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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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FMRIB's Linear Image Registration Tool Resource Report Resource Website 10+ mentions |
FMRIB's Linear Image Registration Tool (RRID:SCR_024922) | FLIRT | data processing software, registration software, software resource, software application, image analysis software | Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration. | linear, affine, intra, inter, modal, brain, image, registration, brain image registration, | is a plug in for: FSL | Free, Freely available | SCR_024922 | 2026-08-04 09:45:38 | 12 | |||||||||
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VERBENA Resource Report Resource Website |
VERBENA (RRID:SCR_024919) | software application, software resource | Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain. | Dynamic Susceptibility Contrast, quantification of perfusion, haemodynamic parameters, Dynamic Susceptibility Contrast perfusion MRI, brain | is a plug in for: FSL | Free, Freely available | SCR_024919 | VERBENA:Vascular Model Based Perfusion Quantification for DSC-MRI | 2026-08-04 09:45:38 | 0 | |||||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software application, software resource | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-08-04 09:45:38 | 2 | ||||||||
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Brain Maps Resource Report Resource Website 1+ mentions |
Brain Maps (RRID:SCR_017314) | atlas, data or information resource | Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community. | atlas, nervous, system, nomenclature, ontology, flatmap, structure, brain, rat | PMID:29277900 | Free, Freely available | SCR_017314 | Brain maps 4.0, Brain maps | 2026-08-04 09:44:10 | 3 | |||||||||
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Autopatcher Resource Report Resource Website 1+ mentions |
Autopatcher (RRID:SCR_017464) | software application, software resource | Software tool for neuronal recording in intact brain. | Neuronal, recording, intact, brain, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH106027 | PMID:29297466 | Free, Available for download, Freely available | SCR_017464 | 2026-08-04 09:44:10 | 2 | ||||||||
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Whole Brain Catalog Blog Resource Report Resource Website |
Whole Brain Catalog Blog (RRID:SCR_000582) | WBC Blog | blog, narrative resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog. | crowdsourcing, mouse, brain, cell, neuron, simulation, microscopy, neuroscience, electron microscopy, light microscopy | has parent organization: Whole Brain Catalog | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144534 | SCR_000582 | 2026-08-04 09:40:10 | 0 | ||||||||
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BrainNavigator Resource Report Resource Website 1+ mentions |
BrainNavigator (RRID:SCR_008289) | BrainNavigator | atlas, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips. | 3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, image | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24037 | SCR_008289 | Brain Navigator | 2026-08-04 09:42:07 | 5 | ||||||||
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Manually Labeled MRI Brain Scan Database Resource Report Resource Website 1+ mentions |
Manually Labeled MRI Brain Scan Database (RRID:SCR_009604) | database, data or information resource | Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks. | collection, neuroanatomical, MRI, brain, scan, data, thalamus, caudate, putamen, hippocampus, ventricle, cerebellum, cortex |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics works with: MRI Neuroanatomy Labeling Services works with: MRI Neuroanatomy Labeling Services |
NIMH R43 MH60507; NIMH R44 MH60507; NIMH R43 MH084358 |
Commercially available | nlx_155805 | http://www.nitrc.org/projects/manuallabels | SCR_009604 | 2026-08-04 09:42:25 | 1 | |||||||
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Discover Magazine Resource Report Resource Website 10+ mentions |
Discover Magazine (RRID:SCR_008787) | Discover | blog, narrative resource, data or information resource | Popular science magazine which includes news and blogs on topics including Health & Medicine, Mind & Brain, Technology, Space, Human origins, Living World, Environment, and Physics & Math. NIF Indexes include: The Brain: DISCOVER blogger, columnist, and contributing editor Carl Zimmer''s monthly column will make your brain happy. Discover Interview: The magazine''s signature in-depth discussion with the leading lights of the world of science Vital Signs: A medical mystery, as written by the doctor involved. | health, medicine, mind, brain, technology, magazine |
is used by: NIF Data Federation is used by: Integrated Blogs is parent organization of: Neuroskeptic is parent organization of: The Loom |
nlx_144214 | SCR_008787 | 2026-08-04 09:42:14 | 15 | |||||||||
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HIV Brain Sequence Database Resource Report Resource Website 1+ mentions |
HIV Brain Sequence Database (RRID:SCR_008819) | HIVBrainSeqDB | database, data or information resource | The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection. | human immunodeficiency virus, hiv, brain, sequence, hiv envelope sequence, brain sequence, clone, tissue, brainstem, spinal cord, meninges, choroid plexus, csf, blood, lymphoid, bone marrow, colon, lung, liver, aids |
is related to: FMA has parent organization: Harvard University; Cambridge; United States |
Human immunodeficiency virus | ARRA ; NIMH 3ROI MH83588-12S1; NIMH MH83588 |
PMID:21156070 | nlx_149217 | SCR_008819 | The HIV Brain Sequence Database | 2026-08-04 09:42:13 | 1 | |||||
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Molecular Brain: Transcription Profiles of Mouse and Human Brains Resource Report Resource Website 1+ mentions |
Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) | database, data or information resource | MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available. | molecular, molecule, brain, transcription, mouse, human, gene, microarray, data, expression, database, tool, expression, molecular neuroanatomy resource | has parent organization: National Institutes of Health | nif-0000-37035 | SCR_008689 | Molecular Brain | 2026-08-04 09:42:12 | 3 | |||||||||
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Functional Neurogenesis Resource Report Resource Website 1+ mentions |
Functional Neurogenesis (RRID:SCR_008830) | Functional Neurogenesis | blog, narrative resource, data or information resource | A blog focusing on the function of adult neurogenesis in the dentate gyrus of the hippocampus, including discussion of scientific research papers, methods and protocols, and other trends or observations about the field. | adult, neurogenesis, dentate gyrus, hippocampus, brain, neuron, anxiety, depressive disorder, memory, plasticity | nlx_144587 | SCR_008830 | Functional Neurogenesis - New neurons in the adult brain. How they work and what they are good for. | 2026-08-04 09:42:15 | 2 | |||||||||
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Pediatric Imaging Neurocognition and Genetics Resource Report Resource Website 50+ mentions |
Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) | PING | database, data or information resource | A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu. | pediatric, neuroimaging, genetics, child, early adult human, adolescent, genetic variant, magnetic resonance imaging, brain, gene, brain structure, connectivity, function, brain development, cognition, experimental protocol, saliva, dna, diffusion tensor imaging, image, genotype, dicom, imaging genomics, magnetic resonance, nifti, FASEB list |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIH Toolbox - Assessment of Neurological and Behavioral Function has parent organization: University of California at San Diego; California; USA has parent organization: Multimodal Imaging Laboratory |
NIDA ; ARRA ; NICHD |
Data Use Agreement required. | nlx_151904 | http://www.nitrc.org/projects/ping | http://ping.chd.ucsd.edu/ | SCR_008953 | PING Study, Pediatric Imaging Neurocognition and Genetics (PING) | 2026-08-04 09:42:15 | 76 | ||||
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Allen Mouse Brain Connectivity Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) | ABA Mouse Connectivity | atlas, spatially referenced dataset, data or information resource | Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses. | brain, connectivity, atlas, neural, projection, mutant, mouse, strain, image, histology, neuroimaging, data |
is used by: NIF Data Federation is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science | Free for academic use, Non-commercial, Acknowledgement required, Commercial use requires permission | nlx_146253 | http://connectivity.brain-map.org/static/brainexplorer | SCR_008848 | Allen Brain Atlas Connectivity Study, Allen Brain Mouse Connectivity, Allen Mouse Connectivity Atlas, Allen Brain Atlas Mouse Connectivity | 2026-08-04 09:42:15 | 186 | |||||
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Multiple Sclerosis Research Australia Brain Bank Resource Report Resource Website |
Multiple Sclerosis Research Australia Brain Bank (RRID:SCR_010747) | MS Research Australia Brain Bank | biomaterial supply resource, material resource, tissue bank | Biomaterial supply resource which provides high quality and well-chracaterized brain tissue samples for MS research. Registered MS brain donors and their families are kept up to date on the latest progress in MS research. | biomaterial supply resource, brain, brain tissue, brain bank, MS, multiple sclerosis | is listed by: Multiple Sclerosis Discovery Forum | Multiple Sclerosis | Trish MS Research Foundation ; University of Sydney ; Collier Charitable Fund ; NSW Government Office for Science and Medical Research ; MS Research Australia |
Free, Freely available | SCR_013840, nlx_99028 | SCR_010747 | 2026-08-04 09:42:46 | 0 | ||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, database, data or information resource | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-08-04 09:43:08 | 1 | |||||
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499 fROI atlas Resource Report Resource Website 50+ mentions |
499 fROI atlas (RRID:SCR_014756) | atlas, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website. | roi, dmn, fmri, atlas, functional roi, gray matter, grey matter, brain | is related to: 90 fROI atlas | PMID:26068849 | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014756 | Willard atlas | 2026-08-04 09:43:31 | 71 | ||||||||
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MicrocircuitDB Resource Report Resource Website |
MicrocircuitDB (RRID:SCR_014577) | database, data or information resource | A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity. | database, microcircuit, micro circuit, brain, neuron, connectivity |
works with: ModelDB works with: NeuronDB |
Researchers may contribute to this resource | SCR_014577 | 2026-08-04 09:43:30 | 0 | ||||||||||
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Drosphila Brain Lineage Atlas Resource Report Resource Website 1+ mentions |
Drosphila Brain Lineage Atlas (RRID:SCR_017507) | atlas, data or information resource, service resource | Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons. | Structure, development, Drosophila, brain, lineage, neuron, brain | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_017507 | 2026-08-04 09:44:10 | 1 | ||||||||||
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Finnish Twin Cohort Study Resource Report Resource Website 1+ mentions |
Finnish Twin Cohort Study (RRID:SCR_017477) | database, data or information resource | Twin panel consists of three nationwide samples of Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use. | Twin, Finnish, nicotine, dependence, eating, disorder, brain, imaginig, alcohol, data, | has parent organization: University of Helsinki; Helsinki; Finland | Restricted | SCR_017477 | 2026-08-04 09:44:14 | 1 |
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