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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Brain and Body Genetic Resource Exchange
 
Resource Report
Resource Website
1+ mentions
Brain and Body Genetic Resource Exchange (RRID:SCR_008959) BB-GRE data or information resource, database A database and associated tools for investigating the genetic basis of neurodisability. It combines phenotype information from patients with neurodevelopmental and behavioral problems with clinical genetic data, and displays this information on the human genome map. Basic access to genetic information (deletions, duplications) relating to participants with neurodevelopmental disorders is provided without an account; access to the full dataset requires an account. The genetic information that is available to view comprises potentially pathogenic copy number variation across the genome, detected by array comparative genome hybridization (aCGH) using a customized 44K oligonucleotide array. developmental disorder, copy number, neurodevelopmental disorder, child, phenotype, genotype-phenotype, brain, genetic, gene, genotype, behavior, clinical, genome, neurodevelopment, behavioral disorder, genetic variant, development has parent organization: King's College London; London; United Kingdom Schizophrenia, Mental retardation, Attention deficit hyperactivity disorder, Developmental language delay, Dyslexia, Sleep disorder, Epilepsy, Dysmorphism, Neurodisability, Autism Acknowledgement required nlx_151987 http://bbgre-dev.iop.kcl.ac.uk/info/about-us SCR_008959 BBGRE.org, Brain & Body Genetic Resource Exchange, BB-GRE database 2026-02-14 02:06:43 1
Neurology Image Library from The Internet Stroke Center
 
Resource Report
Resource Website
1+ mentions
Neurology Image Library from The Internet Stroke Center (RRID:SCR_013633) data or information resource, database The Internet Stroke Center at Washington University is pleased to offer this module for viewing CT, MR, and angiogram images of cerebrovascular and neurological diseases. While this project is still being perfected -- and many more cases have yet to be added -- we hope that you will find this collection useful in your education and practice. The images presented here are for educational use only. This information may not be used for diagnosis or treatment. All images are protected property of the Internet Stroke Center at Washington University and may not be reproduced without permission. Permission may be granted to students and professionals to borrow images from this site for educational purposes and/or presentations; we just ask that an email be sent detailing both the desired material and the intended use. Please direct all comments, questions, and requests to the Site Editor of the Internet Stroke Center. human, stroke, homo sapien, brain, image, clinical data, translational medicine has parent organization: Washington University in St. Louis; Missouri; USA nif-0000-00535 http://www.strokecenter.org/images SCR_013633 Neurology Image Library 2026-02-14 02:06:26 1
Brain Transcriptome Database
 
Resource Report
Resource Website
1+ mentions
Brain Transcriptome Database (RRID:SCR_014457) data or information resource, database A platform that allow users to visualize and analyze transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain. Users can search for cerebellar development genes by name, ID, keyword, expression, and tissue specificity. Search results include general information, links, temporal, spatial, and tissue information, and gene category. transcriptome, brain, database, temporal, spatial, tissue, brain development, brain function, brain dysfunction, genetics NIJC Japan Node of the INCF ;
JST ;
JSPS ;
MEXT
PMID:18603407 Public, Available to the scientific community SCR_014457 Cerebellar Development Transcriptome Database CDT-DB, BrainTX 2026-02-14 02:06:21 1
Brain RNA-Seq
 
Resource Report
Resource Website
100+ mentions
Brain RNA-Seq (RRID:SCR_013736) data or information resource, database Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list has parent organization: Stanford University; Stanford; California NIMH R01MH09955501;
NINDS R01NS08170301;
NIGMS T32GM007365
PMID:25186741
PMID:26687838
Free, Freely available SCR_017483 http://www.brainrnaseq.org/ SCR_013736 Barres Brain RNA-Seq 2026-02-14 02:06:51 109
TissueNet - The Database of Human Tissue Protein-Protein Interactions
 
