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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CTSA-IP Resource Report Resource Website |
CTSA-IP (RRID:SCR_006380) | CTSA-IP | database, data or information resource, community building portal, portal | Database that aggregates and markets technologies from CTSA institutions as well as those of the National Institutes of Health, with the goal of enhancing research activity and private partnerships across the CTSA consortium. Regular, automatic updating with a standardized template facilitates broad participation by CTSA consortium members. Currently, there are over a dozen CTSAs contributing information on their technologies to the site. CTSA-IP Mission * Intellectual Property information exchange * Links publicly available licensing opportunities from CTSI Institutions in an easily searchable format that connects providers & users. * Aim of creating a consortium view of IP, licensing & sponsored research opportunities. * Stimulus to collaboration and partnering with and between CTSA member institutions. | technology, intellectual property, partnership, aggregator, licensing opportunity |
is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Rochester; New York; USA |
NCRR UL1 RR024160 | PMID:22029803 | Open access | nlx_152160 | SCR_006380 | Clinical and Translational Sciences Award Intellectual Property | 2026-07-28 09:41:35 | 0 | |||||
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ResearchMatch Resource Report Resource Website 100+ mentions |
ResearchMatch (RRID:SCR_006387) | ResearchMatch | people resource, community building portal, data or information resource, portal, patient registry | Free and secure registry to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It has been developed by major academic institutions across the country who want to involve you in the mission of helping today''''s studies make a real difference for everyone''''s health in the future. Anyone can join ResearchMatch. Many studies are looking for healthy people of all ages, while some are looking for people with specific health conditions. ResearchMatch can help ''''match'''' you with any type of research study, ranging from surveys to clinical trials, always giving you the choice to decide what studies may interest you. | recruit, volunteer, clinical research, clinical, recruitment registry, registry, patient, clinical study, clinical trial, survey |
is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA |
Healthy, Specific health condition | NIH ; NCATS UL1TR000445; NCRR 1U54RR032646-01 |
PMID:22104055 | nlx_152168 | SCR_006387 | Research Match | 2026-07-28 09:41:35 | 180 | |||||
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Comparative Toxicogenomics Database (CTD) Resource Report Resource Website 1000+ mentions |
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) | CTD | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks. | environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browser, FASEB list |
is used by: DisGeNET is used by: NIF Data Federation is listed by: 3DVC is listed by: Gene Ontology Tools is related to: PharmGKB Ontology is related to: Gene Ontology is related to: BioRAT is related to: Integrated Gene-Disease Interaction is related to: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Mount Desert Island Biological Laboratory has parent organization: North Carolina State University; North Carolina; USA is parent organization of: Interaction Ontology |
Pfizer ; American Chemistry Council ; NIEHS ES014065; NIEHS R01 ES019604; NCRR P20 RR016463; NIEHS U24 ES033155 |
PMID:16902965 PMID:16675512 PMID:14735110 PMID:12760826 |
Free, Freely available | OMICS_01578, nif-0000-02683, r3d100011530 | http://ctd.mdibl.org, https://doi.org/10.17616/R3KS7N | SCR_006530 | CTD - Comparative Toxicogenomics Database | 2026-07-28 09:41:35 | 1188 | ||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | software application, software resource, data processing software, data visualization software, image analysis software | Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction | brain, magnetic resonance, image, analysis, human, topology, segmentation, visualization, cortex, cortical, mri, tissue classification, topological correction, rendering, edit, cortical surface |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network |
NIBIB R01 EB002010; NCRR P41 RR013642; NIMH RO1-MH53213 |
PMID:12045000 | nif-0000-30214 | http://www.nitrc.org/projects/brainsuite | SCR_006623 | Brain Suite | 2026-07-28 09:41:38 | 93 | |||||
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Resource Discovery System Resource Report Resource Website |
