mouse brain (C57BL/6J). Data stored in the database include raw gene expression values as well as results of drug comparison. * Genomic Signature Identification section allows for the identification of drug-specific genomic signatures. * Genomic Signature Analysis section allows for further inspection and visualization of the signatures using multidimensional data analysis (PCA), co-expression analysis and heatmaps. * Single Gene Inspection allows for brief review of expression of specific candidate genes using barplots. | psychotropic drug, gene expression, gene, brain, drug, c57bl/6j, genomic | has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland | Institute of Pharmacology PAS ; Polish Ministry of Science and Higher Education DeMeTer 3.1 POIG; Polish Ministry of Science and Higher Education NN405 274137; European Union FP6 GENADDICT LSHM-CT-2004-005166 |
nlx_149344 | SCR_008872 | 2026-02-16 09:47:17 | 3 | ||||||||
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Baby Brain Toolkit Resource Report Resource Website |
Baby Brain Toolkit (RRID:SCR_009440) | BTK | software application, data processing software, software toolkit, image processing software, image analysis software, software resource | Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development. | computational neuroscience, magnetic resonance, fetus, brain, development, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | ERC | PMID:23036854 | CeCILL license, v2 | nlx_155584 | SCR_009440 | BTK : Baby Brain Toolkit | 2026-02-16 09:47:24 | 0 | |||||
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3DBar Resource Report Resource Website 1+ mentions |
3DBar (RRID:SCR_008896) | 3dBAR | reference atlas, analysis service resource, atlas, software resource, production service resource, service resource, data or information resource | Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML | 3d, reconstruction, brain structure, brain, algorithm or reusable library, web service, atlas application, three dimensional display, spinal cord, sensory system, waxholm space |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Scalable Brain Atlas is related to: Allen Mouse Brain Reference Atlas is related to: Waxholm Space is related to: Allen Institute for Brain Science has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland |
PMID:22227717 | GNU General Public License | nlx_151380 | http://www.nitrc.org/projects/bar3d http://service.3dbar.org http://www.3dbar.org:8080/ http://3dbar.org |
SCR_008896 | 3D BAR, 3d Brain Atlas Reconstructor | 2026-02-16 09:47:18 | 5 | |||||
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UC Davis Alzheimers Disease Center - Resources Resource Report Resource Website |
UC Davis Alzheimers Disease Center - Resources (RRID:SCR_010699) | UCD ADC Resources | brain bank, tissue bank, material resource, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Support research in Alzheimer's disease (AD) offering pilot grants, recruitment of research subjects, access to database, tissue samples, and statistical and research study design consultation for investigators. The scientific effort of the program seeks to: promote research directed at understanding factors that influence the expression and progression of Alzheimer's disease; develop and maintain cohorts of carefully diagnosed and well characterized research subjects available for research studies on Alzheimer's disease and dementia; provide support to investigators in subject recruitment, clinical research, experimental design, and statistical analysis of data; and maintain a variety of samples (brain, DNA, serum) and an extensive electronic database suitable for developing new research and supporting existing programs. | brain, dna, serum, brain tissue, tissue |
is listed by: One Mind Biospecimen Bank Listing has parent organization: UC Davis Alzheimer's Disease Center |
Alzheimer's disease, Aging | State of California's Department of Public Health ; Martinez Veterans Health Administration ; NIA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_82710 | SCR_010699 | University of California Davis Alzheimer's Disease Center - Resources | 2026-02-16 09:47:56 | 0 | |||||
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Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | software application, data processing software, data analysis software, source code, software resource | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/ https://markmikkelsen.github.io/Gannet-docs/index.html |
http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-02-16 09:48:56 | 149 | ||||||||
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NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | software application, data processing software, software toolkit, data visualization software, data analysis software, software resource | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-02-16 09:49:01 | 0 | ||||||||||
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AFIDs Resource Report Resource Website 1+ mentions |
AFIDs (RRID:SCR_016623) | AFIDs | software application, data processing software, software toolkit, image processing software, training resource, software resource, continuing medical education | Open framework for evaluating correspondence between brain images and teaching neuroanatomy. | evaluate, correspondence, magnetic, images, human, brain, fiducial, placement, neuroanatomy | DOI:10.1002/hbm.24693 | Free, Available for download, Freely available | SCR_016623 | Anatomical Fiducials | 2026-02-16 09:49:04 | 2 | ||||||||
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Colour maps for brain imaging Resource Report Resource Website 1+ mentions |
Colour maps for brain imaging (RRID:SCR_016715) | software application, data processing software, data visualization software, image analysis software, software resource | Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging. | perceptually, uniform, color, map, brain, data, imaging |
is related to: MRIcron is related to: MATLAB has parent organization: University of Western Australia; Perth; Australia |
Free, Available for download, Freely available | SCR_016715 | Colour maps, brain_colours, colour maps, brain colours, Brain colours, colour maps for brain imaging, Colour maps for brain imaging | 2026-02-16 09:49:05 | 1 | |||||||||
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MouseLight Project Resource Report Resource Website 1+ mentions |
MouseLight Project (RRID:SCR_016668) | web service, data analysis service, analysis service resource, data access protocol, database, software resource, portal, production service resource, service resource, data or information resource | Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain. | neuronal, reconstruction, connectomics, projectomics, brain, tissue, image, dataset, mouse, axonal, arbor, individual, neuron |
