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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
BAMS Nested Regions
 
Resource Report
Resource Website
1+ mentions
BAMS Nested Regions (RRID:SCR_000238) BAMS Nested Regions data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships. neural circuitry, brain region, brain is used by: NIF Data Federation
has parent organization: Brain Architecture Management System
NIMH MH61223;
NINDS NS16686;
NINDS/NIMH/NIBIB NS50792-01
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10175 SCR_000238 Brain Architecture Management System Nested Regions 2026-02-14 02:05:59 3
Penn Hippocampus Atlas
 
Resource Report
Resource Website
1+ mentions
Penn Hippocampus Atlas (RRID:SCR_000421) Penn Hippocampus Atlas data or information resource, atlas Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS. magnetic resonance, nifti, hippocampus, mri, postmortem is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Pennsylvania; Philadelphia; USA
NIA AG027785;
NINDS NS061111;
NINDS NS058386;
NINDS NS045839
PMID:18840532 Free, Available for download, Freely available nlx_155920 SCR_000421 2026-02-14 02:05:57 2
UCSF Brain Tumor Tissue Bank
 
Resource Report
Resource Website
UCSF Brain Tumor Tissue Bank (RRID:SCR_000647) biomaterial supply resource, tissue bank, material resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.) tissue, frozen, paraffin-embedded, blood, culture, frozen tissuefrozen serum, serum, paraffin embedded tissue, research, cell, cell line is listed by: One Mind Biospecimen Bank Listing
has parent organization: University of California at San Francisco; California; USA
Tumor NINDS P01 NS94297;
NCI P-50-CA97257
THIS RESOURCE IS NO LONGER IN SERVICE nlx_33528, SCR_006439, nlx_143683 https://gnome.ucsf.edu/tbank/ SCR_000647 UCSF Brain Tumor Research Center Tissue Bank, UCSF Brain Tumor Research Center Tissue Core, UCSF Neurosurgery Tissue Bank, UCSF Neurological Surgery Tissue Bank, UCSF BTRC Tissue Core 2026-02-14 02:05:32 0
Emory ADRC Tissue and Biospecimen Banking Facility
 
Resource Report
Resource Website
Emory ADRC Tissue and Biospecimen Banking Facility (RRID:SCR_000551) biomaterial supply resource, tissue bank, material resource The Alzheimer's Disease Research Center at Emery University maintains an active brain bank to facilitate the acquisition, storage, handling and distribution of well-characterized autopsy brain tissue and other materials to investigators. It contains frozen tissue and brain specimens, formalin fixed tissue, paraformaldehyde fixed tissue, and cryopreserved tissue. The ADRC also has access to tissues and samples related to other neurodegenerative diseases. It contains plasma samples, serum samples, lymphoblast cell lines, and cerebrospinal fluid. brain bank, biomaterial supply resource, brain tissue, plasma, cerebral spinal fluid, serum, lymphoblast cell line, buffy coat isolate, buffy coat, frozen, paraffin block, paraformaldehyde-fixed, cryopreserved, alzheimer's disease, parkinson's disease, neurodegenerative disease, tauopathy, huntington's disease, normal control is listed by: One Mind Biospecimen Bank Listing
is affiliated with: Emory Alzheimer's Disease Research Center
is related to: Emory Neurology Database
has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA
Alzheimer's disease, Parkinson's disease, Neurodegenerative disease, Tauopathy, Huntington's disease, Creutzfeldt-Jakob Syndrome, Dementia, Movement disorder, Sleep disorder, Stroke, Neuromuscular disease, Nervous system disease, Amyotrophic Lateral Sclerosis, Restless Leg Syndrome NINDS P30 NS055077 Public, Investigators must notify the ADRC of data use, Investigators must send a final copy of any accepted manuscript that used data or recruited research participations from the ADRC, Grant acknowledgement required, Institution acknowledgement required nlx_144036 SCR_000551 Emory Tissue and Biospecimen Banking Facilities, Emory Tissue & Biospecimen Banking Facility, Emory ADRC Tissue & Biospecimen Banking Facility 2026-02-14 02:06:00 0
BraVa
 
Resource Report
Resource Website
1+ mentions
BraVa (RRID:SCR_001407) BraVa data or information resource, database A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs). digital reconstruction, morphometric analysis, cerebrum, arterial vasculature, magnetic resonance angiography, adult human, morphology, artery, arborization, circle of willis, cerebral artery, male, female, magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Bravissima
has parent organization: George Mason University: Krasnow Institute for Advanced Study
Healthy NINDS NS39600;
NIBIB EB001955;
NINDS NS061770;
NIMH P20 MH52176
PMID:23727319 Free, Freely Available nlx_152630 http://www.nitrc.org/projects/breva SCR_001407 2026-02-14 02:06:04 8
WTCHG Genome Scan Viewer
 
Resource Report
Resource Website
1+ mentions
WTCHG Genome Scan Viewer (RRID:SCR_001635) GSCANDB data or information resource, service resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression has parent organization: University of Oxford; Oxford; United Kingdom NIAAA U01AA014425;
NCRR R24RR015116;
NIGMS R01GM072863;
NINDS R01NS049445;
NIMH P20-MH 62009;
NIAAA U24AA13513
THIS RESOURCE IS NO LONGER IN SERVICE nlx_153902 SCR_001635 Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database 2026-02-14 02:05:45 3
Convert MNI coordinates to or from XYZ
 
