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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Mouse BIRN Atlasing Toolkit Resource Report Resource Website 1+ mentions |
Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) | MBAT | data processing software, software resource, software application, image analysis software, data visualization software | Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels. | gene expression, microarray, light microscopy, electron microscopy, mri imaging, analyze, gnome, java, kde, magnetic resonance, nifti, os independent, win32 (ms windows), mri, registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse Biomedical Informatics Research Network is related to: 3D MRI Atlas of Mouse Development has parent organization: Laboratory of Neuro Imaging |
NCRR U24 RR021760 | PMID:21176225 | Free, Freely available, Available for download | nif-0000-00039 | http://mbat.loni.ucla.edu/ | SCR_002814 | MouseBIRN Atlasing Toolkit | 2026-08-04 09:40:44 | 2 | ||||
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UMMC Center for Psychiatric Neuroscience Labs and Facilities Resource Report Resource Website |
UMMC Center for Psychiatric Neuroscience Labs and Facilities (RRID:SCR_002688) | UMMC CPN Labs & Facilities, UMMC CPN Labs and Facilities | biomaterial supply resource, brain bank, material resource, tissue bank | Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core. | postmortem, brain, tissue, imaging, molecular biology, genomics |
is listed by: One Mind Biospecimen Bank Listing is listed by: ScienceExchange is related to: University of Mississippi Medical Center Labs and Facilities is related to: University of Mississippi Medical Center Animal Behavior Core Facility has parent organization: University of Mississippi Medical Center; Mississippi; USA |
Depression, Normal, Mental disease | NCRR | Free | SciEx_8930 | SCR_002688 | CPN Research Resource Cores, University of Mississippi Medical Center Center for Psychiatric Neuroscience, UMMC Center for Psychiatric Neuroscience Research Resource Cores, UMMC Center for Psychiatric Neuroscience Labs & Facilities, UMMC CPN Research Resource Cores | 2026-08-04 09:40:42 | 0 | |||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data processing software, data analysis software, software resource, software application, data visualization software | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-08-04 09:40:48 | 23431 | |||||
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VIVO Resource Report Resource Website 50+ mentions |
VIVO (RRID:SCR_005246) | VIVO | portal, software resource, controlled vocabulary, software application, community building portal, service resource, ontology, data or information resource | Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work. | data sharing, network, semantic web, linked data, rdf, owl, database, people resource |
is listed by: BioPortal is related to: Clinical and Translational Science Awards Consortium is related to: DataStaR is related to: CTSAconnect is related to: CTSA ShareCenter has parent organization: University of Florida; Florida; USA |
NCRR U24 RR029822 | Open unspecified license | nlx_144266 | SCR_005246 | VIVO - enabling national networking of scientists | 2026-08-04 09:41:19 | 50 | ||||||
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PubBrain Resource Report Resource Website 1+ mentions |
PubBrain (RRID:SCR_005387) | PubBrain | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | A literature search and visualization tool that allows end users to enter any PubMed query and see that query rendered as a heatmap illustrating which regions of interest are most commonly mentioned within the search results. To use PubBrain, simply enter any valid PubMed search in the search box. | neuroanatomy |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: PubMed has parent organization: Poldracklab Portal |
NIMH RO1MH082795; NIMH PL1MH083271; NIDCR UL1DE019580; NCRR P20RR020750 |
nlx_144484 | http://www.nitrc.org/projects/pubbrain | SCR_005387 | PubBrain Database, pubbrain.org | 2026-08-04 09:41:22 | 8 | ||||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | data processing software, data visualization software, software application, software resource | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-08-04 09:40:13 | 0 | ||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, software resource, workflow software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-08-04 09:40:19 | 11 | |||
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Insight Segmentation and Registration Toolkit Resource Report Resource Website 50+ mentions |
Insight Segmentation and Registration Toolkit (RRID:SCR_001149) | ITK | topical portal, portal, software resource, data or information resource | Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | registration, segmentation, multidimension, image processing, reusable library, analyze, bshort/bfloat, c++, console (text based), dicom, java, minc2, nifti, nrrd, os independent, philips par/rec, python, tcl/tk |
uses: Laplace Beltrami Filter on QuadEdge Meshes uses: VTK is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is used by: Displacement Field Viewer is used by: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Vaa3D is related to: elastix is related to: VMTK in 3D Slicer is related to: NA-MIC Kit is related to: SimpleITK |
NIBIB EB006733; NIBIB EB008374; NIBIB EB009634; NCRR P41RR013218 |
