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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Virtual Atlas of the Honeybee Brain Resource Report Resource Website 1+ mentions |
Virtual Atlas of the Honeybee Brain (RRID:SCR_007133) | Virtual Atlas of the Honeybee Brain | atlas, data or information resource, reference atlas | Standard brain atlas of the honeybee presented as an interactive three-dimensional surface model with integrated neuron and neuronal tracts. The standard atlas was created as an average-shape atlas of 22 neuropils, calculated from 20 individual immunostained whole-mount bee brains. After correction for global size and positioning differences by repeatedly applying an intensity-based nonrigid registration algorithm, a sequence of average label images was created. The Honeybee, Apis mellifera has been studied extensively with respect to its sensory and neural capacities in navigation, communication, visual and olfactory learning and memory processing. The goal is to integrate the entirety of information into a Virtual Atlas of the Honeybee Brain. This common spatial reference map will potentiate the representation of structural and functional data obtained in different experiments and from different individuals. | anatomy, honeybee, brain, insect, insecta, normal, antennal lobe, olfactory | has parent organization: Free University of Berlin; Berlin; Germany | BMBF | PMID:16175557 | nif-0000-00089 | SCR_007133 | 2026-08-29 11:28:45 | 6 | |||||||
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Brainvox Resource Report Resource Website 1+ mentions |
Brainvox (RRID:SCR_009448) | data processing software, image analysis software, software application, software resource | An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997). | magnetic resonance, neuroanatomical analysis, software package, 3d, interactive, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
PMID:9038281 | Available for download | nlx_155592 | SCR_009448 | 2026-08-29 11:28:52 | 1 | ||||||||
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Gene Atlas Resource Report Resource Website 10+ mentions |
Gene Atlas (RRID:SCR_008089) | Geneatlas | atlas, data or information resource, database | This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston. | gene, brain, mouse, protein, spatial expression, molecular neuroanatomy resource, FASEB list |
has parent organization: University of Houston; Texas; USA has parent organization: Baylor University; Texas; USA |
Burroughs Wellcome Fund ; NLM 5T15LM07093; NCRR P41RR02250 |
nif-0000-10987 | SCR_008089 | 2026-08-29 11:30:16 | 47 | ||||||||
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3D surgical atlases of the murine head Resource Report Resource Website 1+ mentions |
3D surgical atlases of the murine head (RRID:SCR_008039) | atlas, data or information resource | 3D interactive atlas of two mouse brains, 129S1/SvImJ and C57Bl/6J. The aim of this resource is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice. These representations of the murine brain and skull, in conjunction with the resource''s development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate off-axis surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambdabregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system. | 129s1/svimj, anatomy, brain, c57bl/6j, central nervous system, digital atlas, imaging assay, in vivo, micro-electroporation, morphometric analysis, skull, sterotactic, transgenic, imaging | has parent organization: University of Toronto; Ontario; Canada | Canadian Institute for Health Research ; Ontario Research Development Challenge ; NARSAD Young Investigator award |
nif-0000-10249 | SCR_008039 | MRI / CT atlases | 2026-08-29 11:30:16 | 1 | ||||||||
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International Consortium of Brain Mapping DTI-81 Atlas Resource Report Resource Website 1+ mentions |
International Consortium of Brain Mapping DTI-81 Atlas (RRID:SCR_008066) | atlas, data or information resource | A stereotaxic probabilistic white matter atlas that fuses DTI-based white matter information with an anatomical template (ICBM-152). This atlas is based on probabilistic tensor maps obtained from 81 normal subjects acquired under an initiative of the International Consortium of Brain Mapping (ICBM). The subjects were normal right-handed adults ranging from 18 to 59 years of age. A hand-segmented white matter parcellation map was created from this averaged map. This map can be used for automated white matter parcellation. The precision of the affine-based image normalization and automated parcellation was measured for a group of normal subjects using manually defined anatomical landmarks. The raw diffusion-weighted images (DWIs) were first co-registered to one of the least diffusion-weighted images and corrected for subject motion with 6-mode rigid transformation with Automated Image Registgration (AIR). The average of all DWIs (aDWI) was calculated and used for a DTI-based anatomic image. For anatomical images to drive the normalization process, aDWIs were used. These images were normalized to the template (ICBM-152) using a 12-mode affine or 4th order polynomial non-linear transformation of AIR. The transformation matrix was then applied to the calculated diffusion tensor field. In the white matter parcellation map (WMPM), deep white matter regions were manually segmented into various anatomic structures based on fiber orientation information. | adult, echo-planar image sequence, external capsule, fornix, stria terminalis, anatomical template, anterior commissure, anterior limb of internal capsule, association fiber, brain, brainstem, cerebral peduncle, cingulum, commissural fiber, corona radiata, corpus callosum, corticospinal tract, inferior cerebellar peduncle, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, inferior fronto-occipital fasciculus, uncinate fasciculus, medial lemniscus, medial longitudinal fasciculus, middle cerebellar peduncle, posterior limb of internal capsule, projection fiber, retrolenticular part of the internal capsule, sagittal stratum, superior cerebellar peduncle, superior fronto-occipital fasciculus, superior longitudinal fasciculus, tapetum, tensor map, tract, white matter, magnetic resonance imaging | has parent organization: University of California at Los Angeles; California; USA | nif-0000-10495 | http://www.loni.ucla.edu/Atlases/Atlas_Detail.jsp?atlas_id=15 | SCR_008066 | ICBM DTI-81 | 2026-08-29 11:30:16 | 3 | ||||||||