is related to: Allen Institute for Brain Science has parent organization: Janelia Research provides: MouseLight Neuron Browser |
Free, Freely available, Tutorial available, Acknowledgement required, Registration required | http://mouselight.janelia.org/ | SCR_016668 | MouseLight, The Mouse Light Project, Janelia MouseLight project, Mouse Light Project, Mouse Light, MouseLight Project | 2026-02-16 09:49:05 | 9 | ||||||||
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Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | data or information resource, atlas, project portal, portal | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-02-16 09:49:08 | 195 | ||||||||
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MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://meshview-for-brain-atlases.readthedocs.io https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases |
SCR_017222 | MeshView for brain atlases | 2026-02-16 09:49:11 | 11 | ||||||
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Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | service resource, data repository, data or information resource, storage service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-02-16 09:49:10 | 14 | |||||||
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Knowing what you know (kwyk) - Bayesian Brain Parcellation Resource Report Resource Website |
Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) | kwyk | software application, data processing software, image analysis software, software resource, segmentation software | Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation. | Deep, neural, network, prediction, FreeSurfer, segmentation, structural, MRI, volume, brain, parcellation, uncertainty, estimation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/neuronets/kwyk | SCR_017470 | knowing what you know | 2026-02-16 09:49:14 | 0 | |||||||
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StimVision Resource Report Resource Website 1+ mentions |
StimVision (RRID:SCR_017457) | software application, data processing software, data visualization software, software resource | Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room. | Tractography, deep, brain, stimulation, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH R01 MH102238; NIMH R01 MH106173 |
PMID:28653482 | SCR_017457 | Stim Vision, StimVision | 2026-02-16 09:49:14 | 1 | ||||||||
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Neuroreader Resource Report Resource Website 10+ mentions |
Neuroreader (RRID:SCR_017309) | NeuroreaderTM | data processing software, software application, software resource, image processing software | Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database. | Brain, volumetry, assessment | is affiliated with: Brainreader | PMID:26484924 | Restricted | https://brainreader.net/p/product/neuroreader | SCR_017309 | Neuro Reader, Neuroreader | 2026-02-16 09:49:12 | 11 | ||||||
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Allen Institute Mouse Diversity Study Resource Report Resource Website 1+ mentions |
Allen Institute Mouse Diversity Study (RRID:SCR_008009) | Allen Mouse Diversity | expression atlas, data or information resource, database, atlas | A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex. | drug target, gene expression, genetic background, adult, brain, developing, diversity, g protein-coupled receptor, ion channel, mouse, neurotransmitter, rna in situ hybridization, sex, molecular neuroanatomy resource, in situ hybridization, male, female, c57bl/6j, comparison |
is listed by: 3DVC has parent organization: Allen Institute for Brain Science |
Free | nif-0000-08695 | SCR_008009 | Mouse Diversity Study | 2026-02-16 09:47:05 | 1 | |||||||
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Animal Imaging Database Resource Report Resource Website |
Animal Imaging Database (RRID:SCR_008002) | AIDB | image repository, data repository, database, storage service resource, service resource, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented October 4, 2017. A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887) |
reconstruction, segmentation, mri, microscopy, brain, magnetic resonance microscopy |
is related to: Integrated Manually Extracted Annotation has parent organization: Cell Centered Database |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07736 | SCR_008002 | 2026-02-16 09:47:05 | 0 | ||||||||
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Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) Resource Report Resource Website 100+ mentions |
Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) (RRID:SCR_008083) | BrainSpan | expression atlas, reference atlas, data or information resource, atlas | Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. Consists of RNA sequencing and exon microarray data profiling up to sixteen cortical and subcortical structures across full course of human brain development, high resolution neuroanatomical transcriptional profiles of about 300 distinct structures spanning entire brain for four midgestional prenatal specimens, in situ hybridization image data covering selected genes and brain regions in developing and adult human brain, reference atlas in full color with high resolution anatomic reference atlases of prenatal (two stages) and adult human brain along with supporting histology, magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) data. | anatomic, gene expression, molecular neuroanatomy, in situ hybridization, human, medial prefrontal cortex, primary visual cortex, hippocampus, amygdala, ventral striatum, postnatal, development, brain development, transcription, brain, rna sequencing, exon microarray, developmental stage, male, female, mrna transcript, developing human, adult human, fetal brain, fetus, histology, transcriptome, magnetic resonance imaging, diffusion tensor imaging, annotation, neuroanatomy, prenatal, development, fiber tract, microarray, mri, dti, methylation, microrna, mrf |
is used by: BICCN is related to: NIH Blueprint NHP Atlas is related to: Allen Developing Mouse Brain Atlas is related to: Developmental Human Brain Atlas Ontology (DHBA) has parent organization: Allen Institute for Brain Science is parent organization of: BrainSpan is parent organization of: BrainSpan |
Neurodevelopmental disorder, Neuropsychiatric disease, Schizophrenia, Epilepsy, Parkinson's disease, Alzheimer's disease, Neurological disease, Autism | NIMH RC2 MH089921; NIMH RC2 MH090047; NIMH RC2 MH089929 |
Free, Freely available | nif-0000-10626 | http://www.developinghumanbrain.org/ | SCR_008083 | BrainSpan - Atlas of the Developing Human Brain, BrainSpan: Atlas of the Developing Human Brain, NIMH Transcriptional Atlas of Human Brain Development | 2026-02-16 09:47:06 | 398 |
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