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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Athens; Athens; Greece Resource Report Resource Website 1+ mentions |
University of Athens; Athens; Greece (RRID:SCR_002607) | UoA | university | Public university in Athens, Greece that offers degree programs in health sciences, law and economics, and theology. | public university in greece |
is related to: EARIP is related to: ORBITO is related to: International AMD Genetics Consortium is parent organization of: Digital Repository Infrastructure Vision for European Research is parent organization of: University of Athens Biophysics and Bioinformatics Laboratory |
Free | ISNI:0000 0001 2155 0800, grid.5216.0, Wikidata:Q547867, Crossref funder ID:501100005187, nlx_94434 | https://ror.org/04gnjpq42 | SCR_002607 | University of Athens, National and Kapodistrian University of Athens | 2026-08-15 11:22:17 | 6 | ||||||
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TurtleSeg Resource Report Resource Website 1+ mentions |
TurtleSeg (RRID:SCR_002605) | TurtleSeg | image analysis software, data processing software, software application, software resource, segmentation software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process. | analyze, c++, computed tomography, dicom, intensity contour, microsoft, minc, magnetic resonance, nifti, segmentation, win32 (ms windows), windows, windows nt/2000, windows vista, windows xp | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156008 | http://www.nitrc.org/projects/turtleseg | SCR_002605 | TurtleSeg - Interactive 3D Image Segmentation Software | 2026-08-15 11:22:16 | 6 | ||||||
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University of Arkansas for Medical Sciences; Arkansas; USA Resource Report Resource Website 10+ mentions |
University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) | UAMS | organization portal, data or information resource, department portal, portal | Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care. | translational medicine, public medical school |
is related to: Alzheimers Disease Genetics Consortium is related to: Clinical and Translational Science Awards Consortium has parent organization: University of Arkansas System; Arkansas; USA is parent organization of: UAMS Experimental Pathology Core Laboratory |
Free | grid.241054.6, nlx_152181, Wikidata:Q941298, Crossref funder ID:100008519, ISNI:0000 0004 4687 1637 | https://ror.org/00xcryt71 | SCR_002522 | University of Arkansas for Medical Sciences | 2026-08-15 11:22:15 | 41 | ||||||
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Open Journal Systems Resource Report Resource Website 1+ mentions |
Open Journal Systems (RRID:SCR_002642) | OJS | software resource | Open source software made freely available to journals worldwide for the purpose of making open access publishing a viable option for more journals, as open access can increase a journal's readership as well as its contribution to the public good on a global scale. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of refereed research. OJS Features # OJS is installed locally and locally controlled. # Editors configure requirements, sections, review process, etc. # Online submission and management of all content. # Subscription module with delayed open access options. # Comprehensive indexing of content part of global system. # Reading Tools for content, based on field and editors' choice. # Email notification and commenting ability for readers. # Complete context-sensitive online Help support. | journal management, publishing system, publication | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_156071 | SCR_002642 | 2026-08-15 11:22:18 | 1 | ||||||||
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PeptideShaker Resource Report Resource Website 100+ mentions |
PeptideShaker (RRID:SCR_002520) | software resource | Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data. | standalone software, proteomics, mass spectrometry, java, search engine, omssa, xtandem, mascot, ms-gf, msamanda, myrimatch, comet, tide |
is listed by: OMICtools is related to: MS Amanda has parent organization: Google Code |
PMID:34709836 | Free, Available for download, Freely available | OMICS_03347 | http://peptide-shaker.googlecode.com | SCR_002520 | 2026-08-15 11:22:16 | 164 | |||||||
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OpenDOAR Resource Report Resource Website 10+ mentions |
OpenDOAR (RRID:SCR_002641) | OpenDOAR | database, data repository, storage service resource, data or information resource, service resource | A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining. | open access, open data, repository, data sharing |
is listed by: FORCE11 is related to: DOAJ - Directory of Open Access Journals has parent organization: University of Nottingham; Nottingham; United Kingdom |