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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 | atlas, data or information resource, 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 | 2026-08-29 11:29:58 | 0 | |||||||
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Database on Brain Map Transformations in Cerebellar Systems Resource Report Resource Website 1+ mentions |
Database on Brain Map Transformations in Cerebellar Systems (RRID:SCR_008052) | data or information resource, database | This site contains the NeSys archive on structure and structure-function data about brain map transformations in the cerebellar system of the rat. This archive presents data not illustrated in the original publications, downloadable original data sets, interactive illustration sequences, including 3-D models. The repository is based on 5 original publications. The publications deal with: - organization of projections to the pontine nuclei from three cortical areas: primary and secondary somatosensory areas (SI and SII), and the primary motor cortex (MI) - organization of pontine neurons projecting to somatosensory representations in the posterior cerebellum The data are also included in the FACCS application, a relational database application with embedded analytical tools, available via the The Rodent Brain Workbench (www.rbwb.org). Sponsors: NeSys Research and Database development is supported by The Research Council of Norway, The European Community (grants QLRT-2000-02256 and QLG3-CT 1999-00763), The Norwegian Consortium for High Performance Computing, and The Jahre Foundation. | brain, cerebellar, cortical, map, organization, ponine nucleus, posterior cerebellum, primary motor cortex, rat, somatosensory, structure, structure-function, system | has parent organization: University of Oslo; Oslo; Norway | nif-0000-10374 | SCR_008052 | NeSys Database | 2026-08-29 11:30:16 | 1 | |||||||||
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University of Kentucky's Alzheimer's Disease Center Resource Report Resource Website 1+ mentions |
University of Kentucky's Alzheimer's Disease Center (RRID:SCR_008766) | UK-ADC, UK ADC | biomaterial supply resource, material resource, tissue bank | An organization which includes a tissue bank, a database, study design consultation, clinical resources, and a community registry database. The UK-ADC shares data with the NIA national database (NACC), as well as with independent, qualified investigators both within and outside the UK-ADC. This resource's associated tissue bank is comprised of anonymized brain tissue, blood, and cerebrospinal fluid samples from patients in the clinic, as well as frozen post-mortem brain tissue samples. This organization also shares research resources with the National Alzheimer's Coordinating Center (NACC), NACC collaborative initiatives, the Alzheimer's Disease Neuroimaging Initiative (ADNI), other Alzheimer Disease Centers (ADCs), and any qualified investigators from either the University of Kentucky or the general scientific community. | post-mortem, brain, brain tissue, cerebral spinal fluid, serum, plasma, buffy coat, blood, alzheimer's disease, dementing disorder, mild cognitive impairment, dementia, frozen, formalin fixed, paraffin embedded slide, clinical, neuropathology, neuropathologic disease, neuropathologic diagnosis, clinical, registry |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Kentucky Alzheimer's Disease Center |
Alzheimer's disease, Dementing disorder, Dementia, Neuropathologic diagnosis | NIA P30 AG028383 | Public | nlx_144056 | http://www.mc.uky.edu/coa/clinicalcore/alzheimercenter.html#neuropathology, http://www.mc.uky.edu/coa/clinicalcore/Neuropathology%20Core.html | SCR_008766 | University of Kentucky Alzheimer's Disease Center Biospecimen Data or Clinical Request, UK-Alzheimer's Disease Center Biospecimen Data or Clinical Request | 2026-08-29 11:30:20 | 1 | ||||
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Experimental Man Blog Resource Report Resource Website |
Experimental Man Blog (RRID:SCR_008378) | Experimental Man | blog, data or information resource, narrative resource | Blog about how leading-edge bio-science and technology is impacting individuals and society. This blog is an outgrowth of David Ewing Duncan''s new book, Experimental Man: What one mans body reveals about youy future, your health, and our toxic world. In the book he reports taking over 250 tests in the realms of genes, environment, brain and body and explore what these tests can tell us about one persons health, past, present, and future. | experimental, blog, bio-science, technology, david ewing duncan, experimental man, health, toxic, world, environment, brain, body, test | has parent organization: Johns Hopkins University; Maryland; USA | nif-0000-30007 | SCR_008378 | Experimental Man Blog, The Experimental Man Blog | 2026-08-29 11:30:18 | 0 | ||||||||
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Rhesus Macaque Atlases for Functional and Structural Imaging Studies Resource Report Resource Website 10+ mentions |
Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) | Rhesus Macaque Atlases | atlas, data or information resource | NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL. | magnetic resonance imaging, macaca mulatta, neuroscience, rhesus macaque, structure, neuroimaging, t1-weighted atlas, t2-weighted atlas, mri, brain, neuroanatomy | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | Aging | Intramural Research Program ; NCRR RR000167; NIA AG11915; NIA AG20013; NIGMS GM007507; NCRR RR00163; NIA AG029612 |
PMID:19059346 | NO LONGER AVAILABLE | nif-0000-33003 | SCR_008650 | 2026-08-29 11:30:26 | 10 | |||||
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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 | 2026-08-29 11:30:20 | 1 | |||||
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Dublin Brain Bank Resource Report Resource Website |
Dublin Brain Bank (RRID:SCR_010597) | biomaterial supply resource, material resource, tissue bank | A biomaterial supply resource that collects and distributes human brain tissue samples. The Dublin Brain Bank is a collaboration between the Neuropathology Department of Beaumont Hospital and the Royal College of Surgeons in Ireland. Investigators interested in applying for tissue samples need to complete tissue requisition forms and provide a record of the research groups'' ethical approval. | brain, tissue, brain tissue |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland has parent organization: Beaumont Hospital; Dublin; Ireland |
Public, Only for research, The community can contribute to this resource | nlx_48304 | http://www.beaumont.ie/index.jsp?a=190&n=142&p=103 | http://www.rcsi.ie/index.jsp?nID=1342&pID=683 | SCR_010597 | 2026-08-29 11:30:35 | 0 | |||||||
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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 | 2026-08-29 11:30:43 | 1 | ||||||||
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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 | r3d100011591 | SCR_014457 | Cerebellar Development Transcriptome Database CDT-DB, BrainTX | 2026-08-29 11:30:44 | 1 | |||||||
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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 | NIGMS T32GM007365; NIMH R01MH09955501; NINDS R01NS08170301 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | Barres Brain RNA-Seq | 2026-08-29 11:30:30 | 156 | |||||
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90 fROI atlas Resource Report Resource Website 10+ mentions |
90 fROI atlas (RRID:SCR_014757) | atlas, data or information resource | Atlas of functional ROI's, including individual networks (auditory network, sensorimotor network, etc.). Atlases of individual networks and combined networks are available for download directly from the website. | froi, roi, dmn, atlas, individual network, brain, brain region, brain network | is related to: 499 fROI atlas | PMID:21616982 | Available for download | SCR_014757 | 2026-08-29 11:30:17 | 30 | |||||||||
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Bravissima Resource Report Resource Website |
Bravissima (RRID:SCR_016229) | atlas, data or information resource | Project that is a translation of the BraVa arterial vasculature database into the NIFTI MRI file format that can be applied to stroke studies, fMRI resting state imaging studies and other clinical neuroscience studies. Group artery region labels and arterial density maps are provided as well. Human Brain Major Artery Atlas 10.7490/f1000research.1114378.1 | brain, neuroanatomy, artery, vascular, vasculature, |
is related to: BraVa is related to: DALAN Atlas has parent organization: U.S. Department of Veterans Affairs |
Free, Available for download | SCR_016229 | Bravissima: Human Brain Artery NIfTI Atlas, Human Brain Major Artery Atlas | 2026-08-29 11:30:21 | 0 | |||||||||
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Waxholm Space Atlas of the Sprague Dawley Rat Brain Resource Report Resource Website 10+ mentions |
Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) | WHS-SD-atlas | atlas, data or information resource, waxholm atlas | Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format. | volumetric, atlas, anatomical, delineation, rat, brain, structural, contrast, isotropic, MIR, DTI, male, Sprague Dawley, image |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP is related to: PMOD Software is related to: Duke University; North Carolina; USA has parent organization: University of Oslo; Oslo; Norway works with: MeshView works with: VisuAlign |
EC Human Brain Project ; NCI U24 CA092656; NIBIB P41 EB015897; Research Council of Norway |
PMID:24726336 PMID:25585022 |
Free, Available for download, Freely available | SCR_017124 | WHS SD rat atlas, WHS_SD_rat_atlas, WHS-SD-rat-atlas | 2026-08-29 11:30:24 | 38 | ||||||
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CATlas Resource Report Resource Website 1+ mentions |
CATlas (RRID:SCR_018690) | atlas, data or information resource | Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans. | Gene, regulatory element, gene regulatory element, adult mouse, cerebrum, Cis-element, chromatin, mouse isocortex, olfactory bulb, hippocampus, cerebral nuclei, cis regulatory DNA element, brain, neurological disease |
is used by: BICCN is related to: BRAIN Initiative Cell Atlas Network |
DOI:10.1101/2020.05.10.087585 | Free, Freely available | SCR_018690 | , Cis-element Atlas, Ren lab web portal for chromatin accessibility data | 2026-08-29 11:30:27 | 4 | ||||||||
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ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | data or information resource, database, service resource | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-08-29 11:30:24 | 405 |
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