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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Pythagorean Displacement and Motion Regressors Resource Report Resource Website 1+ mentions |
Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) | Pythagorean Displacement and Motion Regressors | software resource | Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment. | algorithm, magnetic resonance, matlab, pythagorean theorem, head, motion, position, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155931 | SCR_002525 | SciCrunch Registry | 2026-10-17 01:25:40 | 5 | ||||||||
|
PySurfer Resource Report Resource Website 10+ mentions |
PySurfer (RRID:SCR_002524) | PySurfer | data processing software, data visualization software, software application, software library, software resource, software toolkit | Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, meg, electrocorticography, magnetic resonance, mri, python, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155930 | http://www.nitrc.org/projects/pysurfer, https://sources.debian.org/src/python3-surfer/ | SCR_002524 | SciCrunch Registry | 2026-10-17 01:25:27 | 29 | |||||||
|
RDFaCE Resource Report Resource Website |
RDFaCE (RRID:SCR_002645) | RDFaCE | authoring tool, software application, software resource | A Semantic content editor based on TinyMCE WYSIWYG editor. RDFaCE is created as a proof of concept for WYSIWYM (What You See Is What You Mean) concept. WYSIWYM aims to enable end-users to easily annotate their content using RDFa and Microdata markups. RDFaCE employs external NLP APIs to suggest namespaces, properties, URIs and to automatically annotate content. | annotation, authoring, markup, rdfa |
is listed by: FORCE11 has parent organization: University of Leipzig; Saxony; Germany |
Free, Available for download, Freely available | nlx_156074 | SCR_002645 | SciCrunch Registry | RDFa Content Editor | 2026-10-17 01:25:15 | 0 | |||||||
|
ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | data analysis software, data processing software, sequence analysis software, simulation software, software application, software resource | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | SciCrunch Registry | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-10-17 01:25:13 | 35 | ||||||
|
Spanish Resting State Network Resource Report Resource Website |
Spanish Resting State Network (RRID:SCR_002562) | SRSN | community building portal, data or information resource, portal | Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.) | microsoft word document, magnetic resonance, nifti, pdf, spanish |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project |
Free | nlx_155968 | SCR_002562 | SciCrunch Registry | 2026-10-17 01:25:28 | 0 | ||||||||
|
University of Arkansas System; Arkansas; USA Resource Report Resource Website |
University of Arkansas System; Arkansas; USA (RRID:SCR_002564) | university | The public university system in Arkansas, USA that includes 4-year institutions, 2-year colleges, and affiliated units for agriculture, public service and criminal justice programs. | public university system | is parent organization of: University of Arkansas for Medical Sciences; Arkansas; USA | nlx_152182 | SCR_002564 | SciCrunch Registry | University of Arkansas System, UA System | 2026-10-17 01:25:41 | 0 | |||||||||
|
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 | SciCrunch Registry | Altmetric.com embeds, The Altmetric Badges | 2026-10-17 01:25:13 | 0 | |||||||
|
Slice:Drop Resource Report Resource Website 1+ mentions |
Slice:Drop (RRID:SCR_002557) | Slice:Drop | analysis service resource, production service resource, service resource, software resource, source code | 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 | SciCrunch Registry | 2026-10-17 01:25:41 | 5 | |||||||
|
Gibbs Motif Sampler Resource Report Resource Website 1+ mentions |
Gibbs Motif Sampler (RRID:SCR_002550) | Gibbs Motif Sampler | analysis service resource, data analysis service, production service resource, service resource, software 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 | SciCrunch Registry | The Gibbs Motif Sampler | 2026-10-17 01:25:13 | 2 | ||||||
|
Sleuth Resource Report Resource Website 100+ mentions |
Sleuth (RRID:SCR_002555) | data analysis software, data processing software, data visualization software, software application, software resource, web application | 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 | SciCrunch Registry | Sleuth Version 2.4 | 2026-10-17 01:25:28 | 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 | SciCrunch Registry | 2026-10-17 01:25:13 | 206 | |||||||
|
Volocity 3D Image Analysis Software Resource Report Resource Website 1000+ mentions |
Volocity 3D Image Analysis Software (RRID:SCR_002668) | Volocity Imaging software | commercial organization, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience. | 3d, confocal microscopy, visualization, analyze | THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000112 | SCR_002668 | SciCrunch Registry | 2026-10-17 01:25:15 | 4003 | |||||||||
|
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 | SciCrunch Registry | Meta-analysis Based Allele-Specific Expression Detection, MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection | 2026-10-17 01:25:14 | 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 | SciCrunch Registry | 2026-10-17 01:25:12 | 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 | SciCrunch Registry | ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives | 2026-10-17 01:25:15 | 134 | |||||
|
BioStar Resource Report Resource Website 50+ mentions |
BioStar (RRID:SCR_002580) | Biostar | community building portal, data or information resource, discussion, forum, narrative resource, portal | 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 | SciCrunch Registry | biostars.org | 2026-10-17 01:25:28 | 88 | |||||
|
WFU Biological Parametric Mapping Toolbox Resource Report Resource Website 1+ mentions |
WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) | WFU_BPM, WFU BPM | data processing software, image analysis software, software application, software resource, software toolkit | 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 | SciCrunch Registry | BPM - Integrated Tool for Biological Parametric Mapping, WFU Biological Parametric Mapping, BPM toolbox, BPM | 2026-10-17 01:25:41 | 4 | ||||
|
discoSnp Resource Report Resource Website 1+ mentions |
discoSnp (RRID:SCR_002612) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | DiscoSnp++, discovering Single Nucleotide Polymorphism, discovering Single Nucleotide Polymorphism (discoSNP) | 2026-10-17 01:25:29 | 9 | |||||
|
Etherpad Resource Report Resource Website 1+ mentions |
Etherpad (RRID:SCR_002611) | authoring tool, collaboration tool, software application, software resource, web application | 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 | SciCrunch Registry | 2026-10-17 01:25:14 | 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 is parent organization of: University of Auckland Cytometry Core Facility |
Free | nlx_28115, Crossref Funder ID 501100001537, Wikidata Q492467, GRID grid.9654.e, ISNI 0000 0004 0372 3343 | https://ror.org/03b94tp07 | SCR_002615 | SciCrunch Registry | 2026-10-17 01:25:14 | 2 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