JISC | Free, Freely available | nlx_156070 | SCR_002641 | Directory of Open Access Repositories, The Directory of Open Access Repositories - OpenDOAR | 2026-08-15 11:22:17 | 40 | ||||||
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PHYCAA+: adaptive physiological noise correction for BOLD fMRI Resource Report Resource Website 1+ mentions |
PHYCAA+: adaptive physiological noise correction for BOLD fMRI (RRID:SCR_002514) | PHYCAA+ | data processing software, software application, image processing software, software resource | Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325 | algorithm, matlab, magnetic resonance, nifti, os independent, fmri, bold, bold fmri, multivariate, physiological noise |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Toronto; Ontario; Canada |
PMID:23727534 | GNU Lesser General Public License | nlx_155913 | SCR_002514 | 2026-08-15 11:22:16 | 7 | |||||||
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Memento Resource Report Resource Website 10+ mentions |
Memento (RRID:SCR_002634) | Memento | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An extension for Chrome to see a version of a resource as it existed at some date in the past, by entering that URI in your browser and by specifying the desired date in a browser plug-in. Or you can actually browse the Web of the past by selecting a date and clicking. Whatever you land upon will be versions of Web resources as they were around the selected date. (This will only work if previous versions are available somewhere on the Web.) | versioning, chrome, firefox, bookmarklet |
is listed by: FORCE11 has parent organization: Los Alamos National Laboratory has parent organization: Old Dominion University; Virginia; USA |
Library of Congress | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156058 | SCR_002634 | 2026-08-15 11:22:17 | 38 | |||||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | image repository, database, data repository, storage service resource, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | 2026-08-15 11:22:16 | 14 | |||||
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pIRS Resource Report Resource Website 50+ mentions |
pIRS (RRID:SCR_002519) | software application, simulation software, software resource | Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias. | de novo data simulation, empirical distribution, illumina pair-end read, substitution sequencing error, gc depth bias | is listed by: OMICtools | PMID:22508794 | Free, Available for download, Freely available | OMICS_00254 | SCR_002519 | pIRS (profile based Illumina pair-end Reads Simulator), profile based Illumina pair-end Reads Simulator | 2026-08-15 11:22:15 | 74 | |||||||
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PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-08-15 11:22:13 | 372 | |||
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Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) Resource Report Resource Website 10+ mentions |
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) | PDBP | storage service resource, service resource, biospecimen repository, material storage repository | Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders. | parkinson's, clinical neuroinformatics, magnetic resonance, diagnostic, progression, biomarker, clinical |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NINDS Repository is related to: MIPAV: Medical Image Processing and Visualization has parent organization: National Institute of Neurological Disorders and Stroke |
Parkinson's disease | nlm ; NINDS |
PMID:25976927 | Restricted | nlx_155919 | http://www.nitrc.org/projects/pdbp | http://pdbp.ninds.nih.gov/index.jsp | SCR_002517 | Parkinson's Disease Biomarkers Program, PDBP: Parkinsons Disease Biomarkers Program, Parkinson’s Disease Biomarkers Program Data Management Resource, PDBP DMR | 2026-08-15 11:22:16 | 31 | ||
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Bioassay Ontology Resource Report Resource Website 1+ mentions |
Bioassay Ontology (RRID:SCR_002638) | BAO | ontology, data or information resource, controlled vocabulary | Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation. | chemical biology, drug screening, assay, perturbation, high-throughput screening, owl |
is used by: LINCS Information Framework is listed by: BioPortal is parent organization of: G Protein-Coupled Receptor BioAssays Ontology |
Free, Freely available | nlx_156065 | SCR_002638 | 2026-08-15 11:22:17 | 7 | ||||||||
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GUDMAP Ontology Resource Report Resource Website 1+ mentions |
GUDMAP Ontology (RRID:SCR_002637) | GUDMAP Ontology | ontology, data or information resource, resource, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. | murine, genitourinary tract, development, in situ hybridization, theiler stage, adult mouse, newborn mouse, adolescent mouse, embryonic mouse |