Resource Report
Resource Website
10+ mentions
TissueNet - The Database of Human Tissue Protein-Protein Interactions (RRID:SCR_002052) TissueNet data or information resource, database Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues. protein-protein interaction, protein, tissue, adipose, adrenal, brain, breast, colon, heart, kidney, liver, lung, lymph node, ovary, prostate, skeletal muscle, testis, thyroid, white blood cell, protein expression, dna-microarray is listed by: OMICtools
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: Database of Interacting Proteins (DIP)
is related to: IntAct
is related to: MINT
has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel
PMID:23193266 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01913 SCR_002052 2026-02-14 02:05:46 26
Genes to Cognition Database
 
Resource Report
Resource Website
Genes to Cognition Database (RRID:SCR_002735) G2Cdb data or information resource, database Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain. allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapse Wellcome Trust ;
MRC ;
BBSRC ;
Gatsby Charitable Foundation ;
Human Frontiers Science Programme ;
European Union ;
Framework Programme ;
EPSRC ;
NSF
PMID:18984621 Free, Freely available nif-0000-02864 http://www.genes2cognition.org/cgi-bin/SearchView SCR_002735 Genes-to-Cognition Database 2026-02-14 02:06:11 0
BAMS Cells
 
Resource Report
Resource Website
10+ mentions
BAMS Cells (RRID:SCR_003531) BAMS Cells, BAMS Cell data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein. neuroanatomy, cell, neuron, neural circuitry, brain is used by: NIF Data Federation
has parent organization: Brain Architecture Management System
NIMH ;
NINDS ;
NIBIB
THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-90175 http://brancusi.usc.edu/bkms/ SCR_003531 Brain Architecture Management System Cells 2026-02-14 02:05:50 11
Drug Related Gene Database
 
Resource Report
Resource Website
1+ mentions
Drug Related Gene Database (RRID:SCR_003330) DRG data or information resource, database Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome. drug of abuse, gene expression, brain region, brain, american recovery and reinvestment act, brain, dna microarray, microarray, addiction uses: PubMed
is listed by: NIF Data Federation
is related to: Integrated Manually Extracted Annotation
has parent organization: Neuroscience Information Framework
NIDA Free, Freely available nif-0000-37443 https://confluence.crbs.ucsd.edu/login.action?os_destination=%2Fpages%2Fviewpage.action%3FspaceKey%3DNIF%26title%3DDRG&permissionViolation=true SCR_003330 DRG Database, Drug Dependent Gene Database 2026-02-14 02:06:14 2
Brede Database
 
Resource Report
Resource Website
Brede Database (RRID:SCR_003327) Brede data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments. neuroinformatics, functional neuroimaging, talairach, mni, brain, fmri, neuroimaging, matlab, pet, positron emission tomography, functional magnetic resonance imaging, multichannel electroencephalography, eeg, magnetoencephalography, near infrared spectroscopic imaging, single photon emission computed tomography, mri, coordinate, brain function, brain region, ontology is used by: NIF Data Federation
is related to: Brede Wiki
is related to: Brede Toolbox
is related to: Brede Toolbox
is related to: Brede Wiki
is related to: brainmap.org
is related to: Integrated Manually Extracted Annotation
has parent organization: Technical University of Denmark; Lyngby; Denmark
European Union ;
Project MAPAWAMO QLG3-CT-2000-300161
PMID:19668704
PMID:23666785
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00064 SCR_003327 2026-02-14 02:05:49 0
University of Southern California Brain Project
 
Resource Report
Resource Website
1+ mentions
University of Southern California Brain Project (RRID:SCR_008044) data or information resource, database, software resource The USC Brain Project is engaged in the effort to develop new tools and methodologies for neuroinformatics in modeling neural mechanisms of visuomotor coordination and exploring the evolution of the human language-ready brain, as well as conducting work in both neural modeling and database construction in relation to rehabilitation after stroke. Sponsors: USCBP is funded by the University of Southern California. brain, human, neural, neuroinformatics, stroke, visuomotor coordination, language has parent organization: University of Southern California; Los Angeles; USA nif-0000-10531 http://neuroinformatics.usc.edu/mediawiki/index.php/Main_Page SCR_008044 USCBP 2026-02-15 09:19:27 1
MRTool
 
