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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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CloudReg Resource Report Resource Website |
CloudReg (RRID:SCR_022795) | data processing software, image analysis software, software application, software resource | Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration. | brain volume, nonlinear registration, automatic terabyte scale, cross modal brain volume registration, image analysis pipeline, volumetric datasets with artifacts | is used by: BICCN | AP Giannini Foundation ; Johns Hopkins University Kavli Neuroscience Discovery Institute Postdoctoral Fellowship ; Karen Toffler Charitable Trust ; Kavli Neuroscience Discovery Institute ; Microsoft Research ; NIA P01AG009973; NIA R01 AG066184; NIDA 1K99DA050662; NIMH K08MH113039; NIMH R01 MH099647; NIMH U19MH114821; NINDS K99 NS116122; NSF EEC 1707298 |
PMID:34253927 | Free, Available for download, Freely available | https://github.com/neurodata/CloudReg/ | SCR_022795 | 2026-09-12 01:01:11 | 0 | |||||||
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Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure Resource Report Resource Website 10+ mentions |
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) | SCORE imaging | data or information resource, narrative resource | Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields. | format, authoring tool, embryo, microscopy, publishing format, image |
is listed by: FORCE11 has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIGMS GM63904; NIDA DA14546 |
PMID:20528262 | nif-0000-07749 | SCR_001300 | Specimen in a Corrected Optical Rotational Enclosure imaging | 2026-09-12 01:02:26 | 11 | ||||||
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Substructure Index-based Approximate Graph Alignment Resource Report Resource Website 10+ mentions |
Substructure Index-based Approximate Graph Alignment (RRID:SCR_003434) | SAGA | software application, software resource | SAGA (Substructure Index-based Approximate Graph Alignment) is a tool for querying a biological graph database to retrieve matches between subgraphs of molecular interactions and biological networks. SAGA implements an efficient approximate subgraph matching algorithm that can be used for a variety of biological graph matching problems such as the pathway matching SAGA uses to compare pathways in KEGG and Reactome. You can also use SAGA to find matches in literature databases that have been parsed into semantic graphs. In this use of SAGA, portions of PubMed have been parsed into graphs that have nodes representing gene names. A link is drawn between two genes if they are discussed in the same sentence (indicating there is potential association between the two genes). SAGA lets you match graphs between different databases even though the content is distinct and the databases organize pathways in different ways. This cross-database matching is achieved by SAGA's flexible approximate subgraph matching model that computes graph similarity, and allows for node gaps, node mismatches, and graph structural differences. Comparing pathways from different databases can be a useful precursor to pathway data integration. SAGA is very efficient for querying relatively small graphs, but becomes prohibitory expensive for querying large graphs. Large graph data sets are common in many emerging database applications, and most notably in large-scale scientific applications. To fully exploit the wealth of information encoded in graphs, effective and efficient graph matching tools are critical. Due to the noisy and incomplete nature of real graph datasets, approximate, rather than exact, graph matching is required. Furthermore, many modern applications need to query large graphs, each of which has hundreds to thousands of nodes and edges. TALE is an approximate subgraph matching tool for matching graph queries with a large number of nodes and edges. TALE employs a novel indexing technique that achieves a high pruning power and scales linearly with the database size. | gene, algorithm, alignment, biological, graph, interaction, literature, molecular, pathway, query, reactome, structural, subgraph, substructure, tool, graph similarity |
is listed by: Biositemaps has parent organization: National Center for Integrative Biomedical Informatics has parent organization: University of Michigan; Ann Arbor; USA |
Microsoft ; NIDA 1-U54-DA021519-01A1 |
PMID:17110368 | Access free via the web; Binaries are also freely available. If you use SAGA for any work that leads to a publication you must cite paper. | nif-0000-33157 | SCR_003434 | SAGA (Substructure Index-based Approximate Graph Alignment), SAGA - Substructure Index-based Approximate Graph Alignment, SAGA: A Fast and Flexible Graph Matching Tool | 2026-09-12 01:02:30 | 24 | |||||
