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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BrainU: The Neuroscience Teacher Institute Resource Report Resource Website 1+ mentions |
BrainU: The Neuroscience Teacher Institute (RRID:SCR_008677) | data or information resource, narrative resource, training material, training resource, workshop | A neuroscience training program for Minnesota students and teachers. It provides teachers with three years of neuroscience training, materials, and staff support to bring brain science to their students. In these professional workshops, participants receive updates on the latest in neuroscience research -- discussion is complemented with hands-on activities and lab work. Teachers also receive curriculum materials to aid them in using neuroscience topics in support of Minnesota Intermediate and Middle Level standards. The program was expanded in 2008 to include high school teachers. | brain, curriculum, laboratory, neuroscience, research, student, teacher | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | SEDAPA ; National Center for Research Resources ; ARRA |
nif-0000-33707 | SCR_008677 | BrainU | 2026-08-29 11:23:22 | 1 | ||||||||
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Johns Hopkins Alzheimer's Disease Research Center Resource Report Resource Website |
Johns Hopkins Alzheimer's Disease Research Center (RRID:SCR_008757) | biomaterial supply resource, brain bank, material resource, tissue bank | A Alzheimer's Disease Research Center (ADRC) whose goal is to conduct basic and clinical research aimed at understanding Alzheimer's disease. The Center enrolls a variety of individuals for clinical trials, evaluation and follow-up, including: normal control subjects, individuals with mild memory problems, and patients diagnosed with Alzheimer's Disease or related dementias. Researchers can request data and specimens obtained from ADRC subjects. These include blood or DNA, brain specimens, and cross-sectional or longitudinal clinical and cognitive data, all from ADRC subjects. | alzheimer's disease, mild memory problem, dementia, clinical data, cognitive data, blood, dna, brain, tissue, human, clinical trial, memory |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA |
Alzheimer's disease, Normal control, Mild memory problem, Dementia, Aging | NIA | Public, Researchers can request data and specimens obtained from ADRC subjects | nlx_144105 | SCR_008757 | Johns Hopkins ADRC, Johns Hopkins Alzheimer's Disease Research Center | 2026-08-29 11:23:12 | 0 | ||||||
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Brain Research Institute Biobank Resources Resource Report Resource Website |
Brain Research Institute Biobank Resources (RRID:SCR_008756) | biomaterial supply resource, brain bank, material resource, tissue bank | Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal. | postmortem, brain, coronal, brain tissue, cerebral spinal fluid, blood, cerebral spinal fluid cell, cell-free cerebral spinal fluid, serum, plasma, buffy coat, frozen, formalin fixed, paraformaldehyde-fixed, paraffin-embedded, neurological disease, alzheimer's disease, amyotrophic lateral sclerosis, depressive disorder, suicide, epilepsy, huntington's disease, multiple sclerosis, parkinson's disease, progressive supranuclear palsy, schizophrenia, stroke, cerebrovascular accident, fronto-temporal dementia, neurologically normal, coronal section, control, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Brain Research Institute |
Neurological disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Depressive Disorder, Suicide, Epilepsy, Huntington's disease, Multiple Sclerosis, Parkinson's disease, Progressive Supranuclear Palsy, Schizophrenia, Stroke, Cerebrovascular Accident, Fronto-temporal dementia, Aging | NINDS ; NIMH ; National MS Society ; United States Department of Veterans Affairs ; Veterans Affairs West Los Angeles Healthcare Center ; NIA |
Public, Available to the research community | nlx_143996 | http://www.bri.ucla.edu/bri_research/research_resources.asp | SCR_008756 | Brain Research Institute Research Resources, Brain Research Institute Biobanks, BRI Research Resources, BRI Biobanks, BRI Biobank Resources | 2026-08-29 11:23:33 | 0 | |||||
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Mayo Clinic Jacksonville: Neuropathology and Microscopy Resource Report Resource Website 1+ mentions |
