Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Altmetric Badges Resource Report Resource Website |
Altmetric Badges (RRID:SCR_002558) | commercial organization | A single line of code to add your article pages to include the Altmetric score and donut graphic on your own site with minimal technical effort. Choose from an array of different badge styles, including the colourful and iconic Altmetric donut. Implement article level metrics into your pages in minutes. Their pricing is based on the number of journals you want covered, with significant discounts for larger portfolios. You can try out the badges for free and without any commitment - however, your visitors will only see a subset of activity for each article when they click through. See the technical documentation for details. | altmetrics, count, score, altmetric score, social metric | is listed by: FORCE11 | Free, Freely available | nlx_156029 | http://www.force11.org/node/4719 | SCR_002558 | Altmetric.com embeds, The Altmetric Badges | 2026-08-15 11:22:17 | 0 | |||||||
|
Slice:Drop Resource Report Resource Website 1+ mentions |
Slice:Drop (RRID:SCR_002557) | Slice:Drop | production service resource, source code, software resource, service resource, analysis service resource | A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ). | ascii, clinical neuroinformatics, computed tomography, dicom, javascript, mgh/mgz, magnetic resonance, nifti, nrrd, medical imaging, 3d, visualization, rendering | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155964 | http://www.nitrc.org/projects/slicedrop | SCR_002557 | 2026-08-15 11:22:15 | 5 | |||||||
|
Gibbs Motif Sampler Resource Report Resource Website 1+ mentions |
Gibbs Motif Sampler (RRID:SCR_002550) | Gibbs Motif Sampler | production service resource, data analysis service, software resource, service resource, analysis service resource | Software to identify motifs, conserved regions, in DNA or protein sequences. | dna, protein, motif, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gibbs_motif_sampler, OMICS_00496 | https://bio.tools/gibbs_motif_sampler | SCR_002550 | The Gibbs Motif Sampler | 2026-08-15 11:22:15 | 2 | ||||||
|
Sleuth Resource Report Resource Website 100+ mentions |
Sleuth (RRID:SCR_002555) | data processing software, web application, software application, data analysis software, software resource, data visualization software | Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space. | brain map database, data visualization, neuroscience literature, talairach space, search software, meta-data analysis |
uses: MNI brain and the Talairach atlas uses: MNI brain and the Talairach atlas is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: brainmap.org |
Public, Account required, Available for download | nlx_155963 | http://www.nitrc.org/projects/brainmap | SCR_002555 | Sleuth Version 2.4 | 2026-08-15 11:22:13 | 224 | |||||||
|
Signed Differential Mapping Resource Report Resource Website 100+ mentions |
Signed Differential Mapping (RRID:SCR_002554) | SDM | software resource | Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera). | magnetic resonance, pet, spect, fmri, vbm, meta-analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155962 | http://www.nitrc.org/projects/sdm | SCR_002554 | 2026-08-15 11:22:17 | 206 | |||||||
|
MBASED Resource Report Resource Website 10+ mentions |
MBASED (RRID:SCR_002584) | software resource | Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection. | software package, unix/linux, mac os x, windows, r, gene expression, sequencing, transcription |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25315065 | Free, Available for download, Freely available | OMICS_05502 | http://www.bioconductor.org/packages/release/bioc/html/MBASED.html | SCR_002584 | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-08-15 11:22:17 | 17 | ||||||
|
pymzML Resource Report Resource Website 10+ mentions |
pymzML (RRID:SCR_002500) | software resource | Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: mzML has parent organization: University of Munster; North Rhine-Westphalia; Germany |
PMID:22302572 | Free, Available for download, Freely available | biotools:pymzml, OMICS_03355 | https://bio.tools/pymzml | SCR_002500 | 2026-08-15 11:22:16 | 18 | |||||||
|
ESTHER Resource Report Resource Website 100+ mentions |
ESTHER (RRID:SCR_002621) | ESTHER | data or information resource, database | Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosome |
is listed by: re3data.org is related to: UniProtKB is related to: AceDB has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:23193256 | Free, Available for download, Freely available | nif-0000-30526, SCR_008479, nif-0000-02817, r3d100010542 | https://doi.org/10.17616/R33K77 | SCR_002621 | ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives | 2026-08-15 11:22:17 | 134 | |||||
|
BioStar Resource Report Resource Website 50+ mentions |
BioStar (RRID:SCR_002580) | Biostar | forum, discussion, portal, data or information resource, community building portal, narrative resource | A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply. | bioinformatics, computational genomics, biological data analysis, data analysis, forum, question, answer |
is listed by: OMICtools is related to: NeuroStars |
NIH ; Luma Education ; NHGRI 5R25HG006243-02 |
PMID:22046109 | Free, Freely available | OMICS_01706, nlx_155982 | SCR_002580 | biostars.org | 2026-08-15 11:22:14 | 88 | |||||
|
WFU Biological Parametric Mapping Toolbox Resource Report Resource Website 1+ mentions |
WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) | WFU_BPM, WFU BPM | software toolkit, image analysis software, data processing software, software application, software resource | Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher | analyze, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, statistical operation, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Wake Forest School of Medicine; North Carolina; USA |
Human Brain Project ; NIBIB 1R01EB004673 |
PMID:17070709 | Free, Available for download, Freely available | nlx_156016 | http://www.nitrc.org/projects/wfu_bpm | SCR_002613 | BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM | 2026-08-15 11:22:14 | 4 | ||||
|
discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS). | single nucleotide polymorphism, snp discovery, discover snp, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
SOFIPROTEOL under the FASO project PEAPOL ; INRIA ANR-12-BS02-0008 |
PMID:25404127 | Free, Freely available | biotools:discosnp, OMICS_00267 | https://bio.tools/discosnp, https://sources.debian.org/src/discosnp/ | SCR_002612 | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-08-15 11:22:17 | 9 | |||||
|
Etherpad Resource Report Resource Website 1+ mentions |
Etherpad (RRID:SCR_002611) | web application, software application, software resource, collaboration tool, authoring tool | 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 | 2026-08-15 11:22:16 | 5 | |||||||||
|
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 | 2026-08-15 11:22:16 | 2 | |||||||||
|
peak nii Resource Report Resource Website 1+ mentions |
peak nii (RRID:SCR_002572) | peak_nii | software toolkit, image processing software, data processing software, software application, software resource | 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 | 2026-08-15 11:22:13 | 7 | |||||||
|
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 | 2026-08-15 11:22:17 | 0 | |||||||
|
Vaa3D Resource Report Resource Website 100+ mentions |
Vaa3D (RRID:SCR_002609) | Vaa3D, Vaa3D-Neuron | software toolkit, image analysis software, data management software, data processing software, software application, software resource, data visualization software | 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 | 2026-08-15 11:22:14 | 166 | ||||
|
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 | 2026-08-15 11:22:14 | 11 | ||||||
|
TractoR: Tractography with R Resource Report Resource Website 10+ mentions |
TractoR: Tractography with R (RRID:SCR_002602) | TractoR | data processing software, software application, data visualization software, software resource | 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 | 2026-08-15 11:22:17 | 28 | ||||||
|
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 | 2026-08-15 11:22:16 | 1 | ||||||||
|
Template Image Processing Library Resource Report Resource Website |
Template Image Processing Library (RRID:SCR_002600) | TIPL | software toolkit, image processing software, image analysis software, data processing software, software application, software resource, 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 | 2026-08-15 11:22:14 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
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.
Email: info_at_ dknet.org