Resource Discovery System (RRID:SCR_005554) | RDS | data or information resource, database | Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members | registry, web service, source code, biomedical, software resource, material resource, funding resource, service resource, training resource, people resource | has parent organization: Biositemaps | Clinical and Translational Science Awards Consortium ; National Centers for Biomedical Computing ; NCRR 3UL1RR024153-03S1; NCRR 5UL1RR024128-03S1; NCRR 1UL1RR025008-01; NCRR 1UL1RR024146-01; NCRR 1UL1RR024986-01; NCRR 1UL1RR024153-01; NIDA 3U54DA021519-04S1; NHGRI 3U54HG004028-04S |
nlx_144645 | SCR_005554 | 2026-07-28 09:41:22 | 0 | ||||||||
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Recombinase (cre) Activity Resource Report Resource Website 10+ mentions |
Recombinase (cre) Activity (RRID:SCR_006585) | Recombinase Activity | data or information resource, database | Curated data about all recombinase-containing transgenes and knock-ins developed in mice providing a comprehensive resource delineating known activity patterns and allows users to find relevant mouse resources for their studies. | cre, recombinase, transgene, knock-in, allele, expression, activity pattern, mutagenesis, promoter, driver, image, tissue, specificity assay |
is related to: International Mouse Strain Resource is related to: CREATE is related to: JAX Cre Repository is related to: Allen Institute for Brain Science is related to: CRE Driver Network is related to: Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders is related to: EUCOMMTOOLS has parent organization: Mouse Genome Informatics (MGI) |
NCRR RR03 2656; NICHD HD062499; European Union HEALTH-F4-2009-223487 |
SCR_017520, nlx_152803 | http://www.creportal.org/ | SCR_006585 | Cre Portal | 2026-07-28 09:41:37 | 21 | ||||||
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SHRINE Resource Report Resource Website 1+ mentions |
SHRINE (RRID:SCR_006293) | SHRINE | software application, source code, software resource | Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems. | software network, clinical database, data sharing, clinical, medical record, federated, platform, network |
is related to: i2b2 Cross-Institutional Clinical Translational Research project is related to: i2b2 Research Data Warehouse has parent organization: Harvard Medical School; Massachusetts; USA |
Informatics for Integrating Biology and the Bedside ; NLM 5 U54 LM008748; NCRR 1 UL1 RR025758-01 |
PMID:19567788 | Available under a BSD3 Open unspecified license Software license. | nlx_151949 | SCR_006293 | Shared Health Research Informatics NEtwork | 2026-07-28 09:41:34 | 8 | |||||
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Wake Forest Cynomolgus Breeding Colony Resource Report Resource Website |
Wake Forest Cynomolgus Breeding Colony (RRID:SCR_006605) | CBC, WFU CBC | tissue bank, biomaterial supply resource, material resource | The Wake Forest Cynomolgus Breeding Colony (CBC) is a colony of cynomolgus macaques (crab-eating macaques, Macaca fascicularis). The cynomolgus colony is designed to produce specific pathogen free (SPF) cynomolgus monkeys for use in biomedical research. The colony, supported by a grant from the NCRR, addresses the growing need for investigators to use in their protocols animals defined for the absence of specific diseases including CHV-1 (Herpes B), simian immunodeficiency virus, and simian retroviruses. An additional important characteristic of this colony is that, unlike many breeding colonies, the NHPs will be fed two defined diets. The first diet is a soy-free diet, not commercial monkey chow. The second diet has the same macronutrients but the protein source is from soy; similar in isoflavone content. A drawback of chow diets is that the exact nutritional product composition is unknown from lot to lot. However, they are always rich in soy bean meal, isoflavones and other constituents of soy bean meal that are known confounders of several types of research projects. All research using the cynomolgus colony must be reviewed and approved by the colony''s scientific board and the Wake Forest Animal Care and Use Committee (ACUC) before any work can be initiated. The scientific board meets regularly to assess the scientific value of each request and to determine whether or not animals/samples/data can be made available. This includes all requests for: # The purchase of animals for use outside the colony # The use of animals within the colony for the collection of blood/tissue samples, behavioral observations or other kinds of testing # The use of the CBC sample/tissue repository # The use of the CBC data repository | long-tailed macaque, non-human primate, blood, tissue, macaca fascicularis, animal model |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Wake Forest Primate Center |
Macaca fascicularis | NCRR | Public | nlx_146209 | SCR_006605 | WFU Cynomolgus Breeding Colony, Cynomolgus Breeding Colony | 2026-07-28 09:41:36 | 0 | |||||