Mayo Clinic Jacksonville: Neuropathology and Microscopy (RRID:SCR_008753) | biomaterial supply resource, brain bank, material resource, tissue bank | A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis. | tissue, brain, fixed, frozen, alzheimer's disease, normal aging, memory disorder, motor disorder, parkinson's disease, progressive supranuclear palsy, lewy body disease, corticobasal degeneration, frontotemporal dementia, dementia, mild cognitive impairment, mouse, neurofibrillary degeneration, postmortem, normal control, autopsy |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Mayo Clinic Florida; Florida; USA has parent organization: Mayo Alzheimer's Disease Research Center has parent organization: Florida Alzheimer's Disease Research Center |
Alzheimer's disease, Aging, Memory disorder, Motor disorder, Parkinson's disease, Progressive Supranuclear Palsy, Lewy Body Disease, Corticobasal Degeneration, Frontotemporal dementia, Dementia, Mild Cognitive Impairment | NIA P50-AG16574; NIA P50-AG25711; NINDS P50-40256 |
nlx_143952 | SCR_008753 | Mayo Clinic Jacksonville: Neuropathology Microscopy, Mayo Clinic Florida: Neuropathology and Microscopy, Neuropathology and Microscopy - Dennis W. Dickson, Mayo Clinic Florida: Neuropathology and Microscopy - Dennis W. Dickson | 2026-08-29 11:23:33 | 1 | |||||||
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genes2mind Resource Report Resource Website 1+ mentions |
genes2mind (RRID:SCR_008872) | genes2mind | analysis service resource, data analysis service, data or information resource, database, production service resource, service 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 | 2026-08-29 11:23:35 | 3 | ||||||||
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Connectome Workbench Resource Report Resource Website 50+ mentions |
Connectome Workbench (RRID:SCR_008750) | CWB, wb_view, wb_command, wb_import | software resource, software toolkit, source code | Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas. | visualization, connectivity, brain, human, fMRI, dMRI, brain imaging data, map neuroimaging data, |
is used by: BRAIN Initiative Cell Atlas Network is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: FAIRsharing is related to: BALSA is related to: Washington University in St. Louis; Missouri; USA works with: ConnectomeDB works with: NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation |
NIH Blueprint for Neuroscience Research ; NIMH MH060974 |
Free, Available for download, Freely available | nlx_143924 | http://www.nitrc.org/projects/workbench, https://github.com/Washington-University/workbench, https://www.humanconnectome.org/software/workbench-command, https://www.humanconnectome.org/software/get-connectome-workbench, http://humanconnectome.org/connectome/connectome-workbench.html | SCR_008750 | 2026-08-29 11:23:11 | 95 | ||||||
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Human Connectome Coordination Facility Resource Report Resource Website 1000+ mentions |
Human Connectome Coordination Facility (RRID:SCR_008749) | WU-Minn HCP | data repository, image repository, service resource, storage service resource | Consortium to comprehensively map long-distance brain connections and their variability. It is acquiring data and developing analysis pipelines for several modalities of neuroimaging data plus behavioral and genetic data from healthy adults. | brain, connectivity, adult human, mri, resting-state fmri, functional mri assay, neuroimaging, surface rendering, time domain analysis, tractography, xnat pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Brain Connectivity Toolbox is related to: FieldTrip is related to: BALSA has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: NIH Human Connectome Project has parent organization: University of Minnesota Twin Cities; Minnesota; USA is parent organization of: WU-Minn HCP 500 Subjects MR and MEG Release |
healthy, twin | NIH Blueprint for Neuroscience Research ; NIMH MH091657 |
PMID:23684880 PMID:23702419 PMID:23668970 PMID:23702415 PMID:23702418 PMID:23707591 PMID:23702417 PMID:23684877 |
Free, Freely available | nlx_143922 | http://www.nitrc.org/projects/hcp_wuminn, http://www.humanconnectome.org/documentation/S500/ | SCR_008749 | HCP WU-Minn Consortium, WU-Minn: Human Connectome Project, HUMAN CONNECTOME PROJECT WU-Minn Consortium, WU-Minn Consortium: Human Connectome Project, WU-Minn Consortium: HCP | 2026-08-29 11:23:33 | 1095 | |||
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Mount Sinai Alzheimer's Disease Research Center Resource Report Resource Website |