Free, Available for download, Freely available | nif-0000-00319 | http://www.nitrc.org/projects/insighttoolkit | SCR_001149 | Insight Toolkit, National Library of Medicine Insight Segmentation and Registration Toolkit (ITK), Insight Segmentation and Registration Toolkit | 2026-08-04 09:40:19 | 83 | |||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data processing software, software application, software resource, data analysis software | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-08-04 09:40:28 | 9 | ||||
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Rat Resource and Research Center Resource Report Resource Website 100+ mentions |
Rat Resource and Research Center (RRID:SCR_002044) | NRRRC, RRRC, NCRR RRRC | biomaterial supply resource, material resource, cell repository, organism supplier | Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. | RIN, Resource Information Network, embryo, gamete, animal, drug, biomedical, cryopreserved, disease, genome, genotyping, germplasma, human, hybrid, inbred, infectious, molecular, mutant, nuclear, ovarian, pathogen, rat, research, tissue, rat model, embryonic stem cell, reagent, protocol, cell line, stem cell, strain, database, catalog, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NIH Office of the Director P40 OD011062; NCRR P40 RR016939 |
Free | nif-0000-12085 | http://www.nrrrc.missouri.edu/ | SCR_002044 | National Rat Resource Research Center, National Center for Research Resources, Rat Resource & Research Center, Rat Resource and Research Center, Rat Resource Research Center, NCRR | 2026-08-04 09:40:32 | 219 | |||||
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Yerkes National Primate Research Center Resource Report Resource Website 1000+ mentions |
Yerkes National Primate Research Center (RRID:SCR_001914) | portal, organization portal, data or information resource, service resource | Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders. | NPRC, NPRC Consortium, ORIP, alzheimers disease, brain, immunology, microbiology, neurological disease, parkinsons disease, rodent, non human primate, neuropharmacology, cognitive neuroscience, developmental neuroscience, genetics |
is listed by: National Primate Research Center Consortium is related to: National Chimpanzee Brain Resource has parent organization: Emory University; Georgia; USA has parent organization: National Center for Research Resources - Primate Resources is parent organization of: Yerkes Collection Non-Human Primate Resource |
Neurological disease, Psychiatric disorder, Infectious disease, Non-infectious disease, Drug addiction, Alzheimer's disease, Parkinson's disease, AIDS, Malaria | NCRR P51 RR000165; NIH Office of the Director P51 OD011132; NIH Office of the Director U42 OD011023 |
Public, Available to researchers | nif-0000-10485 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_001914 | Yerkes Primate Research Center, Yerkes Research Center | 2026-08-04 09:40:30 | 1313 | |||||
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Wisconsin National Primate Research Center Resource Report Resource Website 1+ mentions |
Wisconsin National Primate Research Center (RRID:SCR_012987) | WNPRC | topical portal, portal, data or information resource, service resource | Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public. | NPRC, NPRC Consortium, ORIP, ecosystem, embryonic, fertility, fetal, gene, animal, ctl, development, differentiation, disease, hiv, immunodeficiency, immunogenetic, medicine, metabolic, molecular, neuroendocrinology, obesity, ocular, ovarian, parkinson's disease, polycystic, presbyopia, primate, reproduction, restriction, stem cell, t-cell, vaccine, virology, virus, caloric restriction, obesity, diabetes mellitus, osteoporosis, ocular aging, glaucoma, neurodegeneration, gene expression profiling, simian immunodeficiency virus, cytotoxic t cell, embryonic stem cell, fertility regulation, embryonic differentiation, maternal-fetal health, reproductive neuroendocrinology, polycystic ovarian syndrome, endometriosis, reproductive tract, gene therapy |
is listed by: Biositemaps is listed by: National Primate Research Center Consortium is related to: NIA Nonhuman Primate Tissue Bank has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: Primate Info Net is parent organization of: Wisconsin National Primate Research Center Pathology Services Core Facility |
Aging | NCRR RR000167; NIH Office of the Director P51 OD011106 |
Available to the research community | nif-0000-24362 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_012987 | 2026-08-04 09:43:07 | 3 | |||||
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Laplace Beltrami Filter on QuadEdge Meshes Resource Report Resource Website |
Laplace Beltrami Filter on QuadEdge Meshes (RRID:SCR_014133) | data processing software, software application, software resource, data acquisition software | A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface. | data acquisition software, filter, laplace beltrami, surface harmonic |
is used by: Insight Segmentation and Registration Toolkit is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
NIBIB R01-EB008171-01A1; NCRR P41-RR015241 |
Available to the research community | SCR_014133 | Laplace-Beltrami Filter on QuadEdge Meshes | 2026-08-04 09:43:20 | 0 | ||||||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data processing software, software application, software resource, data analysis software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-08-04 09:43:20 | 2805 | ||||||||
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MRM NeAt (Neurological Atlas) Mouse Brain Database Resource Report Resource Website 1+ mentions |
