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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | data processing software, software application, software resource | Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure. | BIDS, NeuroImaging, Neuroscience, check, folder, structure, compliance, data, standard, brain, imaging | is listed by: OMICtools | Laura and John Arnold Foundation ; NIBIB R01 EB020740 |
PMID:28278228 | Free, Available for download, Freely available | http://bids-standard.github.io/bids-validator/ | SCR_017255 | Brain Imaging Data Structure (BIDS) Validator | 2026-09-19 12:56:07 | 26 | ||||||
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brainlife.io Resource Report Resource Website 1+ mentions |
brainlife.io (RRID:SCR_016513) | data or information resource, portal | Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain. | human, brain, life, data, application, technology, share, open, software, reproducible, code, dataset, |
has parent organization: Indiana University Bloomington; Indiana; USA works with: brainlife |
NSF BCS 1734853; NSF IIS 1636893 |
DOI:10.1038/s41597-019-0073-y | Public, Free, Freely available, Login required | https://github.com/brain-life | SCR_016513 | 2026-09-19 12:56:05 | 1 | |||||||
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BraTS Resource Report Resource Website 1+ mentions |
BraTS (RRID:SCR_016214) | data or information resource, organization portal, portal | Organization that provides a conference about the methods for the segmentation of brain tumors in magnetic resonance imaging (MRI) scans. Its conferences utilize multi-institutional pre-operative MRI scans and focus on the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. | brain, neuroscience, tumor, cancer, segmentation, mri, neuroimaging, glioma, patient, conference, event | SCR_016214 | BraTS: Multimodal Brain Tumor Segmentation, Multimodal Brain Tumor Segmentation | 2026-09-19 12:56:05 | 8 | |||||||||||
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Mouse Connectome Project Resource Report Resource Website |
Mouse Connectome Project (RRID:SCR_017313) | MCP | data or information resource, portal, project portal | Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. | mesoscale, connectivity, atlas, C57Black/6, mouse, brain, neural, network |
is used by: BICCN has parent organization: University of Southern California; Los Angeles; USA |
NIH | Free, Freely available | SCR_017313 | The Mouse Connectome Project, Mouse Connectome Project | 2026-09-19 12:56:07 | 0 | |||||||
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Compilation of Genetics Resource Databases Resource Report Resource Website 50+ mentions |
Compilation of Genetics Resource Databases (RRID:SCR_017501) | data or information resource, portal | Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse. | Genetic, data, brain, atlas, information, National, Institute, Drug, Abuse, FASEB list | Restricted | SCR_017501 | 2026-09-19 12:56:07 | 61 | |||||||||||
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HeuDiConv: a heuristic-centric DICOM converter Resource Report Resource Website 10+ mentions |
HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) | HeuDiConv | data processing software, software application, software resource | Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts. | Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layout | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | http://www.nitrc.org/projects/heudiconv/ | SCR_017427 | heudiconv, heuristic-centric DICOM converter | 2026-09-19 12:56:07 | 34 | ||||||||
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Mononucleotide Repeat Frameshift Portal Resource Report Resource Website |
Mononucleotide Repeat Frameshift Portal (RRID:SCR_021125) | MORF | data or information resource, organization portal, portal | Portal devoted to suite of MORF reporter mice labels of Cre positive neurons and glia distributed stochastically throughout brain and can be imaged with endogenous fluorescence (mNeonGreen in MORF1 and EGFP in TIGRE-MORF) or stained for multivalent immunoreporter (Spaghetti Monster fluorescent protein V5, or smFP-V5, in MORF3). MORF technology used to label and reconstruct thousands genetically defined cells per brain for large scale, unbiased classification and quantitative analyses of CNS cell types brainwide. | Sparsely label genetically defined neuronal populations, reporter mouse lines, Cre-dependent sparse cell labeling methodology, MORF stochastic translational switch, integrating molecular, morphological properties, connectomic properties, unbiased classification, neuronal cell types, brain | has parent organization: University of California at Los Angeles; California; USA | PMID:32795398 | Free, Freely available | SCR_021125 | MOnonucleotide Repeat Frameshift, MORF portal | 2026-09-19 12:56:11 | 0 | |||||||
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aBEAT Resource Report Resource Website 1+ mentions |
aBEAT (RRID:SCR_002238) | aBEAT | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing. | analyze, atlas application, magnetic resonance, segmentation, visualization, adult, mri, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:23577105 | nlx_155840, nlx_155542 | http://www.nitrc.org/projects/abeat | SCR_002238 | aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI, Adult Brain Extraction and Analysis Toolbox | 2026-09-19 12:55:04 | 1 | ||||||
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Chronux Resource Report Resource Website 500+ mentions |
