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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clinical and Laboratory Standards Institute Resource Report Resource Website 100+ mentions |
Clinical and Laboratory Standards Institute (RRID:SCR_002382) | CLSI | data or information resource, knowledge environment, narrative resource, standard specification | 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 | 2026-09-12 12:55:40 | 195 | ||||||||
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Neuroscience Course - Atlas Images Resource Report Resource Website 1+ mentions |
Neuroscience Course - Atlas Images (RRID:SCR_002381) | data or information resource, portal, training 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 | 2026-09-12 12:55:40 | 7 | ||||||||
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MCML and CONV Resource Report Resource Website |
MCML and CONV (RRID:SCR_002419) | MCML, MCML & CONV, CONV | simulation software, software application, 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 | 2026-09-12 12:55:40 | 0 | |||||
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Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | book, data or information resource, narrative resource, training material | 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 | 2026-09-12 12:55:40 | 5 | |||||||
|
NPTK Resource Report Resource Website |
NPTK (RRID:SCR_002496) | NPTK | data processing software, image analysis software, registration software, software application, software resource | 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 | 2026-09-12 12:55:41 | 0 | ||||||||
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NITRC Enhanced Services Resource Report Resource Website |
NITRC Enhanced Services (RRID:SCR_002494) | NITRC Enhanced Services | community building portal, data or information resource, portal, 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 | 2026-09-12 12:55:41 | 0 | ||||||||
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realSFS Resource Report Resource Website 10+ mentions |
realSFS (RRID:SCR_002493) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:55:41 | 27 | |||||||||
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IDbases Resource Report Resource Website 10+ mentions |
IDbases (RRID:SCR_002378) | data or information resource, data repository, database, service resource, storage service resource | IDbases are locus-specific databases for immunodeficiency-causing mutations. Our aim is to establish database for every immunodeficiency or provide links to those maintained elsewhere. IDbases contain in addition to gene mutation, also information about clinical presentation. Information has been collected from literature as well as received directly from researchers. It would be most glad if those analyzing mutations would send their information by using the interactive web submission available in each database. A number of articles have been published related to IDbases. IDbases are curated and distributed with proprietary MUTbase software suite. | gene, clinical, database, immunodeficiency, immunological database, locus, mutation, presentation, specific | has parent organization: University of Tampere; Tampere; Finland | PMID:17004234 | nif-0000-21214 | SCR_002378 | IDbases | 2026-09-12 12:55:40 | 16 | ||||||||
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PaleoVu Resource Report Resource Website |
PaleoVu (RRID:SCR_002411) | PaleoVu | data processing software, data visualization software, software application, 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 | 2026-09-12 12:55:40 | 0 | ||||||||
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NIRAL Utilities Resource Report Resource Website |
NIRAL Utilities (RRID:SCR_002490) | NIRAL Utilities | data processing software, image analysis software, image processing software, software application, 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 | 2026-09-12 12:55:41 | 0 | ||||||||
|
ModelGUI Resource Report Resource Website 1+ mentions |
ModelGUI (RRID:SCR_002441) | mgui | data processing software, data visualization software, rendering software, software application, 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 | 2026-09-12 12:55:41 | 1 | |||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-09-12 12:55:41 | 0 | ||||||||
|
MultiTracer Resource Report Resource Website 10+ mentions |
MultiTracer (RRID:SCR_002445) | MultiTracer | data processing software, data visualization software, software application, 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 | 2026-09-12 12:55:41 | 11 | |||||
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Multi-Modal MRI Reproducibility Resource Resource Report Resource Website 10+ mentions |
Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) | Multi-Modal MRI Reproducibility Resource | data or information resource, image collection | Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047 | java image science toolkit, magnetic resonance, nifti, neuroimaging, reproducibility, mprage, flair, dti, resting state fmri, b0 field map, b1 field map, asl, vaso, quantitative t1 mapping, quantitative t2 mapping, magnetization transfer imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit |
Healthy | PMID:21094686 | Free, Available for download, Freely available | nlx_155818 | SCR_002442 | 2026-09-12 12:55:41 | 12 | ||||||
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Medical Image Visualization and Analysis Resource Report Resource Website 1+ mentions |
Medical Image Visualization and Analysis (RRID:SCR_002315) | MIVA | atlas, data or information resource, data processing software, image analysis software, software application, software resource | Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator. | magnetic resonance, fmri, graphical interface, display, segment, align, manipulate, blend, registration, alignment, region of interst, volume of interest, 3d geometry tool, 3d |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Worcester Polytechnic Institute; Massachusetts; USA |
BSD License | nlx_155664 | SCR_002315 | 2026-09-12 12:55:39 | 8 | ||||||||
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Cogprints: Cognitive Sciences EPrint Archive Resource Report Resource Website 1+ mentions |
Cogprints: Cognitive Sciences EPrint Archive (RRID:SCR_002314) | journal article | An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition. | ethnology, anthropology, archeology, biology, cognition, cognitive science, computer science, linguistics, mathematical, medicine, neuroscience, paleontology, philosophy, physical, psychology, science, scientific literature databases and services, social | has parent organization: University of Southampton; Southampton; United Kingdom | nif-0000-21093 | SCR_002314 | Cogprints | 2026-09-12 12:55:39 | 3 | |||||||||
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flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-09-12 12:55:39 | 7 | ||||||||
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MriWatcher Resource Report Resource Website 1+ mentions |
MriWatcher (RRID:SCR_002318) | MriWatcher | data processing software, data visualization software, software application, software resource | This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155667 | SCR_002318 | 2026-09-12 12:55:39 | 2 | ||||||||
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R Tutorial - An R Introduction to Statistics Resource Report Resource Website 10+ mentions |
R Tutorial - An R Introduction to Statistics (RRID:SCR_002394) | R Tutorial | book, data or information resource, narrative resource, training material | Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available. | r, statistics, gpu computing | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01762 | SCR_002394 | R Tutorial (An R Introduction to Statistics) | 2026-09-12 12:55:40 | 23 | |||||||
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MGDM: Multi Geometric Deformable Model Resource Report Resource Website |
MGDM: Multi Geometric Deformable Model (RRID:SCR_002311) | MGDM | data processing software, image analysis software, segmentation software, software application, software resource | An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming. | algorithm, reusable library, computed tomography, java, matlab, magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155658 | SCR_002311 | Multi Geometric Deformable Model | 2026-09-12 12:55:39 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
