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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Open Access Series of Imaging Studies Resource Report Resource Website 100+ mentions |
Open Access Series of Imaging Studies (RRID:SCR_007385) | OASIS | data or information resource, database | Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated. | early, stage, alzheimer, disease, mri, fmri, image, brain, dicom, magnetic, resonance, collection, data, FASEB list |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Automatic Registration Toolbox is related to: 2012 MICCAI Multi-Atlas Labeling Challenge Data has parent organization: Howard Hughes Medical Institute has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Biomedical Informatics Research Network is parent organization of: Cover Pages |
Alzheimer's disease, Dementia, Normal, Nondemented, Aging | NIA P50 AG05681; NIA P01 AG03991; NIA R01 AG021910; NIMH P50 MH071616; NCRR U24 RR021382; NIMH R01 MH56584 |
Free, Acknowledgement required | r3d100012182, nif-0000-00387 | http://www.nitrc.org/projects/oasis https://doi.org/10.17616/R3RS8K |
SCR_007385 | The Open Access Series of Imaging Studies, Open Access Series of Imaging Studies, OASIS | 2026-02-14 02:06:36 | 299 | ||||
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BAMS Connectivity Resource Report Resource Website 1+ mentions |
BAMS Connectivity (RRID:SCR_000561) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | brain, neural circuitry, connectivity, brain region, neuroanatomy, neuronal tract tracing, connectome |
is used by: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Brain Architecture Management System |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144138 | http://brancusi.usc.edu/bkms/, http://brancusi.usc.edu/ | SCR_000561 | Brain Architecture Management System Connectivity Data | 2026-02-14 02:05:32 | 1 | |||||||
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WholeBrainCatalog's Channel - YouTube Resource Report Resource Website |
WholeBrainCatalog's Channel - YouTube (RRID:SCR_005436) | WholeBrainCatalog's Channel - YouTube | data or information resource, video resource | Videos uploaded to YouTube by the Whole Brain Catalog. | brain, mouse, atlas, crowdsourcing, cell, neuron, simulation, microscopy, neuroscience, electron microscopy, light microscopy | has parent organization: Whole Brain Catalog | nlx_144533 | SCR_005436 | Whole Brain Catalogs Channel - YouTube, Whole Brain Catalog's Channel - YouTube | 2026-02-14 02:06:24 | 0 | ||||||||
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sfnvideo - YouTube Resource Report Resource Website |
sfnvideo - YouTube (RRID:SCR_005463) | SFNVideo - YouTube | data or information resource, video resource | The Society for Neuroscience (SfN) is a nonprofit membership organization of scientists and physicians who study the brain and nervous system. SFNVideo - YouTube are videos uploaded to YouTube by the Society for Neuroscience (SfN). Since inception in 1969, the Society has grown from 500 members to more than 41,000. Today, SfN is the world''s largest organization of scientists and physicians devoted to advancing understanding of the brain and nervous system. | neuroscience, brain, nervous system | has parent organization: Society for Neuroscience | nlx_144583 | SCR_005463 | Society for Neuroscience Video - YouTube | 2026-02-14 02:05:56 | 0 | ||||||||
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Laboratory of Neuro Imaging - YouTube Resource Report Resource Website |
Laboratory of Neuro Imaging - YouTube (RRID:SCR_005462) | loniucla - YouTube | data or information resource, video resource | Videos uploaded to YouTube by the Laboratory of Neuro Imaging (LONI). The Laboratory of Neuro Imaging at UCLA strives to improve our understanding of the brain in health and disease. LONI is a leader in the development of advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function. | human, mouse, brain, health, disease, brain structure, brain function | nlx_144582 | http://www.youtube.com/user/loniucla | SCR_005462 | LONI - YouTube | 2026-02-14 02:06:24 | 0 | ||||||||
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Brain Mysteries Resource Report Resource Website |
Brain Mysteries (RRID:SCR_000504) | data or information resource, narrative resource | A blog featuring articles on the brain, consciousness, cognitive science, psychology and neurology. This resource is in Russian. | research, blog, article, psychology, neurology, brain, consciousness, forum, cognitive, russian | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_19443 | SCR_000504 | 2026-02-14 02:06:37 | 0 | ||||||||||
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PubAnatomy Resource Report Resource Website |
PubAnatomy (RRID:SCR_007999) | PubAnatomy | data or information resource, database | An integrated exploration of biomedical literature and data. An anatomy viewer can be accessed and searches of PubMed literature are visualized as to the anatomical regions that they effect. PubAnatomy takes advantage of the 25-micron voxel level mouse brain structure annotation generated by the Allen Brain Institute and integrates Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data. | molecular neuroanatomy resource, literature, paper, publication, pubmed, visual, graphical interface, brain, brain regions, gene expression |
is related to: Allen Mouse Brain Reference Atlas has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21143788 | nif-0000-07729 | SCR_007999 | 2026-02-14 02:06:11 | 0 | ||||||||
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Alternative Exon Database Resource Report Resource Website |
