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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cancer Genomics Consortium Resource Report Resource Website 1+ mentions |
Cancer Genomics Consortium (RRID:SCR_002384) | CGC | portal, community building portal, data or information resource, organization portal | Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. | cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics | is listed by: OMICtools | Cancer | Membership fee, Account required | OMICS_01776 | SCR_002384 | CCMC, Cancer Cytogenomics Microarray Consortium | 2026-08-20 09:25:43 | 6 | ||||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | storage service resource, service resource, data or information resource, data repository, database | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NIGMS R01 GM123489; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA U01 AA014425; NIA R01 AG043930; NIDA P20 DA21131; NCI U01 CA105417; NCRR U24 RR021760 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-08-20 09:25:46 | 499 | |||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | software application, data processing software, software resource, data analysis software | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-08-20 09:25:47 | 17 | ||||||
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Clinical and Laboratory Standards Institute Resource Report Resource Website 100+ mentions |
Clinical and Laboratory Standards Institute (RRID:SCR_002382) | CLSI | narrative resource, knowledge environment, standard specification, data or information resource | A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world. | clinical, laboratory testing, quality, clinical laboratory testing standard, laboratory, testing | is listed by: OMICtools | Membership fee | OMICS_01777 | SCR_002382 | 2026-08-20 09:25:50 | 195 | ||||||||
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Neuroscience Course - Atlas Images Resource Report Resource Website 1+ mentions |
Neuroscience Course - Atlas Images (RRID:SCR_002381) | portal, training resource, data or information resource | Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections. | anatomy atlas, brain dissection, spinal cord dissection | has parent organization: University of Arkansas; Arkansas; USA | Public, Unauthorized use is prohibited | nif-0000-00117 | SCR_002381 | Neuroscience Course Atlas Images | 2026-08-20 09:25:43 | 7 | ||||||||
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Resource Ontology Discussion Group Resource Report Resource Website |
Resource Ontology Discussion Group (RRID:SCR_002536) | Resource Ontology Discussion Group | narrative resource, discussion, knowledge environment, data or information resource | Project to discuss, debate, develop and deploy ontological practices for the fMRI community. | community, ontology, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155943 | SCR_002536 | 2026-08-20 09:25:47 | 0 | ||||||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | software application, simulation software, software resource | MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications. | optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Oregon Health and Science University; Oregon; USA |
PMID:9421660 PMID:19256707 |
Free, Available for download, Freely available | nlx_155791 | http://www.nitrc.org/projects/mcml | SCR_002419 | Monte Carlo for Multi-Layered media | 2026-08-20 09:25:51 | 0 | |||||
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Rodent Cortical Thickness Analysis Resource Report Resource Website |
Rodent Cortical Thickness Analysis (RRID:SCR_002539) | software application, image processing software, data processing software, image analysis software, software resource | An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling | microscopy, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155946 | http://www.nitrc.org/projects/rodentthickness | SCR_002539 | RodentThickness | 2026-08-20 09:25:47 | 0 | |||||||
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Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | narrative resource, data or information resource, training material, book | Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. | r, programming language, code | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01760 | SCR_002417 | Quick-R - accessing the power of R | 2026-08-20 09:25:47 | 5 | |||||||
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Rodent Brain Extraction Tool Resource Report Resource Website |
Rodent Brain Extraction Tool (RRID:SCR_002538) | rBET | software application, image processing software, data processing software, software resource | A modified version of the Brain Extraction Tool (BET) that can process rodent brains. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: King's College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_155945 | http://www.nitrc.org/projects/rbet | SCR_002538 | 2026-08-20 09:25:50 | 0 | |||||||
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NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | software application, data processing software, software resource, image analysis software, registration software | Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. | analyze, artifact removal, c++, image-to-image, intermodal, linux, macos, microsoft, magnetic resonance, nifti, nonlinear warp, posix/unix-like, registration, spatial transformation, warping, windows, windows xp, fmri, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155893 | SCR_002496 | 2026-08-20 09:25:46 | 0 | ||||||||
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NITRC Enhanced Services Resource Report Resource Website |
NITRC Enhanced Services (RRID:SCR_002494) | NITRC Enhanced Services | portal, community building portal, data or information resource, service resource | Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data. | data, database, data resource, dicom, domain independent, information resource, nifti, platform or development environment, software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NITRC Computational Environment is related to: NITRC-IR has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155890 | SCR_002494 | 2026-08-20 09:25:49 | 0 | ||||||||
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realSFS Resource Report Resource Website 10+ mentions |
realSFS (RRID:SCR_002493) | software application, data processing software, software resource, data analysis software | Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | allele frequency estimation, snp calling | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00071 | SCR_002493 | 2026-08-20 09:25:53 | 27 | |||||||||
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PaleoVu Resource Report Resource Website |
PaleoVu (RRID:SCR_002411) | PaleoVu | software application, data visualization software, data processing software, software resource | A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data. | browse, visualization, paleo, paleoclimatology, ecology, paleoclimate, climate, query, windows, macintosh, paleoecological |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
Free | SciRes_000130 | SCR_002411 | 2026-08-20 09:25:51 | 0 | ||||||||
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NIRAL Utilities Resource Report Resource Website |
NIRAL Utilities (RRID:SCR_002490) | NIRAL Utilities | image processing software, software application, data processing software, image analysis software, software resource | Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images | analyze, c++, console (text based), linux, macos, microsoft, magnetic resonance, nrrd, posix/unix-like |
is used by: NeoSegPipeline is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Free, Freely avaialble | nlx_155884 | SCR_002490 | 2026-08-20 09:25:49 | 0 | ||||||||
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PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | software application, data processing software, data visualization software, software toolkit, software library, software resource | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer, https://sources.debian.org/src/python3-surfer/ | SCR_002524 | 2026-08-20 09:25:54 | 29 | |||||||
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ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | software application, data processing software, data analysis software, simulation software, sequence analysis software, software resource | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-08-20 09:25:50 | 35 | ||||||
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ModelGUI Resource Report Resource Website 1+ mentions |
ModelGUI (RRID:SCR_002441) | mgui | software application, data processing software, rendering software, data visualization software, software resource | An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework | clipping, database application, domain independent, gifti, image display, java, nifti, os independent, platform, development environment, rendering, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, java | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155816 | http://www.nitrc.org/projects/modelgui | SCR_002441 | 2026-08-20 09:25:47 | 1 | |||||||
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Spanish Resting State Network Resource Report Resource Website |
Spanish Resting State Network (RRID:SCR_002562) | SRSN | portal, community building portal, data or information resource | Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.) | microsoft word document, magnetic resonance, nifti, pdf, spanish |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project |
Free | nlx_155968 | SCR_002562 | 2026-08-20 09:25:51 | 0 | ||||||||
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MultiTracer Resource Report Resource Website 10+ mentions |
MultiTracer (RRID:SCR_002445) | MultiTracer | software application, data visualization software, data processing software, software resource | A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set. | analyze, computed tomography, image display, java, manual, magnetic resonance, nifti, os independent, pet, spect, region growing, segmentation, three dimensional display, two dimensional display, visualization, volumetric analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA has parent organization: Laboratory of Neuro Imaging |
PMID:12948737 | Free, Available for download, Freely available | nlx_155819 | http://www.nitrc.org/projects/multitracer2 | SCR_002445 | MultiTracer version 2 | 2026-08-20 09:25:52 | 11 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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