Resource Report
Resource Website
Convert MNI coordinates to or from XYZ (RRID:SCR_000406) Convert MNI coordinates to or from XYZ software resource, data processing software, software application Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other. magnetic resonance is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) NINDS K23NS083741;
Stiftung Charité ;
Berlin Institute of Health ;
Prof. Klaus Thiemann Foundation ;
German Research Agency
Free, Available for download, Freely available nlx_155600 SCR_000406 2026-02-14 02:05:23 0
nTracer
 
Resource Report
Resource Website
nTracer (RRID:SCR_023032) image processing software, software resource, data processing software, software application Software tool as plug-in for ImageJ software. Used for tracing microscopic images. tracing microscopic images is a plug in for: ImageJ Michigan miBRAIN initiative ;
NIAID R01AI130303;
NSF NSF-1707316;
NIMH R01MH110932;
NIGMS F31GM116517;
NINDS R01NS095367;
NIMH P50MH09427;
NIH Office of the Director DP2OD006514;
NINDS R01NS076467;
NINDS U01NS090449;
NIGMS P41GM10371;
Multidisciplinary University Research Initiative Army Research Office
PMID:30715234 Free, Available for download, Freely available SCR_023032 2026-02-14 02:05:00 0
rMATS
 
Resource Report
Resource Website
10+ mentions
rMATS (RRID:SCR_023485) software resource Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. detection of differential alternative splicing, replicate RNA-Seq data, analysis of paired and unpaired replicates, clinical RNA-Seq datasets, genome studies, NIGMS R01GM088342;
NINDS R01NS076631;
NIEHS R01ES024995;
NIGMS R01GM105431;
NSF DMS1055286;
NSF DMS1310391;
Alfred Sloan Research Fellowship
PMID:25480548 Free, Available to download, Freely available SCR_023485 2026-02-14 02:05:11 18
powereQTL
 
Resource Report
Resource Website
1+ mentions
powereQTL (RRID:SCR_021653) data processing software, data analysis software, data analytics software, software toolkit, software application, software resource Software R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. sample size calculation, bulk tissue, calculation, single-cell eQTL analysis is listed by: CRAN NINDS U01 NS120637;
American Parkinson Disease Association ;
NINDS R01 NS115144;
NINDS U01 NS095736;
NINDS U01 NS10 0603;
Michael J. Fox Foundation for Parkinson Research
DOI:10.1093/bioinformatics/btab385 Free, Available for download, Freely available https://cran.r-project.org/web/packages/powerEQTL/index.html
https://github.com/sterding/powerEQTL
SCR_021653 2026-02-14 02:04:41 3
Minian
 
Resource Report
Resource Website
1+ mentions
Minian (RRID:SCR_022601) data processing software, data analysis software, software toolkit, software application, software resource Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output. Miniscope, analysis pipeline, calcium imaging, mouse, Visualization, OpenBehavior is listed by: OpenBehavior
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
NIMH DP2MH122399;
NIMH R01MH120162;
NIBIB R01EB028166;
NSF 1926800;
NSF 2046583;
NINDS U01NS094286;
NSF 1700408;
NIA F32AG067640;
NINDS R03 NS111493;
NIDA R21 DA049568;
NINDS R01 NS116357
PMID:35642786 Free, Available for download, Freely available https://edspace.american.edu/openbehavior/project/minian/ SCR_022601 2026-02-14 02:04:45 4
Brain atlas of the common marmoset
 
Resource Report
Resource Website
Brain atlas of the common marmoset (RRID:SCR_005135) Brain Atlas of the Common Marmoset data or information resource, atlas THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman. callithrix jacchus jacchus, marmoset, primate neuroanatomy, callitrichidae, female, forebrain, thalamus, midbrain, brainstem, magnetic resonance imaging, adult, callithrix, histological section, nissl staining, brain, mri has parent organization: NICHD Developmental Neuroethology - Laboratory of Comparative Ethology NIH ;
NICHD ;
NINDS
PMID:19744521 THIS RESOURCE IS NO LONGER IN SERVICE. nlx_144140 SCR_005135 Brain Atlas of the Common Marmoset Callithrix jacchus jacchus 2026-02-14 02:06:25 0
High Resolution Mouse Brain Atlas
 
Resource Report
Resource Website
10+ mentions
High Resolution Mouse Brain Atlas (RRID:SCR_006063) High Resolution Mouse Brain Atlas data or information resource, atlas 2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas. adult mouse, hippocampal formation, image, leaf lumina camera, mouse, normal, nuclei of the limbic thalamus, c57bl/6, nissel, myelin, neuroanatomy, olfactory bulb, frontal pole, pyriform cortex, septo-striatal, septo-diencephalic, rostral diencephalon, caudal diencephalon, rostral cerebellum, caudal cerebellum, medula, spinal cord, diencephalon, cerebellum, mesencephalon has parent organization: Harvard University; Cambridge; United States Human Brain Project ;
NINDS RO1 NS36041
nif-0000-00087 SCR_006063 2026-02-14 02:05:58 24
FuncAssociate: The Gene Set Functionator
 
