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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Etherpad Resource Report Resource Website 1+ mentions |
Etherpad (RRID:SCR_002611) | web application, collaboration tool, software application, authoring tool, software resource | Web application for real-time collaborative editing. It provides customizable options, a documented API and the ability to convert to various data exchange formats. | online word processor, collaborative application, writing tool | is listed by: FORCE11 | Free, Available for download, Freely available | nlx_156044 | SCR_002611 | 2026-08-01 12:02:11 | 4 | |||||||||
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University of Auckland; Auckland; New Zealand Resource Report Resource Website 1+ mentions |
University of Auckland; Auckland; New Zealand (RRID:SCR_002615) | university | Public university in New Zealand that offers degrees in areas such as the arts, business, education, medical and health science, and law. | public university system, new zealand, degree program |
is related to: University of Auckland Biomedical Imaging Research Unit Molecular Devices ImageXpress Micro XLS is parent organization of: CellML is parent organization of: BEAST2 is parent organization of: ApiNATOMY |
Free | nlx_28115 | SCR_002615 | 2026-08-01 12:02:11 | 2 | |||||||||
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peak nii Resource Report Resource Website 1+ mentions |
peak nii (RRID:SCR_002572) | peak_nii | software toolkit, software application, data processing software, software resource, image processing software | Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command. | magnetic resonance, pet, spect | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Personal License | nlx_155975 | SCR_002572 | peak_nii: Statistical image clustering peak detection and data extraction, peak nii | 2026-08-01 12:02:11 | 7 | |||||||
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University of Barcelona; Barcelona; Spain Resource Report Resource Website |
University of Barcelona; Barcelona; Spain (RRID:SCR_002575) | UB | university | Public university in Barcelona, Spain that offers degree programs in social sciences, engineering, and arts and humanities. | public university, barcelona, spanish university, degree program |
uses: Scizzle is related to: European Gram Negative AntiBacterial Engine is parent organization of: DnaSP is parent organization of: Bellvitge Biomedical Research Institute is parent organization of: University of Barcelona Statistics and Bioinformatics Research Group is parent organization of: SerbGO is parent organization of: nucleR |
Free | nlx_21784 | SCR_002575 | University of Barcelona, Universitat de Barcelona | 2026-08-01 12:01:50 | 0 | |||||||
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Vaa3D Resource Report Resource Website 100+ mentions |
Vaa3D (RRID:SCR_002609) | Vaa3D, Vaa3D-Neuron | image analysis software, data visualization software, software toolkit, data management software, software application, data processing software, software resource | A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools. | reusable library, atlas application, c, c++, cygwin, fiber tracking, gnome, image display, kde, linux, macos, microsoft, magnetic resonance, neuronal characterization, development environment, position, posix/unix-like, quantification, registration, rendering, resampling, segmentation, shape analysis, spatial transformation, surface analysis, tractography, visualization, volumetric analysis, warping, win32 (ms windows), windows, windows 95/98/2000, windows nt/2000, windows vista, windows xp, 3d neuron reconstruction, 3d, neuron, reconstruction, microscopy |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Insight Segmentation and Registration Toolkit has parent organization: Janelia Research |
Howard Hughes Medical Institute | PMID:20231818 | Free, Available for download, Freely available | nlx_156012 | http://www.nitrc.org/projects/v3d | SCR_002609 | V3D, Vaa3D: A Swiss army knife for bioimage visualization & analysis, V3D-Neuron, Vaa3D: A Swiss army knife for bioimage visualization and analysis, 3D Visualization-Assisted Analysis, Vaa3D and Vaa3D-Neuron | 2026-08-01 12:02:11 | 157 | ||||
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Triangle BioSystems Resource Report Resource Website 10+ mentions |
Triangle BioSystems (RRID:SCR_002603) | TBSI | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software | computational neuroscience, eeg, eeg, meg, electrocorticography, hardware, other software resource, physiological recording, software | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156006 | http://www.nitrc.org/projects/tbsi | SCR_002603 | Triangle BioSystems International | 2026-08-01 12:02:11 | 11 | ||||||
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TractoR: Tractography with R Resource Report Resource Website 10+ mentions |
TractoR: Tractography with R (RRID:SCR_002602) | TractoR | software resource, software application, data processing software, data visualization software | Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R. | analyze, atlas application, c, dicom, linux, macos, modeling, magnetic resonance, nifti, other unix-like, posix/unix-like, quantification, r, segmentation, sh, bash, statistical operation, tractography, unix shell, visualization, diffusion mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | nlx_156005 | http://www.nitrc.org/projects/tractor | SCR_002602 | Tractography with R | 2026-08-01 12:01:51 | 28 | ||||||
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TetraMetrix Resource Report Resource Website 1+ mentions |
TetraMetrix (RRID:SCR_002601) | TetraMetrix | software resource | An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left. | magnetic resonance, 3d, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
Free, Available for download, Freely available | nlx_156004 | SCR_002601 | 2026-08-01 12:02:11 | 1 | ||||||||
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Template Image Processing Library Resource Report Resource Website |
Template Image Processing Library (RRID:SCR_002600) | TIPL | image analysis software, software toolkit, software application, data processing software, software resource, image processing software, software library | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM) | reusable library, analyze, c++, dicom, format conversion, magnetic resonance, nifti, os independent, segmentation, spatial transformation, visualization, win32 (ms windows) |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Carnegie Mellon University; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156003 | http://www.nitrc.org/projects/tipl | SCR_002600 | 2026-08-01 12:02:11 | 0 | |||||||
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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 | 2026-08-01 12:01:51 | 4 | ||||||
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TurtleSeg Resource Report Resource Website 1+ mentions |
TurtleSeg (RRID:SCR_002605) | TurtleSeg | image analysis software, segmentation software, software application, software resource, data processing 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 | 2026-08-01 12:02:11 | 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 | portal, organization portal, data or information resource, department 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 | 2026-08-01 12:02:09 | 38 | ||||||
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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 | 2026-08-01 12:01:52 | 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 | 2026-08-01 12:01:50 | 160 | |||||||
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OpenDOAR Resource Report Resource Website 10+ mentions |
OpenDOAR (RRID:SCR_002641) | OpenDOAR | data or information resource, data repository, storage service resource, database, 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 | 2026-08-01 12:02:12 | 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+ | software resource, software application, image processing software, data processing software | 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 | 2026-08-01 12:01:49 | 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 | 2026-08-01 12:01:52 | 38 | |||||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data or information resource, data repository, storage service resource, image repository, database, 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 | 2026-08-01 12:02:12 | 14 | |||||
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pIRS Resource Report Resource Website 50+ mentions |
pIRS (RRID:SCR_002519) | software resource, software application, simulation software | 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 | 2026-08-01 12:02:09 | 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 | 2026-08-01 12:02:11 | 349 |
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