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lapdftext Resource Report Resource Website |
lapdftext (RRID:SCR_006167) | lapdftext, LA-PDFText, | software application, text extraction software, software resource | Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. | text mining, pdf, text extraction, natural language processing |
is listed by: FORCE11 has parent organization: University of Southern California; Los Angeles; USA |
NSF 0849977; NIGMS RO1-GM083871; NIMH 1R01MH079068-01A2; NCRR U24 RR025736-01 |
PMID:22640904 | Acknowledgement requested, GNU General Public License, v3 | nlx_151668 | SCR_006167 | Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles | 2026-07-28 09:41:28 | 0 | |||||
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Alternative Splicing Annotation Project II Database Resource Report Resource Website 1+ mentions |
Alternative Splicing Annotation Project II Database (RRID:SCR_000322) | ASAP II | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also search human data for tissue- and cancer-specific splice forms at the bottom of the gene summary page. The p-values for tissue-specificity as log-odds (LOD) scores, and highlight the results for LOD >= 3 and at least 3 EST sequences are all also reported. | exon, gene structure, genome, alternative splicing, cancer genome alignment, intron, isoform, orthologous exon, orthologous gene, orthologous intron, protein sequence, splice site, tissue, genome alignment, cancer |
is related to: ASAP: the Alternative Splicing Annotation Project has parent organization: University of California at Los Angeles; California; USA |
NCRR U54 RR021813; NIDCR DE-FC02-02ER63421 |
PMID:17108355 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02572 | SCR_000322 | ASAP II Database, Alternative Splicing Annotation Project II | 2026-07-28 09:39:58 | 2 | |||||
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Bioscholar Resource Report Resource Website 1+ mentions |
Bioscholar (RRID:SCR_001380) | BioScholar | software application, source code, software resource | Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server. | knowledge engineering from experimental design, protocol, lab data management, knowledge engineering, kefed, experimental design, curate, model, scientific experiment, data repository, experimental variable, biomedical, bioinformatics |
is related to: Knowledge Engineering from Experimental Design has parent organization: University of Southern California; Los Angeles; USA |
NCRR 1 U24 RR025736; NIGMS R01-GM083871 |
PMID:21859449 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152541 | SCR_001380 | 2026-07-28 09:40:14 | 1 | ||||||
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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 | 2026-07-28 09:40:14 | 3 | ||||||
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EcoCyc Resource Report Resource Website 100+ mentions |
EcoCyc (RRID:SCR_002433) | EcoCyc, EcoCyc REF | data or information resource, database | Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms. | genome, metabolic pathway, transcription, transporters, escherichia coli, transcriptional regulation, metabolism, pathway, FASEB list |
uses: Pathway Tools is used by: NIF Data Federation is listed by: OMICtools is listed by: BioCyc is related to: MultiFun is related to: BioCyc is related to: BioCyc is related to: AmiGO is related to: NCBI BioSystems Database is related to: Pathway Tools has parent organization: Stanford Research Institute International |
NCRR ; NIGMS GM077678; NIGMS GM71962 |
PMID:23143106 PMID:21097882 |
Free, Freely available | OMICS_01645, nif-0000-02783, r3d100011277 | https://doi.org/10.17616/R34K99 | SCR_002433 | EcoCyc REF | 2026-07-28 09:40:25 | 482 | ||||
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Homophila Resource Report Resource Website |
Homophila (RRID:SCR_007717) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions. | homolog, human disease, human disease gene, human, gene, cognate |
is related to: OMIM has parent organization: University of California at San Diego; California; USA |
NCRR P 41 RR08605-06 | PMID:11752278 PMID:11381037 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02976 | SCR_007717 | Human disease to drosophila database | 2026-07-28 09:41:54 | 0 | ||||||
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Gene Atlas Resource Report Resource Website 10+ mentions |
Gene Atlas (RRID:SCR_008089) | Geneatlas | data or information resource, database, atlas | 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 | 2026-07-28 09:42:16 | 47 | ||||||||
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3D MRI Atlas of Mouse Development Resource Report Resource Website 1+ mentions |