is used by: GATACA GUDMAP Gene Explorer is used by: Kidney Development Database lists: GOA lists: EuReGene lists: Embryo Images Normal and Abnormal Mammalian Development lists: Stem Cell Genome Anatomy Projects lists: Eurexpress lists: Gene Expression Database lists: ToppGene Suite is related to: eMouseAtlas is related to: GenePaint Interactive Anatomy Atlas is related to: EMAGE Gene Expression Database is related to: Gene Expression Omnibus has parent organization: GenitoUrinary Development Molecular Anatomy Project |
NIDDK DK070136-02; NIDDK DK070181; NIDDK DK07020001; European Union FP6 005085 |
PMID:17452023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156063 | SCR_002637 | 2026-08-15 11:22:17 | 2 | ||||||
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Subject Library Resource Report Resource Website |
Subject Library (RRID:SCR_002595) | Subject Library | software toolkit, image processing software, data management software, data processing software, software application, software resource, software library | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks. | reusable library, analyze, database application, magnetic resonance, os independent, python, workflow, mri, organize, process, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155999 | http://www.nitrc.org/projects/subjectlibrary | SCR_002595 | 2026-08-15 11:22:14 | 0 | |||||||
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PANDA Resource Report Resource Website 100+ mentions |
PANDA (RRID:SCR_002511) | PANDA | software toolkit, software resource | Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface). | analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National Natural Science Foundation of China ; Beijing Nova Program ; 973 program ; State Key Laboratory of Cognitive Neuroscience and Learning |
PMID:23439846 | Free, Available for download, Freely available | nlx_155911 | http://www.nitrc.org/projects/panda | SCR_002511 | PANDA: a pipeline tool for diffusion MRI, PANDA (Pipeline for Analyzing braiN Diffusion imAges), Pipeline for Analyzing braiN Diffusion imAges, PANDA: Pipeline for Analyzing braiN Diffusion imAges, panda-tool | 2026-08-15 11:22:14 | 427 | ||||
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TAPIR Resource Report Resource Website 50+ mentions |
TAPIR (RRID:SCR_002596) | TAPIR | image analysis software, data processing software, registration software, software application, software resource | A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_156001 | SCR_002596 | Tools for Advanced Parameterized Image Registration | 2026-08-15 11:22:16 | 67 | |||||||
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Segmentation Validation Engine Resource Report Resource Website |
Segmentation Validation Engine (RRID:SCR_002591) | SVE | production service resource, data analysis service, software application, software resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site. | analyze, dice coefficient, information resource, loni/sve terms of use, magnetic resonance, nifti, os independent, other/proprietary license, overlap metrics, quality metrics, quantification, segmentation, tanomoto coefficient, web environment, web resource, web service, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA |
PMID:19073267 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155995 | http://www.nitrc.org/projects/sve | SCR_002591 | 2026-08-15 11:22:14 | 0 | ||||||
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Nirfast Resource Report Resource Website 10+ mentions |
Nirfast (RRID:SCR_002503) | NIRFAST | software toolkit, software resource | Software package for modeling Near-Infrared light transport in tissue and image reconstruction. This includes: Standard single wavelength absorption and reduced scatter, Multi-wavelength spectrally constrained models and Fluorescence models. | optical imaging, tissue |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Dartmouth College; New Hampshire; USA |
PMID:20182646 PMID:23942632 |
Free, Available for download, Freely available | nlx_155902 | http://www.nitrc.org/projects/nirfast | SCR_002503 | 2026-08-15 11:22:14 | 35 | ||||||
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Web Interfaces for Multiscale Images Resource Report Resource Website |
Web Interfaces for Multiscale Images (RRID:SCR_002589) | Web Interfaces for Multiscale Images | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web. | magnetic resonance, interoperability, microscopy, standard specification, forum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156020 | SCR_002589 | 2026-08-15 11:22:17 | 0 |
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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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