Alternative Exon Database (RRID:SCR_008157) | AEdb | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs. | element, exon, expression, gene, alignment, alternative, brain, conservation, cross-specie, disease, isoform, mechanism, minigene, pattern, peptide, regulatory, sequence, signal, splice, splicing, structure intron, tissue, transcript, nucleotide sequence, gene structure, intron, splice site, alternative splicing, sequence, alternative exon, function, constitutive exon, alternative exon, regulatory sequence, transcript regulatory motif, minigene, disease | has parent organization: European Bioinformatics Institute | PMID:16381912 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21009 | SCR_008157 | 2026-02-14 02:06:34 | 0 | |||||||
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Electroencephalogram Database: Prediction of Epileptic Seizures Resource Report Resource Website |
Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM). | electrode, electroencephalogram (eeg), epilepsy, epileptic seizure, focal, algorithm, analysis, behavioral, brain, cardiac, computational, data, defibrillator, hippocampus, medically, modeling, neocortical, neuroscience, patient, predict, seizure, stimulation, structure, surgical, model |
is listed by: 3DVC has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
University of Freiburg; Baden-Wurttemberg; Germany | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10217 | SCR_008032 | EEG Database | 2026-02-14 02:06:11 | 0 | |||||||
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HIV Brain Sequence Database Resource Report Resource Website 1+ mentions |
HIV Brain Sequence Database (RRID:SCR_008819) | HIVBrainSeqDB | data or information resource, database | 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 | 2026-02-14 02:06:10 | 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) | data or information resource, database | 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 | 2026-02-14 02:06:43 | 3 | |||||||||
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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) | data or information resource, database | 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 | 2026-02-14 02:06:11 | 1 | |||||||
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Pediatric Imaging Neurocognition and Genetics Resource Report Resource Website 50+ mentions |
Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) | PING | data or information resource, database | 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) | 2026-02-14 02:06:36 | 76 | ||||
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MicrocircuitDB Resource Report Resource Website |
MicrocircuitDB (RRID:SCR_014577) | data or information resource, database | 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 | 2026-02-14 02:06:52 | 0 | ||||||||||
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Finnish Twin Cohort Study Resource Report Resource Website 1+ mentions |
Finnish Twin Cohort Study (RRID:SCR_017477) | data or information resource, database | 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 | 2026-02-14 02:06:48 | 1 | ||||||||||
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Single Cell Portal Resource Report Resource Website 100+ mentions |
Single Cell Portal (RRID:SCR_014816) | SCP | data or information resource, portal | Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes. | Single cell data visualization, disseminating single cell data, single cell data, brain, RNA, rna seq, multiple gene expression, spatial transcriptomics, open science |
is used by: BRAIN Initiative is used by: BICCN is related to: BICCN Anatomy and Morphology Project is related to: Allen Institute for Brain Science has parent organization: Broad Institute has organization facet: Terra |
Free, Available for download, Freely available | https://portals.broadinstitute.org/single_cell?utf8=✓&search_terms=e+coli&order=&commit= | SCR_014816 | Single-Cell RNA-Seq Portal for Brain Research | 2026-02-14 02:05:34 | 237 | |||||||
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brainhack.org Resource Report Resource Website 1+ mentions |
brainhack.org (RRID:SCR_000195) | brainhack.org | data or information resource, portal | Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way. | magnetic resonance imaging assay, image, fmri, brain, science, neuroimaging, project |
is affiliated with: HBM Hackathon has parent organization: Neuro Bureau |
PMID:27042293 PMID:33932337 |
The community can contribute to this resource | nlx_149390 | SCR_000195 | BrainHack | 2026-02-14 02:05:12 | 1 | ||||||
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Brainreader Resource Report Resource Website 1+ mentions |
Brainreader (RRID:SCR_017308) | software resource | Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain. | Company, Denmark, medical, image, analysis, processing, software, brain | is affiliated with: Neuroreader | SCR_017308 | brainreader, BrainReader | 2026-02-14 02:03:26 | 3 | ||||||||||
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Leica CM1520 Cryostat Resource Report Resource Website 1+ mentions |
Leica CM1520 Cryostat (RRID:SCR_017543) | instrument resource | Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided. | Leica, cryostat, histology, surgery, brain, sectioning | This product has been discontinued | https://www.leicabiosystems.com/sites/default/files/media_product-download/2022-01/Leica_CM1520_IFU_2v4O_en.pdf | SCR_017543 | 2026-02-14 02:03:21 | 3 | ||||||||||
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BICCN Cell Registry Resource Report Resource Website 10+ mentions |
BICCN Cell Registry (RRID:SCR_017267) | data or information resource | Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols. | data, dataset, brain, initiative, cell, registry |
is related to: BRAIN Cell Data Center is related to: BRAIN Cell Data Center has parent organization: Allen Institute for Brain Science is provided by: BICCN |
NIH | Free, Freely available, Available for download | http://www.brainimagelibrary.org/download.html https://nemoarchive.org/resources/data-download.php |
SCR_017267 | BRAIN Initiative Cell Census Network Cell Registry, BICCN Cell Registry | 2026-02-14 02:03:25 | 11 |
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