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Harmonized DRG and TG Reference Atlas Resource Report Resource Website 1+ mentions |
Harmonized DRG and TG Reference Atlas (RRID:SCR_025720) | atlas, data or information resource, reference atlas, software resource, source code | Harmonized cell atlases using sc/snRNA-seq data obtained from dorsal root ganglia and trigeminal ganglio mammalian datasets. | Harmonized cell atlas, peripheral nervous system, RNA-Seq, dorsal root ganglion, trigeminal ganglia, | is related to: NIH PRECISION Human Pain Network | Pain | Barry Family Harvard Stem Cell Institute Award ; Burroughs Wellcome Fund ; BWH Neurotechnology Studio ; BWH Women’s Brain Initiative ; Edwards PhD Studentship in Pain Research ; MGB Gene and Cell Therapy Institute ; Migraine Research Foundation ; NEI U01EY034709; NIDA DP1DA054343; NINDS R01NS119476; NINDS U19NS130607; NINDS U19NS130608; NINDS U19NS130617; Rita Allen Foundation ; Teva Pharmaceuticals |
DOI:10.1126/sciadv.adj9173 | Free, Freely available | https://github.com/Renthal-Lab/harmonized_atlas | SCR_025720 | 2026-09-12 01:04:50 | 4 | ||||||
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GSEApy Resource Report Resource Website 100+ mentions |
GSEApy (RRID:SCR_025803) | software resource, software toolkit, source code | Software Python package for performing gene set enrichment analysis. Used for characterizing gene expression changes by analysis of large single-cell datasets. | gene set enrichment analysis, characterizing gene expression changes, large single-cell datasets, | NIDA 5U01DA04439902 | PMID:36426870 | Free, Available for download, Freely available | https://github.com/zqfang/GSEApy | SCR_025803 | Gene Set Enrichment Analysis python | 2026-09-12 01:04:52 | 185 | |||||||
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Antibody Watch Resource Report Resource Website |
Antibody Watch (RRID:SCR_027424) | knowledge base | Text mining antibody specificity from literature. Helps researchers identify potential problems with antibody specificity. By mining the scientific literature and linking findings to Research Resource Identifiers (RRIDs), it provides alerts on antibodies that may yield unreliable results, supporting reproducibility in biomedical research. | Text mining antibody specificity, identify potential problems with antibody specificity, identify potential problems, antibody specificity, antibody, scientific literature, | Ministry of Science and Technology ; Taiwan ; NIDA U24DA039832; NIDDK U24DK097771 |
PMID:34043624 | Free, Freely available | SCR_027424 | 2026-09-12 01:05:27 | 0 | |||||||||
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hdWGCNA Resource Report Resource Website 10+ mentions |
hdWGCNA (RRID:SCR_027496) | software resource, software toolkit, source code | Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. | weighted gene co-expression network, high dimensional transcriptomics data, single-cell RNA-seq, transcriptomics | NIA 1RF1AG071683; NIA 3U19AG068054; NIA U54 AG054349; NIDA 1U01DA053826; NINDS P01NS084974 |
PMID:37426759 | Free, Available for download, Freely available | SCR_027496 | hd Weighted Gene Co-expression Network Analysis | 2026-09-12 01:05:28 | 10 | ||||||||
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Baby Open Brains Resource Report Resource Website |
Baby Open Brains (RRID:SCR_027836) | data or information resource, data set | Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD. | MRI, image, dataset of infant brain segmentations, infant brain, brain segmentation, manually curated infant brain segmentations, | uses: OpenNeuro | Bill & Melinda Gates Foundation ; NIDA U01DA041148; NIDA U24DA055330; NIMH R01 MH104324; NIMH R01MH096773; NIMH R01MH125829; NIMH R37MH125829; NIMH U01 MH110274; NINDS T32 NS109604 |
PMID:40813378 | Free, Freely available, | SCR_027836 | , BOBs, Baby Open Brains (BOBs) Dataset | 2026-09-12 01:05:37 | 0 | |||||||
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Conditioned Taste Aversion: An Annotated Bibliography Resource Report Resource Website 1+ mentions |
Conditioned Taste Aversion: An Annotated Bibliography (RRID:SCR_005953) | CTA | bibliography, data or information resource, database | A searchable, keyword-indexed bibliography on conditioned taste aversion learning, the avoidance of fluids and foods previously associated with the aversive effects of a variety of drugs. The database includes articles as early as 1951, and papers just published given that the database is ongoing and constantly updated. In the mid 1950''s, John Garcia and his colleagues at the Radiological Defense Laboratory at Hunters Point in San Francisco assessed the effects of ionizing radiation on a myriad of behaviors in the laboratory rat. One of their behavioral findings was that radiated rats avoided consumption of solutions that had been present during radiation, presumably