3D MRI Atlas of Mouse Development (RRID:SCR_008090) | MRI Atlas of Mouse Development, | data or information resource, atlas |
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on October, 01, 2019. 3D digital atlas of normal mouse development constructed from magnetic resonance image data. The download is a zipped file containing the six atlases Theiler Stages (ts) 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo. To view the atlases, download and install MBAT from: http://mbat.loni.ucla.edu Specimens were prepared in aqueous, isotonic solutions to avoid tissue shrinkage. Limited specimen handling minimized physical perturbation of the embryos to ensure accurate geometric representations of developing mouse anatomy. Currently, the atlas contains orthogonal sections through MRI volumes, three stages of embryos that have annotated anatomy, photographs of several stages of development, lineage trees for annotated embryos and a gallery of images and movies derived from the annotations. Anatomical annotations can be viewed by selecting a transverse section and selecting a pixel on the displayed slice. |
embryo, embryogenesis, development, magnetic resonance imaging, mouse, developing, c57bl/6, development, anatomy, embryonic mouse | is related to: Mouse BIRN Atlasing Toolkit | Normal | Human Brain Project ; Biomedical Informatics Research Network ; Beckman Institute at Caltech ; NCRR ; NIBIB |
PMID:10091864 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10989 | SCR_008090 | Caltech micro MRI Atlas of Mouse Development, microMRI Atlas of Mouse Development, Caltech MRI Atlas of Mouse Development, micro MRI Atlas of Mouse Development | 2026-07-28 09:41:59 | 1 | ||||
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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 | data or information resource, atlas | 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 | 2026-07-28 09:42:13 | 10 | |||||
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Eagle I Resource Report Resource Website 10+ mentions |
Eagle I (RRID:SCR_013153) | eagle-i, eagle i, eaglei | data or information resource, database | Web application to discover resources available at participating networked universities. This distributed platform for creating and sharing semantically rich data is built around semantic web technologies and follows linked open data principles. | ontology, semantic web, rdf, sparql endpoint, linked open data, distributed platform, protocol |
lists: BWH Partners Tissue and Blood Repository lists: MSU Subzero Science and Engineering Research Core Facility lists: OHSU MRI Support Core Laboratory lists: Penn Cell and Developmental Biology Zebrafish Core lists: Penn Clinical Research Computing Unit lists: Penn Community Outreach Using Health System Informatics Core lists: UPR Medical Mycology Laboratory lists: Vanderbilt Bradykinin Core Laboratory lists: BWH Surgical Planning Laboratory lists: Children's Hospital Informatics Program lists: DF/HCC Health Communication Core lists: DF/HCC Specialized Histopathology Services Core lists: Dartmouth College Clinical Pharmacology Shared Resource Core Facility lists: Dartmouth Geospatial Shared Resource lists: FAMU Drug Discovery Core Facility lists: FAMU Flow cytometry laboratory lists: HMS NERCE FACSCalibur Flow Cytometer Resource lists: Harvard HSCI iPS Cell Core Facility lists: Harvard NeuroDiscovery Center - Biomarker Study lists: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility lists: Hunter NMR Spectroscopy Facility lists: JSU Environmental Toxicology Core Lab lists: MGH Center for Morphometric Analysis lists: MGH Vector Development and Production Core Facility lists: MSU Magnetic Resonance Core Laboratory lists: Penn Diabetes Research Center Mouse Phenotyping Physiology and Metabolism Core lists: Penn Research Instrumentation Shop lists: Penn Small Animal Imaging Facility: PET/SPECT/CT Sub-Core lists: Penn Translational Biomarker Core lists: UH Manoa Insect Museum lists: UTEP BSL 3 Laboratory lists: UTSA Engineering Core lists: Vanderbilt Flow Cytometry Core Laboratory lists: Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core lists: Vanderbilt X-Ray Photoelectron Spectroscopy Lab lists: Wyss Institute Imaging Core lists: XULA Materials Research - Shared Instrumentation Facilities lists: Hunter Genomic Facility lists: UPR Analysis Resource Center Confocal Microscopy Core Laboratory lists: UPR Conrado F. Asenjo Library lists: UPR Confocal Microscope Facility lists: UPR Department of Environmental Health Core Laboratory lists: HSPH Trace Metals Laboratory lists: Dartmouth Science Division Electronics Shop lists: Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab lists: Arnold Arboretum of Harvard University: Weld Hill Molecular Lab lists: BWH Cell Culture and Microscopy Core lists: Hunter