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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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IDbases Resource Report Resource Website 10+ mentions |
IDbases (RRID:SCR_002378) | data or information resource, database, service resource, storage service resource, data repository | 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 | 2026-08-08 11:57:40 | 16 | ||||||||
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ModelGUI Resource Report Resource Website 1+ mentions |
ModelGUI (RRID:SCR_002441) | mgui | software resource, software application, rendering software, data visualization software, data processing software | 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 | 2026-08-08 11:57:41 | 1 | |||||||
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MultiTracer Resource Report Resource Website 10+ mentions |
MultiTracer (RRID:SCR_002445) | MultiTracer | software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 11:57:41 | 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 | 2026-08-08 11:57:41 | 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 | data or information resource, image analysis software, atlas, software resource, software application, data processing software | 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 | 2026-08-08 11:57:40 | 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 | 2026-08-08 11:57:40 | 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 | 2026-08-08 11:57:49 | 7 | ||||||||
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MriWatcher Resource Report Resource Website 1+ mentions |
MriWatcher (RRID:SCR_002318) | MriWatcher | software resource, software application, data visualization software, data processing software | 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 | 2026-08-08 11:57:40 | 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 | training material, narrative resource, data or information resource, book | 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) | 2026-08-08 11:57:41 | 23 | |||||||
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VS-Lite Resource Report Resource Website 1+ mentions |
VS-Lite (RRID:SCR_002431) | VS-Lite | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation. | model, mathematical model, tree ring, dendrochronology, tree ring width, tree, ring, ring growth model |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
NOAA ; NSF 0724802 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000128 | SCR_002431 | Vaganov-Shashkin-Lite, Vaganov-Shashkin-Lite Model of Tree-Ring Width | 2026-08-08 11:57:41 | 2 | ||||||
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ANOVA Resource Report Resource Website 100+ mentions |
ANOVA (RRID:SCR_002427) | ANOVA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided. | model program, anomaly, anomaly, climate, variance, climate anomaly, matlab |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
PMID:27406694 PMID:15866832 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000129 | SCR_002427 | Analysis of Variance | 2026-08-08 11:57:50 | 346 | ||||||
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MS lesion segmentation challenge 2008 Resource Report Resource Website 1+ mentions |
MS lesion segmentation challenge 2008 (RRID:SCR_002425) | MS Lesion Segmentation 08 | training material, narrative resource, data or information resource, data set | Training material for the MS lesion segmentation challenge 2008 to compare different algorithms to segment the MS lesions from brain MRI scans. Data used for the workshop is composed of 54 brain MRI images and represents a range of patients and pathology which was acquired from Children's Hospital Boston and University of North Carolian. Data has initially been randomized into three groups: 20 training MRI images, 24 testing images for the qualifying and 8 for the onsite contest at the 2008 workshop. The downloadable online database consists now of the training images (including reference segmentations) and all the 32 combined testing images (without segmentations). The naming has not been changed in comparison to the workshop compeition in order to allow easy comparison between the workshop papers and the online database papers. One dataset has been removed (UNC_test1_Case02) due to considerable motion present only in its T2 image (without motion artifacts in T1 and FLAIR). Such a dataset unfairly penalizes methods that use T2 images versus methods that don't use the T2 image. Currently all cases have been segmented by expert raters at each institution. They have significant intersite variablility in segmentation. MS lesion MRI image data for this competition was acquired seperately by Children's Hospital Boston and University of North Carolina. UNC cases were acquired on Siemens 3T Allegra MRI scanner with slice thickness of 1mm and in-plane resolution of 0.5mm. To ease the segmentation process all data has been rigidly registered to a common reference frame and resliced to isotrophic voxel spacing using b-spline based interpolation. Pre-processed data is stored in NRRD format containing an ASCII readable header and a separate uncompressed raw image data file. This format is ITK compatible. If you want to join the competition, you can download data set from links here, and submit your segmentation results at http://www.ia.unc.edu/MSseg after registering your team. They require team name, password, and email address for future contact. Once experiment is completed, you can submit the segmentation data in a zip file format. Please refer submission page for uploading data format. | magnetic resonance, competition, challenge, segmentation, segment, ms lesion, brain, mri scan, mri, image collection |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
Multiple Sclerosis | NIH Roadmap for Medical Research ; NIBIB U54 EB005149-01 |
Free, Available for download, Freely available | nlx_155799 | SCR_002425 | 2008 MICCAI MS Lesion Segmentation Challenge | 2026-08-08 11:57:41 | 1 | |||||
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CIBEX: Center for Information Biology gene EXpression database Resource Report Resource Website 1+ mentions |
CIBEX: Center for Information Biology gene EXpression database (RRID:SCR_002307) | CIBEX | data or information resource, database, service resource, storage service resource, data repository | Gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. It serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data. | gene expression, gene, mass spectrometry, microarray, mrna, proteomic, miame, serial analysis of gene expression |
is related to: MIAME has parent organization: DNA DataBank of Japan (DDBJ) |
Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; JST-BIRD |
PMID:14744116 PMID:15669238 |
Public, The community can contribute to this resource | nif-0000-21088 | http://cibex.nig.ac.jp/index.jsp | SCR_002307 | Center for Information Biology gene EXpression database | 2026-08-08 11:57:49 | 7 | ||||
