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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-08-29 11:21:02 | 0 | |||||||
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Confocal Microscopy Image Gallery - Rat Brain Tissue Sections Resource Report Resource Website |
Confocal Microscopy Image Gallery - Rat Brain Tissue Sections (RRID:SCR_002432) | data or information resource, image collection | An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy. | image collection, gallery, function, amygdala, anatomy, blood vessel, brain, cerebellum, cerebral cortex, coronal, digital image, hippocampus, horizontal, hypothalamus, immunofluorescence, microscopy, model, neuron microscopy, rat, receptor, sagittal, thalamus, tissue | is provided by: Olympus | Free, Freely available | nif-0000-21299 | http://www.olympusconfocal.com/gallery/ratbrain/ | SCR_002432 | Olympus Rat Brain Tissue Sections | 2026-08-29 11:21:05 | 0 | |||||||
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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 | 2026-08-29 11:21:14 | 2 | ||||||
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GLIRT Resource Report Resource Website |
GLIRT (RRID:SCR_002390) | GLIRT | data processing software, image analysis software, registration software, software application, software resource | Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously. | analyze, application, c++, image-to-image, intersubject, linux, microsoft, motion analysis, magnetic resonance, posix/unix-like, registration, software, spatial transformation, temporal transformation, win32 (ms windows), windows |
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 |
Free | nlx_155763 | http://www.nitrc.org/projects/glirt | SCR_002390 | Groupwise and Longitudinal Image Registration Toolbox | 2026-08-29 11:21:19 | 0 | ||||||
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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 | 2026-08-29 11:21:20 | 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 | data or information resource, data set, narrative resource, training material | 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 | 2026-08-29 11:21:05 | 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, data repository, database, service resource, storage service resource | 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 | 2026-08-29 11:21:17 | 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 | 2026-08-29 11:21:18 | 53 | |||||||
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Public Health Image Library Resource Report Resource Website 100+ mentions |
Public Health Image Library (RRID:SCR_002463) | PHIL | data or information resource, database, 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) | 2026-08-29 11:21:15 | 109 | |||||
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BEETL-fastq Resource Report Resource Website |
BEETL-fastq (RRID:SCR_002341) | software resource | Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads. | Searchable compressed archive, DNA reads, compresses FASTQ-formatted DNA reads, bio.tools, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:24950811 | Free, Available for download, Freely available | OMICS_04900, biotools:beetl | https://bio.tools/beetl | SCR_002341 | 2026-08-29 11:21:03 | 0 | |||||||
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BRAINSFit Resource Report Resource Website 10+ mentions |
BRAINSFit (RRID:SCR_002340) | BRAINSFit | data processing software, image analysis software, registration software, software application, software resource | 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 | 2026-08-29 11:21:13 | 20 | |||||||
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HIBAL Resource Report Resource Website |
HIBAL (RRID:SCR_002461) | HIBAL | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. FORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002) | d18o, hydrologic isotopic balance model, paleolake, hydrology, hydrologic, isotopic, balance, model, fortran, discharge, evaporation, precipitation, fluid flux, record |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000127 | ftp://ftp.ncdc.noaa.gov/pub/data/paleo/softlib/hibal/hibal.txt | SCR_002461 | Hydrologic Isotopic Balance, HIBAL Hydrologic Isotopic Balance Model for Paleolake Systems | 2026-08-29 11:21:05 | 0 | ||||||
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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 | 2026-08-29 11:21:21 | 4 | ||||||
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Blood Group Antigen Gene Mutation Database Resource Report Resource Website |
Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) | BGMUT | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive. | blood, gene, genetic, allele, allelic, alteration, antigen, blood group, human, mutation, genetic variation, non-human animal, orthologous gene, orthologue, phenotype, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI dbRBC has parent organization: Albert Einstein College of Medicine; New York; USA has parent organization: Roswell Park Comprehensive Cancer Center has parent organization: Medical University of Graz; Graz; Austria has parent organization: Human Genome Variation Society |
Albert Einstein College of Medicine; New York; USA ; David Opochinsky/Blumenfeld Family Fund ; NIH |
PMID:22084196 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-21064, biotools:bgmut | https://bio.tools/bgmut | http://www.bioc.aecom.yu.edu/bgmut/index.htm, http://www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut | SCR_002297 | Blood Group Antigen Gene Mutation Database (BGMUT), BGMUT - Blood Group Antigen Gene Mutation Database | 2026-08-29 11:21:02 | 0 | |||
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NeuroScope Resource Report Resource Website 50+ mentions |
NeuroScope (RRID:SCR_002455) | NeuroScope | data processing software, data visualization software, software application, software resource | 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 | 2026-08-29 11:21:20 | 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 | 2026-08-29 11:21:03 | 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 | 2026-08-29 11:21:17 | 2 | ||||||||
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Multicomponent T2 estimation with stimulated echo correction Resource Report Resource Website |
Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) | Multicomponent T2 estimation with stimulated echo correction | software resource | Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches. | algorithm, matlab, magnetic resonance, mri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:23629849 | Free, Available for download, Freely available | nlx_155820 | SCR_002446 | 2026-08-29 11:21:05 | 0 | |||||||
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Variant Reporter Software Resource Report Resource Website 50+ mentions |
Variant Reporter Software (RRID:SCR_002329) | data analysis software, data processing software, sequence analysis software, software application, software resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation. |
comparative sequencing, mutation detection, snp discovery, sequence confirmation |
is listed by: OMICtools is listed by: Thermo Fisher Scientific has parent organization: Life Technologies |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01818 | http://www.lifetechnologies.com/order/catalog/product/4385261 | SCR_002329 | 2026-08-29 11:21:13 | 85 | ||||||||
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Hardin MD Resource Report Resource Website |
Hardin MD (RRID:SCR_002364) | data or information resource, database, image collection | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. A medical database with lists, or directories, of information in health and medicine and images of medical conditions. Users may search Hardin MD, browse through the Medical picture gallery, and sort search results by disease or alphabetical letter. | disease, health, medicine, database, directory, gallery, image collection | has parent organization: University of Iowa; Iowa; USA | AIDS, Autoimmune disease, Childrens disease, Herpes, Infectious disease, Skin disease, Sexually transmitted disease, Cancer, Heart disease | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-21186, r3d100011208 | https://doi.org/10.17616/R3G62Z | http://www.lib.uiowa.edu/hardin/md/ | SCR_002364 | Hardin Meta Directory | 2026-08-29 11:21:04 | 0 |
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