due to the association of the taste of the solution with the aversive effects of the radiation. These results were published in Science and introduced to the literature the phenomenon of conditioned taste aversion learning (or the Garcia Effect). Subsequently, Garcia and his colleagues demonstrated that such learning appeared unique in a number of respects, including the fact that these aversions were acquired often in a single conditioning trial, selectively to gustatory stimuli and even when long delays were imposed between access to the solution and administration of the aversive agent. Together, these unique characteristics appeared to violate the basic tenets of traditional learning theory and along with a number of other behavioral phenomena (e.g., bird song learning, species-specific defense reactions, tonic immobility and schedule-induced polydipsia) introduced the concept of biological constraints on learning that forced a reconceptualization of the role evolution played in the acquisition of behavior (Garcia and Ervin, 1968; Revusky and Garcia, 1970; Rozin and Kalat, 1971). Although the initial investigations into conditioned taste aversion learning focused on these biological and evolutionary issues and their relation to learning, research in this area soon assessed the basic generality of the phenomenon, specifically, under what conditions such learning did or did not occur. With such research, a wide variety of gustatory stimuli were reported as effective conditioned stimuli and an extensive list of drugs with diverse consequences were reported as effective aversion-inducing agents. Aversions were established in a range of strains and species and under many experimental conditions. Research in this area continues to extend the conditions under which such learning occurs and to demonstrate its biological, neurochemical and anatomical substrates. Although the conditions under which aversion learning are reported to occur appear to generalize from the specific conditions under which they were originally reported, a number of factors including sex, age, training and testing procedures, deprivation level and drug history, all affect the rate of its acquisition and its terminal strength (Riley, 1998). In addition to these experimental demonstrations and assessments of generality, research on conditioned taste aversions has expanded to include investigations into its research and clinical applications (Braveman and Bronstein, 1985). In so doing, taste aversion learning has been applied to the characterization and classification of drug toxicity, the demonstration of the stimulus properties of abused drugs, the management of wildlife predation, the assessment of the etiology and treatment of cancer anorexia, the study of the biochemistry and molecular biology of learning, the etiology and control of alcohol use and abuse, the receptor characterization of the motivational effects of drugs, the occurrence of drug interactions, the characterization of drug withdrawal, the determination of taste psychophysics, the treatment of autoimmune diseases and the evaluation of the role of malaise in drug-induced satiety and drug-induced behavioral deficits. The speed with which aversions are acquired and the relative robustness of this preparation have made conditioned taste aversion learning a widely used, highly replicable and sensitive tool. In 1976, we published the first of three bibliographies on conditioned taste aversion learning. In this initial publication (see Riley and Baril, 1976), we listed and annotated 403 papers in this field. Subsequent lists published in 1977 (Riley and Clarke, 1977) and 1985 (Riley and Tuck, 1985) listed 632 and 1373 papers, respectively. Since that time, we have maintained a bibliography on taste aversion learning utilizing a variety of journal and on-line searches as well as benefiting from the generous contribution of preprints, reprints and pdf files from many colleagues. To date, the number of papers on conditioned taste aversion learning is approaching 3000. The present database lists these papers and provides a mechanism for searching the articles according to a number of search functions. Specifically, it was constructed to provide the reader access to these articles via a variety of search terms, including Author(s), Key Words, Date, Article Title and Journal. One can search for single or multiple items within any specific category. Further, one can search a single or combination of categories. The database is constantly being updated, and any feedback and suggestions are welcome and can be sent to CTALearning (at) american.edu. | taste aversion, learning, drug, aversive effect, literature, research, association, article, conditioned taste aversion, food avoidance | has parent organization: American University; Washington D.C.; USA | NIDA DA-04376 | PMID:15006479 | nif-0000-00085 | SCR_005953 | Conditioned Taste Aversion, Conditioned Taste Aversion Bibliography | 2026-09-12 12:56:33 | 3 | ||||||