MRM NeAt (Neurological Atlas) Mouse Brain Database (RRID:SCR_007053) | MRM NeAt | image collection, reference atlas, atlas, database, data or information resource | Comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. This database consists of: Individual MRI images of mouse brains; three types of atlases: individual atlases, minimum deformation atlases and probabilistic atlases; the associated quantitative structural information, such as structural volumes and surface areas. Quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, have been computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities. You must register First (Mandatory) and then you may Download Images and Data. | phenotype, mouse, brain, computational biology, in vivo, mouse brain atlas, magnetic resonance microscopy, mouse brain morphometry, image registration, in vitro, 3d brain atlas, adult mouse, male, c57bl/6j, autosegmentation, probabilistic atlas, t2 weighted protocol |
is related to: Mouse Brain Image Visualizer (MBIV) is related to: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery has parent organization: University of Florida; Florida; USA is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database Image Gallery |
National High Magnetic Field Laboratory ; NIBIB R01 EB 0023304; NCRR P41 RR16105; NIMH P50 MH58911 |
PMID:16165303 PMID:18958199 |
Registration required | nlx_59497 | http://brainatlas.mbi.ufl.edu | SCR_007053 | Magnetic Resonance Microimaging Neurological Atlas Mouse Brain Database, MRM Neurological Atlas Mouse Brain Database, C57BL/6J Mouse Atlas, Atlas of Adult C57BL/6J Mouse Brain, MRM NeAt Mouse Brain Database | 2026-08-04 09:41:45 | 8 | ||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | topical portal, portal, data or information resource | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-08-04 09:41:49 | 2 | |||||
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BIRN Coordinating Center Resource Report Resource Website |
BIRN Coordinating Center (RRID:SCR_007290) | BIRN-CC | portal, systems interoperability software, software resource, software application, organization portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. It was established to develop, implement and support the information infrastructure necessary to achieve large-scale data sharing among the test bed participants (function, morphometry and mouse birn). The BIRN-CC consists of a unique and well-established partnership between computer scientists, neuroscientists and engineers. This partnership addresses a large array of technical, policy, and architectural issues to fundamentally enable a new suite of information technology supported database and analysis tools that allow scientists to analyze and interpret significantly larger sets of data than is possible in the traditional single-institution study paradigm. | fmri, 3d models, anatomy, atlas, data management, data storage, dohhs architecture, imaging, map, model, mri, neuroinformatics, ontology, portal, software, talairach, warping |
has parent organization: University of Southern California; Los Angeles; USA has parent organization: University of Chicago; Illinois; USA has parent organization: University of California at Irvine; California; USA has parent organization: University of California at Los Angeles; California; USA |
NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00068 | SCR_007290 | 2026-08-04 09:41:49 | 0 | |||||||
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Manual Align RTS2000 Resource Report Resource Website |
Manual Align RTS2000 (RRID:SCR_007107) | data processing software, software application, image processing software, software resource | Software program to adjust the alignment of two adjacent images. Allows to correct for any misalignment that may occur during auto-alignment step. Serves as a bootstrap to get the images in approximately the right place. | alignment, process, image, adjust, correct, misalignment |
is affiliated with: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Center for Microscopy and Imaging Research |
NCRR P41 RR04050 | Free, no longer available | nif-0000-10514 | SCR_007107 | 2026-08-04 09:41:45 | 0 | ||||||||
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Stimulate Resource Report Resource Website 10+ mentions |
Stimulate (RRID:SCR_007375) | data processing software, data analysis software, software resource, software application, data visualization software | An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays. | fmri, workflow, data visualization software, data analysis software | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | NCRR RR08079 | Free for use by non-profit research institutions, Not to be sold or used for profit. | nif-0000-00344 | SCR_007375 | 2026-08-04 09:41:51 | 10 | ||||||||
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Madison Metabolomics Consortium Database Resource Report Resource Website 50+ mentions |
Madison Metabolomics Consortium Database (RRID:SCR_007803) | MMCD | resource, database, data or information resource | A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria. | database, metabolomics, metabolite, consortium, nmr, mas spectroscopy, FASEB list |
is listed by: 3DVC has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NIDDK R21 DK070297; NCRR P41 RR02301 |
PMID:18259166 | Public | nif-0000-03148 | SCR_007803 | Madison Metabolomics Consortium Database (MMCD) | 2026-08-04 09:42:00 | 60 |
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