Mount Sinai Alzheimer's Disease Research Center (RRID:SCR_008780) | Mount Sinai ADRC | biomaterial supply resource, brain bank, material resource, tissue bank | A research facility and clinical program that is dedicated to the study and the treatment of both normal aging and Alzheimer's disease. This facility will accommodate requests for its resources (for example, data or tissue) from investigators that are not funded by the ADRC. Their team is composed of experts in geriatrics, geriatric psychiatry and psychology, neurology, pathology, and radiology. All team members work to provide services to those with memory disorders. This center sponsors educational programs for healthcare professionals and community groups. Data from the ADRC cores are available to all ADRC investigators after approval from the PI who collected the data. Data generated by the ADRC cores are communicated to the National Alzheimer's Coordinating Center (NACC) and can be available through them. Tissue can be distributed after approval of the Tissue Allocation Committee, and can be used for further research. | normal aging, alzheimer's disease, late adult human, memory disorder, memory, dementia, healthy, brain tissue, brain, tissue, paraffin embedded, block, stain, clinical |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
Alzheimer's disease, Aging, Healthy | NIA | Public / Collaborator: The ADRC at Mount Sinai School of Medicine is receptive to requests of ADRC resources (data, Tissue, And so on). The ADRC welcomes requests for tissue from Investigators not currently funded by the ADRC. Tissues needed for conduct of ADRC projects are distributed directly to PIs. Distribution of tissue will be made on a collaborative basis only and determined on a case by case basis by the Tissue Allocation Committee. | nlx_144162 | SCR_008780 | Mount Sinai School of Medicine ADRC, Mount Sinai School of Medicine Alzheimer's Disease Research Center, Mount Sinai Alzheimer's Disease Research Center | 2026-08-29 11:23:25 | 0 | |||||
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3DBar Resource Report Resource Website 1+ mentions |
3DBar (RRID:SCR_008896) | 3dBAR | analysis service resource, atlas, data or information resource, production service resource, reference atlas, service resource, software 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 | 2026-08-29 11:23:35 | 5 | |||||
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Michigan Alzheimer's Disease Center Brain Bank Resource Report Resource Website |
Michigan Alzheimer's Disease Center Brain Bank (RRID:SCR_008774) | MADC | biomaterial supply resource, brain bank, material resource, tissue bank | An organization that provides scientists with human tissue from Alzheimer's patients and patients with related brain disorders. Brain tissue is collected from research studies at the University of Michigan, as well as other research centers, and are donated by the families of the patients or the participants themselves. Tissues that are present in the Brain Bank are pre-characterized by pathologists and can be provided to researchers upon request. | alzheimer's disease, dementia, late adult human, brain, tissue, brain tissue, autopsy, brain donation, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Michigan Alzheimer's Disease Center |
Alzheimer's disease, Dementia, Aging | Available to research staff upon request | nlx_144107 | http://www.med.umich.edu/alzheimers/research/brain_bank.htm | SCR_008774 | MADC Brain Bank | 2026-08-29 11:23:12 | 0 | |||||
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Institute for Basic Research in Developmental Disabilities Resource Report Resource Website |
Institute for Basic Research in Developmental Disabilities (RRID:SCR_008806) | IBR, NYS IBR, NYS-OPWDD IBR | biomaterial supply resource, brain bank, material resource, tissue bank | A research arm of the New York State Office for People with Developmental Disabilities (OPWDD), which conducts basic and clinical research into the causes, treatment, and prevention of intellectual disabilities and other developmental disabilities. The goals of the IBR's research, services and education program are designed to provide prevention, earlier detection, and improved treatment of intellectual disabilities and other developmental disabilities. This research program has a total of 46 laboratories over 7 departments. These programs include the George A. Jervis Clinic (a tertiary-level diagnostic and research clinic), the Specialty Clinical Laboratories (conduct specialty testing for genetic, metabolic, neurodegenerative disorders), and the Comprehensive Genetic Disease Program at Richmond County (provides genetics and genetic counseling services). This institute provides educational activities in the graduate studies program, and the Programs in Developmental Neuroscience and Developmental Disabilities (PDNDD). The PDNDD collaborates with the faculty from the City University of New York and the State University of New York. The IBR staff regularly conducts public education workshops and professional seminars about developmental disabilities. | brain tissue, brain, tissue, developmental disability, late adult human, alzheimer's disease, autism, fragile x syndrome, taurine, fetal alcohol syndrome, batten disease, phenylketonuria, fetal development, down's syndrome, infant, development, biochemistry, neurobiology, genetics, molecular biology, neurochemistry, psychology, neuroscience |