Chronux (RRID:SCR_005547) | Chronux | data analysis software, data processing software, software application, software resource | Open-source software package for the analysis of neural data. Chronux routines may be employed in the analysis of both point process and continuous data, ranging from preprocessing, exploratory and confirmatory analysis. The current release is implemented as a MATLAB library. Chronux offers several routines for computing spectra and coherences for both point and continuous processes. In addition, it also offers several general purpose routines that were found useful such as a routine for extracting specified segments from data, or binning spike time data with bins of a specified size. Since the data can be continuous valued, point process times, or point processes that are binned, methods that apply to all these data types are given in routines whose names end with ''''c'''' for continuous, ''''pb'''' for binned point processes, and ''''pt'''' for point process times. Thus, mtspectrumc computes the spectrum of continuous data, mtspectrumpb computes a spectrum for binned point processes, and mtspectrumpt compute spectra for data consisting of point process times. Hybrid routines are also available and similarly named - for instance coherencycpb computes the coherency between continuous and binned point process data. | fmri, brain mapping, brain, matlab |
is related to: Zebra Finch Song Learning Consortium has parent organization: Cold Spring Harbor Laboratory |
NIMH | Open-source. Please cite. | nif-0000-00082 | SCR_005547 | Chronux Analysis Software | 2026-09-19 12:55:08 | 571 | ||||||
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VA Biorepository Brain Bank Resource Report Resource Website 1+ mentions |
VA Biorepository Brain Bank (RRID:SCR_006546) | VABBB | biomaterial supply resource, brain bank, material resource, tissue bank | A human tissue bank that collects, processes, stores and gives out research specimens for future scientific studies. Presently, the VABBB is obtaining neurologic tissue specimens from Veterans who suffer from amyotrophic lateral sclerosis (ALS) and other illnesses that affect Veterans, along with relevant clinical data, essential for research. Currently, neither the cause nor prevention of ALS is known. Medical researchers are currently examining environmental, toxic, genetic, traumatic, medical, and occupational influences as possible contributors to the development and progression of ALS. Veterans have a higher risk of developing ALS compared with non-Veterans; however, the reasons for this higher risk are currently unknown. Any Veteran with ALS in the U.S. may enroll in the VABBB. | brain, spinal cord, veteran, brain tissue, spinal cord tissue, neurologic tissue, clinical |
is listed by: One Mind Biospecimen Bank Listing has parent organization: U.S. Department of Veterans Affairs |
Amyotrophic Lateral Sclerosis, Post-Traumatic Stress Disorder | ALS researchers are invited to apply for tissue and data | nlx_156782 | SCR_006546 | 2026-09-19 12:55:09 | 1 | |||||||
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University of Texas at Dallas School of Behavioral and Brain Sciences Resource Report Resource Website |
University of Texas at Dallas School of Behavioral and Brain Sciences (RRID:SCR_004645) | UT Dallas BBS | data or information resource, department portal, organization portal, portal | Mission of the School of Behavioral and Brain Sciences is to understand the intersection of mind, brain and behavior; enhance the health, education, and quality of life of children and families; and create and implement technologies and therapies that repair and strengthen human abilities. The School is housed in Green Hall on the main UT Dallas campus in Richardson. It also has satellite research centers and facilities in downtown Dallas. | behavior, brain | has parent organization: University of Texas at Dallas; Texas; USA | nif-0000-02104 | SCR_004645 | University of Texas at Dallas School of Behavioral Brain Sciences, UT Dallas School of Behavioral and Brain Sciences | 2026-09-19 12:55:07 | 0 | ||||||||
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CRCNS Resource Report Resource Website 100+ mentions |
CRCNS (RRID:SCR_005608) | CRCNS | collaborative tool, data or information resource, data repository, funding resource, service resource, storage service resource | Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources. | collaborative research, data sharing, computational model, brain, computational neuroscience, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is recommended by: National Library of Medicine is listed by: DataCite is related to: Integrated Manually Extracted Annotation has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
NIH ; NSF 0636838; NSF IIS-0749049 |
PMID:18259695 | Free, Freely available | nif-0000-00255, r3d100011269 | https://api.datacite.org/dois?prefix=10.6080, https://doi.org/10.17616/R31S7P | SCR_005608 | CRCNS Data sharing, Collaborative Research in Computational Neuroscience - Data sharing, Collaborative Research in Computational Neuroscience, CRCNS - Data sharing | 2026-09-19 12:55:08 | 123 | ||||
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Digital Brain Atlas of the Common Marmoset Resource Report Resource Website 1+ mentions |
Digital Brain Atlas of the Common Marmoset (RRID:SCR_005069) | DBACM | atlas, data or information resource, image collection | Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques. | primate, immunolabeling, nissl stain, brain atlas, virtual microscopy, high-resolution digital image, brain, callithrix, marmoset |
has parent organization: Tokyo Metropolitan Institute of Medical Science; Tokyo; Japan has parent organization: RIKEN |