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Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | data analysis software, data processing software, data visualization software, software application, software resource | A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality. | epigenomics, genome browser, clustering, visualization, genome, computation, pattern discovery, cluster |
is related to: Genboree Discovery System is related to: Roadmap Epigenomics Project has parent organization: BC Cancer Agency |
Canadian Institutes of Health Research ; Michael Smith Foundation for Health Research ; Natural Sciences and Engineering Research Council of Canada ; NIDA U01 DA025956; NIEHS 5U01ES017154-02; NHGRI HG004558 |
PMID:22960372 | Available for download without charge. Please cite. | nlx_151753 | SCR_006207 | Sparkinsight | 2026-09-12 12:56:36 | 417 | |||||
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Antibody Registry Resource Report Resource Website 100+ mentions |
Antibody Registry (RRID:SCR_006397) | data or information resource, data repository, database, service resource, storage service resource | Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload. | RIN, Resource Information Network, antibody, reagent, unique identifiers, RRID Community Authority, |
is used by: Resource Identification Portal is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: OMICtools is listed by: FORCE11 is listed by: re3data.org is listed by: Resource Information Network is related to: Novus Biologicals is related to: DOMEO is related to: Journal of Comparative Neurology Antibody database is related to: Integrated Manually Extracted Annotation has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Creative Commons Attribution License, The community can contribute to this resource | biodbcore-000182, nif-0000-07730, OMICS_01768, r3d100010408 | https://doi.org/10.17616/R3XG7N | SCR_006397 | AntibodyRegistry, AB Registry, The Antibody Registry, ABRegistry | 2026-09-12 12:56:39 | 111 | ||||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | catalog, data or information resource, data set, database, narrative resource, service resource, standard specification | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NCI ; NHGRI U01 HG004597; NHGRI U24 HG012556; NHGRI U41HG007050; NHLBI ; NIDA ; NIMHD ; NIMH ; NINDS ; OBSSR ; ODP ; TRSP |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-09-12 12:56:41 | 73 | ||||
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Eutectic NTS Resource Report Resource Website |
Eutectic NTS (RRID:SCR_008062) | Eutectic NTS | resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A hardware and software package with which a scientist could trace the structure of neurons and other neuroscientific features directly from tissue sections or from a stack of their images into a computer. Then it also could edit, merge, filter, display in 3D, and make realistic plots of the structures. The NTS also includes a substantial statistical package that provided many, now standardized, mathematical and statistical summaries that described each neuron and compared one population to another. Additionally, NTS also provided an embryonic electrotonic modeler that simulates and displayes the electrical functioning of a cell. The NTS uses a special purpose graphics display processor called the VDP3 whose output is presented on a very high resolution CRT. During tracing, the VDP3 presents a variable-diameter cursor and other information directly in the microscope and enables tracing at a high spatial resolution and with measurement of process diameters limited only by the microscope''s optics. Control of tracing is done with a 3D joystick that allows easy control of five input variables: X,Y,Z position, cursor diameter, and a numeric tag. Finally, superb 3D interactive displays of completed cells are provided on the VDP3. | embryonic electronic modeler, cell, hardware, microscope, neuron, optics, software, neuronal tree structure, dendritic tree, segmentation, instrument, equipment | NIDA contract HHSN271200577531C | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10453 | SCR_008062 | The Eutectic Neuron Tracing System | 2026-09-12 12:56:59 | 0 | |||||||
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Transdisciplinary Tobacco Use Research Centers Resource Report Resource Website |
Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) | TTURC | data or information resource, disease-related portal, portal, topical portal | A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment. | gene, genetic factor, addiction gene, behavioral treatment, biomarker, molecule, nicotine use disorder, prevention, psychosocial factor, smoking, smoking cessation, tobacco exposure, treatment, nicotine, prevention, tobacco, intervention | has parent organization: National Cancer Institute | Nicotine use disorder, Addiction | NCI ; NIDA ; NIAAA |