is listed by: One Mind Biospecimen Bank Listing has parent organization: NYS Office for People With Developmental Disabilities |
Developmental disability, Aging | nlx_144385 | http://www.opwdd.ny.gov/ws/ws_ibr_resources.jsp | SCR_008806 | NYS-OPWDD: Institute for Basic Research in Developmental Disabilities, New York State Institute for Basic Research in Developmental Disabilities | 2026-08-29 11:23:13 | 0 | ||||||
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MUSC Center on Aging Campbell Neuropathology Laboratory Resource Report Resource Website 1+ mentions |
MUSC Center on Aging Campbell Neuropathology Laboratory (RRID:SCR_008826) | MUSC Center on Aging Neuropathology Lab | biomaterial supply resource, brain bank, material resource, tissue bank | A brain bank and biospecimen repository that provides research materials to clinicians, scientists and pathologists in South Carolina. The bank provides both control and diseased biospecimens and brain tissue needed for research in Alzheimer's disease, Parkinson's disease and other related neurological disorders. The Campbell Laboratory coordinates the brain tissue donation program, provides post-mortem confirmation of a patient having neurological disorders, and leads research trials. Any South Carolina resident can choose to sign up as a tissue donor and have their brain tissue donated post-mortem to be used for neurological disorder research. The tissue bank will process and analyze these tissue samples and send the results to the deceased person's family. | brain tissue, brain, tissue, alzheimer's disease, parkinson's disease, neurological disorder, stroke, dementia, normal control, late adult human, clinical trial |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Medical University of South Carolina Center on Aging |
Alzheimer's disease, Parkinson's disease, Neurological disorder, Stroke, Aging, Dementia | Account required | nlx_144505 | http://academicdepartments.musc.edu/brainbank/ | SCR_008826 | MUSC Center on Aging Carroll A. Campbell Jr. Neuropathology Laboratory, Carroll A. Campbell Jr. Neuropathology Laboratory (Brain Bank), Medical University of South Carolina Center on Aging Carroll A. Campbell Jr. Neuropathology Laboratory, Carroll A. Campbell Jr. Neuropathology Laboratory at MUSC, Carroll A. Campbell Jr. Neuropathology Laboratory | 2026-08-29 11:23:34 | 2 | |||||
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MassGeneral Institute for Neurodegenerative Disease Resource Report Resource Website 1+ mentions |
MassGeneral Institute for Neurodegenerative Disease (RRID:SCR_008746) | MIND | biomaterial supply resource, brain bank, material resource, tissue bank | An institute whose mission is to translate laboratory discoveries into prevention, treatment and cures for Alzheimer's, ALS, Huntington's, Parkinson's and other neurodegenerative diseases. MIND seeks to accelerate therapies that lessen the toll of disease on patients and families. Researchers of the institute collaborate, strategize, and share technology to find treatment for these diseases. As promising leads are developed in one area, they are tested in the other neurodegenerative disorders. | memory disorder, movement disorder, neuromuscular disease, alzheimer's disease, amyotrophic lateral sclerosis, huntington's disease, parkinson's disease, neurodegenerative disease, brain tissue, tissue, brain |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Harvard Medical School; Massachusetts; USA |
Memory disorder, Movement disorder, Neuromuscular Disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Parkinson's disease, Neurodegenerative disease, Aging | Available to the research community | nlx_144103 | http://www.massgeneral.org/mind/ | SCR_008746 | Massachusetts General Institute for Neurodegenerative Disease, Massachusetts General Hospital Institute for Neurodegenerative Disease | 2026-08-29 11:23:11 | 2 | |||||
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BrainPeps Resource Report Resource Website 1+ mentions |