Resource Report
Resource Website
1+ mentions
MRTool (RRID:SCR_015956) data or information resource, topical portal, portal Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. brain, imaging, neuroimaging, analysis, magnetic, resonance, mr requires: SPM DOI:10.1007/s12021-018-9355-3 Free, Available for download, Runs on MAC OS, Runs on Windows SCR_015956 2026-02-15 09:21:00 8
Neuro Bureau - Berlin Mind and Brain Sample
 
Resource Report
Resource Website
Neuro Bureau - Berlin Mind and Brain Sample (RRID:SCR_003537) Neuro Bureau/Berlin Mind and Brain Sample data or information resource, topical portal, portal Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file). morophometry, affective trait scale, resting state fmri, mprage, adult human, early adult human, late adult human, neuroimaging, brain, fmri, ics, panas, affective behavior scale, siemens, demographic has parent organization: 1000 Functional Connectomes Project
has parent organization: Neuro Bureau
has parent organization: Humboldt University of Berlin; Berlin; Germany
Berlin School of Mind and Brain Creative Commons Attribution-NonCommercial License nlx_157646 SCR_003537 Neuro Bureau - Berlin: Mind & Brain Sample, Neuro Bureau/Berlin Mind and Brain Institute Sample 2026-02-15 09:18:32 0
BrainTrap: Fly Brain Protein Trap Database
 
Resource Report
Resource Website
1+ mentions
BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) BrainTrap data or information resource, database, d spatial image This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download. brain, exon, expression, 3d confocal, affinity, antibody, dataset, immunohistochemical, microscopy, image, protein, protein-trap, gene has parent organization: University of Edinburgh; Scotland; United Kingdom EPSRC ;
British society for Developmental Biology ;
Society for Experimental Biology ;
Virtual Fly Brain e-Science Institute Theme ;
BBSRC ;
MRC
PMID:20624714 Free, Freely available nif-0000-32989 http://fruitfly.inf.ed.ac.uk/braintrap/ SCR_003398 Fly Brain Protein Trap Database, Brain Trap 2026-02-15 09:18:30 1
exact Low Resolution Electromagnetic Tomography
 
Resource Report
Resource Website
100+ mentions
exact Low Resolution Electromagnetic Tomography (RRID:SCR_013830) eLORETA software application, software resource Software application which computes cortical three-dimensional distribution of current density of the brain based on the scalp-recorded electric potential distribution. The exact low resolution brain electromagnetic tomography method has the property of exact localization to test point sources, yielding images of current density with exact localization, albeit with low spatial resolution. eLORETA has no localization bias even in the presence of structured noise. Deep structures, such as the anterior cingulate cortex and mesial temporal lobes, can be correctly localized with these methods. LORETA, EEG, MEG, brain, image, electromagnetic tomography is related to: Low Resolution Electromagnetic Tomography
is related to: sLORETA
is related to: sLORETA
has parent organization: University of Zurich; Zurich; Switzerland
Free, Not ready for public distribution, Must have administrator rights http://www.uzh.ch/keyinst/loretaOldy.htm SCR_013830 Exact Low Resolution Brain Electromagnetic Tomography 2026-02-15 09:20:48 265
Hierarchical Region Splitting
 
Resource Report
Resource Website
1+ mentions
Hierarchical Region Splitting (RRID:SCR_016398) HRS algorithm resource, software resource Algorithm for computational imaging of MRI data that detects and quantifies ischemic core–penumbra using only a single MRI modality (T2- or diffusion-weighted imaging, T2WI/DWI). It can be used with 3D data on lesions and normal-appearing brain matter (NABM) volumes. mri, neuroimaging, modality, t2, diffusion, 3d, brain, lesion, nabm, core, penumbra, computation, hypoxia, ischemic PMID:22929436 Freely available SCR_016398 Hierarchical Region Splitting (HRS) 2026-02-15 09:21:51 1
INCF Japan Node
 