Resource Report
Resource Website
10+ mentions
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) FuncAssociate data analysis service, production service resource, service resource, analysis service resource A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool gene, gene ontology, statistical analysis, web service, bio.tools is listed by: Gene Ontology Tools
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Roth Laboratory
NIH ;
Canadian Institute for Advanced Research ;
NINDS NS054052;
NINDS NS035611;
NHLBI HL081341;
NHGRI HG0017115;
NHGRI HG004233;
NHGRI HG003224
PMID:19717575
PMID:14668247
Free for academic use, Acknowledgement requested biotools:funcassociate, OMICS_02264, nlx_149233 http://llama.mshri.on.ca/cgi/func/funcassociate
https://bio.tools/funcassociate
SCR_005768 2026-02-14 02:05:53 36
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility
 
Resource Report
Resource Website
1+ mentions
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility (RRID:SCR_001712) Duke-UNC BIAC, BIAC core facility, access service resource, service resource BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill. Imaging methodology development, analysis techniques, cognitive neurosciences application, clinical neurosciences application, imaging service has parent organization: Duke University; North Carolina; USA National Institutes of Health ;
Autism Speaks ;
NINDS
Restricted nif-0000-10210 SCR_001712 Duke University of North Carolina Brain Imaging and Analysis Center, Brain Imaging and Analysis Center, Brain Imaging and Analysis Center (BIAC) 2026-02-14 02:07:28 2
Wellcome-CTC Mouse Strain SNP Genotype Set
 
Resource Report
Resource Website
1+ mentions
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) Wellcome-CTC Mouse Strain SNP Genotype Set data or information resource, data set THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain has parent organization: Wellcome Trust Centre for Human Genetics Wellcome Trust ;
NCRR R24RR015116;
NIGMS R01GM072863;
NIAAA U01AA014425;
NINDS R01NS049445;
NIMH P20-MH 62009;
NIAAA U24AA13513
THIS RESOURCE IS NO LONGER IN SERVICE nlx_156947 SCR_003216 2026-02-14 02:07:20 3
Neurophysiology Imaging Facility
 
Resource Report
Resource Website
Neurophysiology Imaging Facility (RRID:SCR_004080) NIF core facility, access service resource, service resource Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates. mri, fmri, neuroimaging, neurophysiology, brain has parent organization: National Institute of Mental Health NIMH ;
NINDS ;
NEI
nlx_158530 SCR_004080 Neurophysiology Imaging Facility (NIF) 2026-02-14 02:07:21 0
Lab Streaming Layer
 
Resource Report
Resource Website
50+ mentions
Lab Streaming Layer (RRID:SCR_017631) LSL software resource, software application System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG has parent organization: University of California at San Diego; California; USA Army Research Laboratory ;
NINDS R01 NS047293
Free, Freely available SCR_017631 Lab Streaming Layer 2026-02-14 02:07:29 67
MIRACL
 
Resource Report
Resource Website
1+ mentions
MIRACL (RRID:SCR_020945) software resource, software toolkit Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation. Image registration, CLARITY, multimodal image registration, connectivity analysis, connectomic data integration, MRI data, connectivity atlases, histological features analysis, mice clarity data is related to: Allen Institute for Brain Science
works with: Allen Mouse Brain Reference Atlas
NINDS R01 NS095985;
NIMH R01 MH111444;
NIA R01 AG061120;
NINDS R01 NS093057;
Stanford Radiology Angel Funds ;
Stanford Neurosciences Institute ;
HHMI ;
U.S. Army Research Laboratory and Defense Advanced Research Projects Agency ;
American Society for Neuroradiology ;
Boerger Research Fund for Alzheimer Disease and Neurocognitive Disorders ;
GE Healthcare ;
Bernard and Ronni Lacroute ;
William Randolph Hearst Foundation ;
Marc Paskin
PMID:31796741 Free, Available for download, Freely available https://github.com/mgoubran/MIRACL/blob/master/docs/index.rst SCR_020945 Multi modal Image Registration And Connectivity anaLysis 2026-02-14 02:07:32 1
Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain
 
Resource Report
Resource Website
Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain (RRID:SCR_008065) Voxelation Map of Gene Expression in a Coronal Section of the Mouse Brain data or information resource, atlas, database Two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 cubic mm gene expression patterns in the brain obtained through voxelation. Voxelation employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. molecular neuroanatomy resource, gene expression, striatum, voxelation, gene, brain, coronal, microarray, adult mouse, male, c57bl/6j has parent organization: David Geffen School of Medicine at UCLA; California; USA Staglin Music Festival and NARSAD Young Investigator Award ;
Tobacco-Related Disease Research Program 11RT-0172;
Alzheimer's Association IIRG-02-3609;
NIDA RO1-DA-015802;
NINDS RO1-NS-050148
PMID:17504947 nif-0000-10493 SCR_008065 2026-02-14 02:06:11 0

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