BrainPeps (RRID:SCR_008851) | Brainpeps | data or information resource, data repository, database, service resource, storage service resource | Database of blood-brain barrier properties of peptides including structure, method, responses, physicochemical properties and related literature. The database is linked to a manuscript entitled Brainpeps: the blood-brain barrier peptide database, in which the BBB methods and responses are clarified and correlated to each other. Data may be submitted for addition to the database. | peptide, intravenous injection, efflux study, immortal cell line, brain slice, ultracentrifugation, bui method, capillary depletion, iam-hplc, indicator diffusion, bmec, shake flask, non-cerebral cell line, in vitro equilibrium dialysis, microdialysis, imaging techniques, quantitative autoradiography, antinociception, hplc, in situ brain perfusion, (co)-culture, mbua, ultrafiltration, cisternal puncture, bei method, gibbs adsorption isotherm, pampa, blood-brain barrier, brain, permeability, distribution, data set |
is listed by: 3DVC has parent organization: Ghent University; Ghent; Belgium |
Institute for the Promotion of Innovation through Science and Technology in Flanders IWT-Vlaanderen 73402 | PMID:22205159 | Acknowledgement requested, The community can contribute to this resource | nlx_149082 | SCR_008851 | Brain Peps | 2026-08-29 11:23:26 | 2 | |||||
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Roadmap Epigenomics Project Resource Report Resource Website 100+ mentions |
Roadmap Epigenomics Project (RRID:SCR_008924) | Roadmap Epigenomics Project | consortium, data or information resource, organization portal, portal, project portal | 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 | 2026-08-29 11:23:15 | 323 | ||||||
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DOTS WM tract segmentation Resource Report Resource Website 100+ mentions |
DOTS WM tract segmentation (RRID:SCR_009459) | DOTS | data processing software, image analysis software, segmentation software, software application, software resource | 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 | 2026-08-29 11:23:18 | 116 | |||||
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Baby Brain Toolkit Resource Report Resource Website |
Baby Brain Toolkit (RRID:SCR_009440) | BTK | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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 | 2026-08-29 11:23:36 | 0 | |||||
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MultiXplore Resource Report Resource Website 1+ mentions |
MultiXplore (RRID:SCR_014814) | data analysis software, data processing software, software application, software resource | Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data. | gui, graphical user interface, cortical region, functional connectivity matrix, 3d, brain, grey matter, fiber bundle |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Western University; Ontario; Canada is a plug in for: 3D Slicer |
NSERC | Available for download | SCR_014814 | 2026-08-29 11:24:53 | 1 | |||||||||
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Automatic Tractography-based Parcellation Pipeline Resource Report Resource Website 1+ mentions |
Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) | ATPP | data processing software, software application, software resource, workflow software | Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). " | pipeline, integrated pipeline, tractography, brain, parcel, gui, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179 | Available for download | https://doi.org/10.5281/zenodo.239705, https://doi.org/10.5281/zenodo.239702 | https://github.com/haililihai/ATPP_CLI, https://github.com/haililihai/ATPP_GUI | SCR_014815 | Automatic Tractography-based Parcellation Pipeline (ATPP) | 2026-08-29 11:24:53 | 3 | |||||
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BluePyOpt Resource Report Resource Website 10+ mentions |
BluePyOpt (RRID:SCR_014753) | simulation software, software application, software resource | An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms. | python, optimization, framework, library, brain, model parameter, neuroscience | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | European Union FP7 604102 | Acknowledgement requested | http://www.nitrc.org/projects/bluepyopt/ | SCR_014753 | Blue Brain Python Optimization Library, Blue Brain Python Optimisation Library (BluePyOpt), Blue Brain Python Optimisation Library | 2026-08-29 11:24:52 | 31 |
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If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
