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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MNE software Resource Report Resource Website 50+ mentions |
MNE software (RRID:SCR_005972) | MNE | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. | Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MNE-BIDS is related to: MATLAB is related to: NumPy is related to: SciPy is related to: Matplotlib is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project is related to: NiBabel |
NIBIB R01 EB009048; NIBIB P41 EB015896; NCRR P41 RR014075; NIDCD F32DC012456; NSF 0958669; NSF 1042134; European Research Council (ERC) StG-263584 |
PMID:24161808 PMID:24431986 |
Free, Available for download, Freely available | nlx_151346 | https://sources.debian.org/src/python3-mne/, http://www.nitrc.org/projects/mne, http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html, https://github.com/mne-tools/, https://mne.tools/ | SCR_005972 | Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python | 2026-08-04 09:41:28 | 97 | ||||
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ResearchMatch Resource Report Resource Website 100+ mentions |
ResearchMatch (RRID:SCR_006387) | ResearchMatch | portal, community building portal, people resource, patient registry, data or information resource | 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 | 2026-08-04 09:41:35 | 180 | |||||
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CTSA-IP Resource Report Resource Website |
CTSA-IP (RRID:SCR_006380) | CTSA-IP | portal, community building portal, database, data or information resource | 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 | 2026-08-04 09:41:35 | 0 | |||||
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BrainSuite Resource Report Resource Website 50+ mentions |
BrainSuite (RRID:SCR_006623) | BrainSuite | data processing software, software resource, software application, image analysis software, data visualization 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 | 2026-08-04 09:41:39 | 93 | |||||
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Comparative Toxicogenomics Database (CTD) Resource Report Resource Website 1000+ mentions |
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) | CTD | data analysis service, analysis service resource, production service resource, service resource, database, data or information 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 | 2026-08-04 09:41:37 | 1188 | ||||
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redcap-to-nda Resource Report Resource Website |
redcap-to-nda (RRID:SCR_016008) | data processing software, data management software, software resource, software application, data transfer software | Software for metadata-driven electronic data capture to export REDCap data dictionaries and data to the NIMH National Data Archive (NDA). Prepares data submissions as csv formatted spreadsheets for data dictionary spreadsheets and for data spreadsheets. | metadata, spreadsheet, format, electronic, capture, export, dictionary, bioinformatic |
is related to: Vanderbilt University; Tennessee; USA is related to: University of California at San Diego; California; USA |
NCRR ; NIDA U24 DA041123 |
Free, Available for download, Freely available | SCR_016010, SCR_016009 | SCR_016008 | Redcap: Research electronic data capture | 2026-08-04 09:43:47 | 0 | |||||||
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Leginon Resource Report Resource Website 10+ mentions |
Leginon (RRID:SCR_016731) | image acquisition software, data processing software, portal, storage service resource, software resource, software application, data repository, service resource, data acquisition software, data or information resource | System designed for automated collection of images from a transmission electron microscope. | automated, collection, acquisition, data, image, electron, microscope |
uses: Python Programming Language has parent organization: Scripps Research Institute |
NCRR RR17573; NIGMS GM61939; NSF DBI0352386; NSF DBI9730056; NSF DBI9904547 |
PMID:15890530 | Free, Available for download, Freely available, Registration suggested | SCR_016731 | 2026-08-04 09:43:58 | 42 | ||||||||
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | topical portal, portal, disease-related portal, data or information resource | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380; NCRR M01 RR00080 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-08-04 09:43:56 | 3 | ||||||
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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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MAPPFinder Resource Report Resource Website 10+ mentions |
MAPPFinder (RRID:SCR_005791) | MAPPFinder | data processing software, software application, software resource, data analysis software | MAPPFinder is an accessory program for GenMAPP. This program allows users to query any existing GenMAPP Expression Dataset Criterion against GO gene associations and GenMAPP MAPPs (microarray pathway profiles). The resulting analysis provides the user with results that can be viewed directly upon the Gene Ontology hierarchy and within GenMAPP, by selecting terms or MAPPs of interest. Platform: Windows compatible | gene, gene ontology, gene association, gene expression, profile, microarray, pathway, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at San Francisco; California; USA has parent organization: Gene Map Annotator and Pathway Profiler |
University of California at San Francisco; California; USA ; San Francisco General Hospital; California; USA ; NHLBI ; NCRR MO1RR00083 |
PMID:12540299 | Free for academic use | nlx_149270 | SCR_005791 | 2026-08-04 09:41:26 | 26 | ||||||
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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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IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | data processing software, source code, software resource, software application, image processing software, image analysis software | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-08-04 09:40:52 | 1585 | ||||
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i2b2 Cross-Institutional Clinical Translational Research project Resource Report Resource Website |
i2b2 Cross-Institutional Clinical Translational Research project (RRID:SCR_003367) | i2b2CICTR, i2b2-CICTR | topical portal, portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies. | exchange, biomedical, clinical, medical, pilot, retrospective, translational, integration, interoperability, information exchange environment, software network, data sharing, network, federation |
is listed by: Biositemaps is related to: SHRINE has parent organization: Informatics for Integrating Biology and the Bedside has parent organization: University of Washington; Seattle; USA |
NCRR Contract HHSN268200700031C | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33108 | SCR_003367 | 2026-08-04 09:40:53 | 0 | |||||||
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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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