nif-0000-24133 | SCR_006858 | 2026-09-12 12:56:46 | 0 | |||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web application, web service | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NCI U24 CA159988; NIAAA U01 AA013512; NIAAA U01 AA016662; NIDA P01 DA015027; NIGMS R01 GM088822; NIMH P50 MH078028; NIMH P50 MH096972 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-09-12 12:56:45 | 3155 | ||||
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BMAP - Brain Molecular Anatomy Project Resource Report Resource Website 1+ mentions |
BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) | BMAP | data or information resource, funding resource, portal, topical portal | The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee |
has parent organization: National Institutes of Health is parent organization of: BMAP cDNA Resources |
Aging | NINDS ; NIMH ; NIDA ; NEI ; NIA ; NIAAA ; NICHD ; NIDCD ; NIEHS ; NHGRI ; NIGMS |
nlx_149083 | SCR_008852 | Brain Molecular Anatomy Project, Trans-NIH Brain Molecular Anatomy Project | 2026-09-12 12:57:09 | 6 | |||||||
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DOTS WM tract segmentation Resource Report Resource Website 100+ mentions |
DOTS WM tract segmentation (RRID:SCR_009459) | DOTS | data processing software, image analysis software, segmentation software, software application, software resource | A fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions. DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats. | magnetic resonance, diffusion tensor mr imaging, dti, fiber tract, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MIPAV: Medical Image Processing and Visualization is related to: JIST: Java Image Science Toolkit has parent organization: Johns Hopkins University; Maryland; USA |
NIDA K25DA025356 | PMID:21718790 | Free | nlx_155605 | SCR_009459 | Diffusion-Oriented Tract Segmentation White Matter tract segmentation, Diffusion-Oriented Tract Segmentation | 2026-09-12 12:57:12 | 116 | |||||
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ProbeMatchDB 2.0 Resource Report Resource Website |
ProbeMatchDB 2.0 (RRID:SCR_003433) | ProbeMatchDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. | experiment, human, microarray, mouse, oligo, operon, platform, probe, protein, proteomic, rate, sequence, study, gene, est, cdna, sts marker, orthologous gene, ortholog, microarray probe, nucleotide sequence |
is related to: UniGene is related to: HomoloGene has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan Microarray Network ; Nancy Pritzker Depression Research Network ; Department of Psychiatry pilot study ; NIMH L99 MH60398; NIDA R21 DA13754-01 |
PMID:11934751 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33156 | SCR_003433 | 2026-09-12 12:55:58 | 0 | ||||||
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Consortium for Reliability and Reproducibility Resource Report Resource Website 1+ mentions |
Consortium for Reliability and Reproducibility (RRID:SCR_003774) | CoRR | data or information resource, data set, portal | Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans | consortium, connectomics, reproducibility, resting state fmri, fmri, diffusion mri, neuroimaging, metadata standard, functional image, dti, anatomical image, functional, anatomical |
uses: Mind Research Network - COINS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project |
NIDA ; National Natural Science Foundation of China ; Child Mind Institute ; Institute of Psychology ; Chinese Academy of Sciences ; Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Registration required, (NITRC), Open unspecified license | nlx_158048 | SCR_003774 | Consortium for Reliability and Reproducibility (CoRR) | 2026-09-12 12:56:02 | 6 | ||||||
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Synapse Web Resource Report Resource Website 50+ mentions |
Synapse Web (RRID:SCR_003577) | atlas, data or information resource, image collection, narrative resource, training material | A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy. | electron microscopy, 3d reconstruction, neuroanatomy, astrocyte, axon, brain, cellular, dendrite, hippocampus, micrograph, microscopy, neurocytology, organelle, structure, synapse, tissue, ultrastructural, light microscopy, neuron, rat, experimental protocol, synapse structure |
is used by: NIF Data Federation has parent organization: University of Texas at Austin; Texas; USA |
The Human Brain Project ; NIDA R01 MH/DA 57351; NIMH R01 MH/DA 57351; NIBIB EB002170 |
Copyrighted, Acknowledgement required | nif-0000-00026 | SCR_003577 | SynapseWeb | 2026-09-12 12:56:00 | 73 |
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