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DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-08-08 11:57:49 | 53 | |||||||
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Public Health Image Library Resource Report Resource Website 100+ mentions |
Public Health Image Library (RRID:SCR_002463) | PHIL | database, data or information resource, image collection | Database of CDC's pictures organized into hierarchical categories of people, places, and science, presented as single images, image sets, and multimedia files. Much of the information critical to the communication of public health messages is pictorial rather than text-based. Created by a Working Group at the Centers for Disease Control and Prevention (CDC), the PHIL offers an organized, universal electronic gateway to CDC's pictures. Public health professionals, the media, laboratory scientists, educators, students, and the worldwide public are welcome to use this material for reference, teaching, presentation, and public health messages. | illustration, multimedia, people, place, public health, electron micrograph, environmental health, bio-terrorism, health behavior, photograph, influenza, natural disaster, FASEB list |
is related to: MeSH has parent organization: Centers for Disease Control and Prevention |
Centers for Disease Control and Prevention | Free, Freely available | nif-0000-21325 | http://phil.cdc.gov/phil/default.asp | SCR_002463 | Public Health Image Library (PHIL) | 2026-08-08 11:57:42 | 109 | |||||
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BRAINSFit Resource Report Resource Website 10+ mentions |
BRAINSFit (RRID:SCR_002340) | BRAINSFit | registration software, image analysis software, software resource, software application, data processing software | A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3 | affine warp, analyze, c++, console (text based), dicom, image-to-image, intermodal, intersubject, linear warp, macos, microsoft, magnetic resonance, nifti, os independent, posix/unix-like, registration, spatial transformation, warping, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155701 | http://www.nitrc.org/projects/multimodereg | SCR_002340 | 2026-08-08 11:57:40 | 20 | |||||||
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University of Arizona; Arizona; USA Resource Report Resource Website 1+ mentions |
University of Arizona; Arizona; USA (RRID:SCR_002459) | UA | university | Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine. | public research university, arizona |
is related to: University of Arizona CBC Glassblowing Core Facility is parent organization of: Bio Resource for Array Genes Database is parent organization of: Plantagora is parent organization of: Center for Gamma Ray Imaging is parent organization of: TCW is parent organization of: Bird Base is parent organization of: Arizona Cancer Center Tumor Bank is parent organization of: Tree of Life Web Project is parent organization of: HIV and its Coreceptors is parent organization of: Arizona Center for Education and Research on Therapeutics is parent organization of: AGI is parent organization of: GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database is parent organization of: UA Neuroscience GIDP is parent organization of: ChromDB- the chromatin database is parent organization of: Newbler is parent organization of: Arizona Genetics Core is parent organization of: UA Department of Chemistry and Biochemistry Labs and Facilities is parent organization of: University of Arizona Labs and Facilities is parent organization of: UA Infectious Disease Resource Core is parent organization of: University of Arizona Nuclear Magnetic Resonance Core Facility is parent organization of: PhenoGO is parent organization of: FlyBrain is parent organization of: MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System is parent organization of: CyVerse is parent organization of: iMicrobe is parent organization of: Arizona University Genetics Core Facility is parent organization of: University of Arizona Molecular Structures Core Facility is parent organization of: University of Arizona Electron Photoemission Spectroscopy and Imaging Laboratory for Observation at the Nanoscale Core Facility is parent organization of: University of Arizona Xray Diffraction Core Facility is parent organization of: University of Arizona Laboratory for Electron Spectroscopy and Surface Analysis Core Facility is parent organization of: University of Arizona W.M. Keck Center for Nano Scale Imaging Core Facility is parent organization of: University of Arizona Electron Paramagnetic Resonance Core Facility is parent organization of: University of Arizona CBC Electronics Core Facility is parent organization of: University of Arizona CBC Machine Shop Core Facility is parent organization of: University of Arizona Imaging Cores Electron Core Facility is parent organization of: University of Arizona Imaging Cores Optical Core Facility is parent organization of: University of Arizona Analytical and Biological Mass Spectrometry Core Facility is parent organization of: University of Arizona Functional Genomics Core Facility is parent organization of: University of Arizona Flow Cytometry and Human Immune Monitoring Shared Resource Core Facility is parent organization of: University of Arizona Phenotyping Core Facility is parent organization of: Planet Microbe is parent organization of: University of Arizona Molecular Clinical Core Facility |
Free | ISNI:0000 0001 2168 186X, grid.134563.6, nlx_13022, Crossref funder ID:100007899, Wikidata:Q503419 | https://ror.org/03m2x1q45 | SCR_002459 | U of A, University of Arizona, UofA | 2026-08-08 11:57:50 | 4 | ||||||
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NeuroScope Resource Report Resource Website 50+ mentions |
NeuroScope (RRID:SCR_002455) | NeuroScope | software resource, software application, data visualization software, data processing software | An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. | eeg, meg, electrocorticography, behavior, neuronal spike, behavioral event, edit |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Buzsaki Lab |
PMID:16580733 | Free, Freely available | nlx_155828 | SCR_002455 | 2026-08-08 11:57:50 | 88 | |||||||
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RepARK Resource Report Resource Website 1+ mentions |
RepARK (RRID:SCR_002333) | software resource | Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome. | standalone software | is listed by: OMICtools | PMID:24634442 | OMICS_03446 | SCR_002333 | Repetitive motif detection by Assembly of Repetitive K-mers | 2026-08-08 11:57:40 | 7 | ||||||||
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Advanced Targeting Systems Resource Report Resource Website 1+ mentions |
Advanced Targeting Systems (RRID:SCR_002328) | ATS | commercial organization | Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders. | antibody supplier, biomedical research resource, targeting reagent | Commercially available | nlx_152256, grid.422052.3 | https://ror.org/01tzmft44 | SCR_002328 | 2026-08-08 11:57:49 | 2 |
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