Nanoscale Analytical Facility lists: Dartmouth SYNERGY Clinical Research Unit lists: Dartmouth Shared Instruments Core Laboratory lists: Vanderbilt Energy Balance Core Laboratory lists: BWH Circulating Tumor Cell Core lists: University of Pennsylvania School of Medicine Penn Diabetes Research Center Pancreatic Islet Cell Biology Core Facility lists: HSPH Molecular Analysis Facility lists: HSPH Organic Chemistry Laboratory lists: Boston Area Diabetes Endocrinology Research Center Metabolic Physiology and Energy Balance Core Facility lists: Harvard FAS Magnetic Resonance Laboratory lists: 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Core lists: Wyss Institute Materials Characterization Core lists: XULA Animal Care Facility lists: XULA Center for Nanomedicine and Drug Delivery lists: XULA RCMI Cell and Molecular Biology Core lists: XULA RCMI Molecular Structure and Modeling Core lists: Harvard FAS Bauer Core Laboratory lists: BWH Research Imaging Core lists: Penn Induced Pluripotent Stem Cell Core Facility lists: HNDC Enhanced NeuroImaging Core lists: University of Pennsylvania Genomics Analysis Core lists: Meharry Proteomics Core lists: Meharry Microarray and Bioinformatics Core lists: Dartmouth DartLab lists: MGH NextGen Sequencing Core lists: Joslin Diabetes Center Islet Isolation Core lists: MGH Psychiatric and Neurodevelopmental Genetics Unit Core Lab lists: HMS Research Imaging Solutions lists: Harvard SERI Graphic Services Core lists: DFCI Confocal and Light Microscopy Core Facility lists: BWH Specimen Bank lists: MGH Martinos Center for Biomedical Imaging Core Facility lists: HNDC NeuroBehavior Laboratory Core lists: Harvard Chan Bioinformatics Core lists: HNDC Advanced Tissue Resource Center lists: DF/HCC DNA Resource Core lists: HNDC Drug Discovery in Neurodegeneration lists: DFCI Center for Cancer Computational Biology lists: HMS Systems Biology Flow Cytometry Facility lists: OHSU Molecular Virology Support Core is listed by: FORCE11 is related to: CTSAconnect is related to: Clinical and Translational Science Awards Consortium has parent organization: Harvard University; Cambridge; United States has parent organization: Oregon Health and Science University; Oregon; USA is parent organization of: eagle-i research resource ontology |
NCRR U24 RR029825; ARRA |
PMID:22434835 | Available to external user, The community can contribute to this resource | r3d100011564, nlx_143592 | https://www.eagle-i.org/, https://www.force11.org/node/4661 | SCR_013153 | 2026-07-28 09:43:23 | 10 | |||||
|
VALiDATe29 Squirrel Monkey Brain Atlas Resource Report Resource Website 1+ mentions |
VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) | data or information resource, atlas | Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. | squirrel brain, squirrel monkey brain, squirrel brain atlas, squirrel mri | has parent organization: Vanderbilt University; Tennessee; USA | NINDS RO1 NS058639; NINDS RO1 NS069909; NINDS RO1 NS078680; NCRR 1S10 RR 17789 |
Available for download | SCR_015542 | VALiDATe29 Atlas | 2026-07-28 09:44:05 | 1 | ||||||||
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Layton Alzheimers Disease Center Biomarkers and Genetics Core Lab Resource Report Resource Website |
Layton Alzheimers Disease Center Biomarkers and Genetics Core Lab (RRID:SCR_009911) | access service resource, service resource, core facility | In cooperation with the Data and Clinical Cores at the Layton Center, the Biomarkers and Genetics Core generates and maintains biomarker data for select biomarkers which have established roles in the characterization of subjects with or at risk of dementia. Biological markers of brain aging, dementia risk, and neurodegeneration have the potential to accelerate the identification of disease mechanisms and treatment strategies. Biomarkers may include genes, proteins, or other metabolites, and may be identified in DNA, cerebrospinal fluid (CSF), or plasma. Apolipoprotein E (APOE) genotype is generated for all research subjects. Sub-groups of subjects have other types of biomarker data. Many subjects have had genome-wide SNP data generated. In order to foster collaborative research as well as expand resources and expertise, samples (DNA, CSF, and plasma) and data are distributed to qualified investigators worldwide. Most of these researchers are pursuing the causes and modifiers of dementia. Data and samples are collected from well characterized research subjects including the healthy elderly and dementia patients. |
is listed by: Eagle I has parent organization: OHSU Layton Aging and Alzheimer's Disease Center |
Aging | NCRR 5U24RR029825-02 | nlx_156376 | SCR_009911 | Layton Alzheimer''s Disease Center Biomarkers & Genetics Core Lab | 2026-07-28 09:42:32 | 0 |
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