PMID:19428691 | Free, Account required | nlx_144084 | http://marmoset-brain.org:2008 | SCR_005069 | Brain/MINDS Data Portal | 2026-09-19 12:55:07 | 6 | |||||
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V3D Resource Report Resource Website 1+ mentions |
V3D (RRID:SCR_008646) | V3D | d visualization software, data processing software, data visualization software, image analysis software, segmentation software, software application, software resource | V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily. | 3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, image |
is listed by: SoftCite has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | nif-0000-32975 | SCR_008646 | V3D: A Swiss army knife for bioimage visualization & analysis | 2026-09-19 12:55:11 | 3 | ||||||
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NIMH Brain Tissue Collection Resource Report Resource Website 1+ mentions |
NIMH Brain Tissue Collection (RRID:SCR_008726) | NIMH Brain Bank | biomaterial supply resource, brain bank, material resource, tissue bank | A collection of brain tissue from individuals suffering from schizophrenia, bipolar disorder, depression, anxiety disorders, and substance abuse, as well as healthy individuals. The research mission of the NIMH Brain Bank is to better understand the underlying biological mechanisms and pathways that contribute to schizophrenia and other neuropsychiatric disorders, as well as to study normal human brain development. | schizophrenia, bipolar disorder, depressive disorder, anxiety disorder, substance abuse, healthy, neurological disorder, mental disease, suicide, tourette's syndrome, dementia, brain development, brain, brain tissue, tissue, post-mortem, normal control, ClinicalTrials.gov Identifier: NCT00001260 |
is listed by: One Mind Biospecimen Bank Listing has parent organization: NIMH Intramural Research Program Clinical Brain Disorders Branch |
Schizophrenia, Bipolar Disorder, Depressiive Disorder, Anxiety Disorder, Drug Abuse, Healthy, Neurological disorder, Mental disease, Suicide, Tourette's Syndrome, Dementia, Normal control, Aging | NIMH | Samples available to investigators approved by an NIMH Oversight Committee, Molecular and genetic data available to the scientific community | nlx_143684 | http://cbdb.nimh.nih.gov/neuropath.htm | SCR_008726 | 2026-09-19 12:55:11 | 1 | |||||
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UT Southwestern ADC Brain Tissue Donation Program Resource Report Resource Website |
UT Southwestern ADC Brain Tissue Donation Program (RRID:SCR_008837) | UTSW Brain Tissue Donation Program, UTSW ADC Brain Tissue Donation Program | biomaterial supply resource, brain bank, material resource, tissue bank | Brain tissue donation program at the UT Southwestern Memory Clinic that aims to utilize these contributions for research on Alzheimer's. Diagnosis of Alzheimer's disease or other dementias are made through autopsy, the results of which are available to family members. | brain tissue, tissue, brain, alzheimer's disease, late adult human, mild cognitive impairment, dementia, frontotemporal dementia, autopsy, research |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Texas Southwestern Medical Center - Alzheimer's Disease Center |
Alzheimer's disease, Mild Cognitive Impairment, Aging, Dementia, Frontotemporal Dementia | Private | nlx_144639 | SCR_008837 | 2026-09-19 12:55:11 | 0 | |||||||
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Brain Imaging Analysis Kit Resource Report Resource Website 10+ mentions |
Brain Imaging Analysis Kit (RRID:SCR_014824) | BrainIAK | data processing software, image analysis software, software application, software resource, software toolkit | Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data. | brain, python, module, imaging, fmri, data, analysis, neuroimaging |
is related to: Intel has parent organization: Princeton University; New Jersey; USA |
Free, Available for download, Freely available | https://github.com/brainiak/brainiak | SCR_014824 | BrainIAK, Brain Imaging Analysis Kit, Brain Imaging Analysis Kit (BrainIAK) | 2026-09-19 12:55:14 | 30 | |||||||
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Braineac Resource Report Resource Website 50+ mentions |
Braineac (RRID:SCR_015888) | data or information resource, database, software resource, web application | Database for the UK Brain Expression Consortium (UKBEC) dataset that comprises of brains from individuals free of neurodegenerative disorders. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders. | neurodegenerative, brain, disorder, mrna, dna, eqtl, snp, gene, visualization, expression | has parent organization: UK Brain Expression Consortium | Normal | PMID:25174004 | Public, Free, Available for download | SCR_015888 | 2026-09-19 12:55:15 | 52 | ||||||||
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QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-09-19 12:55:16 | 1 | |||||||||
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Brain Gene Expression Analysis toolbox Resource Report Resource Website 1+ mentions |
Brain Gene Expression Analysis toolbox (RRID:SCR_017438) | data analysis software, data processing software, software application, software resource | Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain. | Quantitative, analysis, digitized, brain, gene, expression, data, Allen Atlas, adult, mouse, brain, BRAIN Initiative |
is recommended by: BRAIN Initiative is related to: MATLAB is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
Free, Available for download, Freely available | SCR_017438 | , Brain, Gene, Expression, Analysis, toolbox | 2026-09-19 12:55:17 | 1 |
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