Resource Report
Resource Website
1+ mentions
INCF Japan Node (RRID:SCR_006569) INCF Japan Node data or information resource, topical portal, portal The Japan Node of the INCF coordinates neuroinformatics activities within Japan and represents Japanese efforts in INCF. This site provides information about Japanese neuroinformatics platforms (NI Platforms) and the techniques and tools available from the International Neuroinformatics Coordinating Facility (INCF). The Neuroinformatics Japan Center (NIJC) will also supply techniques and tools developed at RIKEN BSI and at other research groups in Japan. INCF expects each national node to: 1. Actively formulate and implement the INCF Work Programs, 2. Coordinate and facilitate local neuroinformatics research activities at the national level, 3. Encourage neuroinformatics data sharing that conforms with INCF standards, and 4. Promote neuroinformatics development that supports the goals of INCF. The Neuroinformatics Japan Center (NIJC) represents the Japan Node. Together with the Japan Node Committee and the Platform Subcommittees, we promote domestic activities of neuroinformatics. Platform Subcommittee members collaborate to develop databases that are available for use on the website. Standing at the intersection of neuroscience and information science, the field of neuroinformatics develops the tools to house, share and analyze neuroscientific data, and to create computational models of brain. NIJC supports researchers developing and maintaining neuroscience databases, provides a portal for these databases and Neuroinformatics, and is designing the infrastructure for Neuroinformatics. It is also developing database technologies, and facilitates cooperation and distribution of the information stored in those databases. The activities of the Japan Node * Shaping domestic neuroinformatics research and directions (Japan Node Committee) * Advising on Intellectual Property Rights and protecting experimental subjects (Japan Node Committee) * Developing and publishing brain science databases (Platform Subcommittee) * Coordinating database management (Platform Subcommittee) * Disseminating neuroinformatics information via the web portal * Developing the infrastructure for brain science information and neuroinformatics * Supporting the development and diffusion of neuroinformatics technology event, brain, collaborate, data sharing, neuroinformatics, news, research, neuroscience is related to: Dynamic Brain Platform
has parent organization: International Neuroinformatics Coordinating Facility
has parent organization: RIKEN Brain Science Institute
is parent organization of: Visiome Platform
is parent organization of: Invertebrate Brain Platform
International Neuroinformatics Coordinating Facility nif-0000-10264 SCR_006569 International Neuroinformatics Coordinating Facility - Japan Node: The Portal System for Neuroinformatics in Japan, International Neuroinformatics Coordinating Facility Japan Node, Neuroinformatics Japan Center, NIJC, INCF Japan-Node 2026-02-16 09:46:45 3
HUPO Brain Proteome Project
 
Resource Report
Resource Website
1+ mentions
HUPO Brain Proteome Project (RRID:SCR_007302) HBPP data or information resource, topical portal, portal An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI). molecular neuroanatomy resource, brain, proteome, gene expression, expression profiling, proteomics, standard has parent organization: HUPO - Human Proteome Organisation Healthy, Neurodiseased, Aged, Alzheimer's disease, Parkinson's disease, Aging BMBF nif-0000-00173 SCR_007302 Human Brain Proteom Project, HUPO BPP 2026-02-16 09:46:56 1
MonkeyCBP
 
Resource Report
Resource Website
1+ mentions
MonkeyCBP (RRID:SCR_017640) MonkeyCBP algorithm resource, software resource, software toolkit Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community. MonkeyCBP, Atlas, Parcellation Atlas, neuroimaging pipeline, brain, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Free, Freely available SCR_017675 http://www.nitrc.org/projects/monkey-cbp/ SCR_017640 Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain 2026-02-16 09:49:17 1
Kymata Atlas
 
Resource Report
Resource Website
1+ mentions
Kymata Atlas (RRID:SCR_000269) data or information resource, atlas THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU). data visualization software, database, adult human, brain, function, computational model, sensory information, post-synaptic dendritic current is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: MRC Cognition and Brain Sciences Unit
THIS RESOURCE IS NO LONGER IN SERVICE nlx_158115 http://www.nitrc.org/projects/kymata_atlas SCR_000269 2026-02-16 09:45:13 1
Neuroanatomy Atlas
 
Resource Report
Resource Website
Neuroanatomy Atlas (RRID:SCR_002402) Neuroanatomy Atlas data or information resource, atlas Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan. magnetic resonance imaging, neuroanatomy, brain has parent organization: University of South Carolina; South Carolina; USA Free, Available for download, Freely available nif-0000-00121 SCR_002402 2026-02-16 09:45:45 0

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