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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) Resource Report Resource Website |
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) (RRID:SCR_014178) | VERTEX | software resource, software application, simulation software | A Matlab tool for simulating extracellular potential recordings in spiking neural network (SNN) models. VERTEX is designed to facilitate the simulation of extracellular potentials generated by activity in SNNs; in particular, spatially-organised networks containing thousands or hundreds of thousands of neurons. It has a limited scope but has a simpler user interface so that a simulation can be specified simply by setting some parameters and run using a few function calls. | simulation software, matlab, extracellular potential, spiking neural network model, snn model |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24863422 | Available to the research community | SCR_014178 | Virtual Electrode Recording Tool for EXtracellular potentials | 2026-08-08 12:00:07 | 0 | |||||||
|
FluoView FV10-ASW software Resource Report Resource Website 100+ mentions |
FluoView FV10-ASW software (RRID:SCR_014215) | image processing software, software resource, software application, data processing software | Image processing software used to modify and clarify sample images for FluoView FV1000 range of confocal laser scanning microscopes and Fluoview FV1000MPE multiphoton excitation systems. The software incorporates high-dynamic-range imaging, minimized signal-to-noise ratios, partial stitching with multiarea time-lapse imaging, and channel unmixing. The software also allows users to select specific areas of the whole sample, which can stitched together. | image processing software, microscopy, laser scanning microscopy, high dynamic range imaging | is provided by: Olympus | Pay for product, Fully compatible with Windows 7 | http://www.olympus-lifescience.com/en/ | SCR_014215 | Olympus Fluoview FV10-ASW 3.0, FV10-ASW 3.0 Software | 2026-08-08 12:00:29 | 295 | ||||||||
|
Phaser Resource Report Resource Website 1000+ mentions |
Phaser (RRID:SCR_014219) | image reconstruction software, image analysis software, data acquisition software, software resource, software application, data processing software | Crystallographic software which solves structures using algorithms and automated rapid search calculations to perform molecular replacement and experimental phasing methods. | crystallographic software, molecular replacement, experimental phasing method, data acquisition software, image analysis software, image reconstruction software |
is listed by: SoftCite is affiliated with: Phenix has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:19461840 | Available through Phenix, Available through CCP4, Acknowledgement requested | http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software | SCR_014219 | 2026-08-08 12:00:29 | 2664 | ||||||||
|
iMosflm Resource Report Resource Website 100+ mentions |
iMosflm (RRID:SCR_014217) | image processing software, software resource, software application, data processing software | Software which processes diffraction data/images and produces an MTZ file of reflection indices with their intensities, standard deviations, and other parameters. The MTZ file is passed onto other programs of the CCP4 program suite for further data reduction. iMosflm processes data from CCD and pixel detectors. It is available for Windows, Mac OSX and Linux platforms. Tutorials are available at the website. | image processing software, diffraction image, mtz file |
is affiliated with: Pointless has parent organization: MRC Laboratory of Molecular Biology |
SCR_014217 | 2026-08-08 12:00:07 | 332 | |||||||||||
|
Coot Resource Report Resource Website 10000+ mentions |
Coot (RRID:SCR_014222) | COOT | data or information resource, model, software toolkit, software resource, software application, simulation software | Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available. | software toolkit, simulation software, model manipulation, protein modeling, bio.tools |
is used by: PDB-REDO is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MolProbity has parent organization: MRC Laboratory of Molecular Biology |
PMID:15572765 | Available for download, Acknowledgement requested | biotools:coot | http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot, https://bio.tools/coot | SCR_014222 | Crystallographic Object-Oriented Toolkit | 2026-08-08 12:00:29 | 15682 | |||||
|
SHELX Resource Report Resource Website 500+ mentions |
SHELX (RRID:SCR_014220) | image reconstruction software, image analysis software, software resource, software application, standalone software, data processing software | A set of software programs that utilizes dual spaces algorithms for the determination of small and macromolecular crystal structures by single crystal X-ray and neutron diffraction. Libraries, extra files and environment variables are not required for the executables. SHELX is intended to be run on a command prompt but may be called from GUIs such as shelXle, Olex2, Oscail or WinGX, or hkl2map., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, image reconstruction software, image analysis software, crystal structure, crystal xray, neutron diffraction, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1107/S2053273314026370 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shelx | https://bio.tools/shelx | SCR_014220 | 2026-08-08 12:00:07 | 523 | |||||||
|
MolProbity Resource Report Resource Website 5000+ mentions |
MolProbity (RRID:SCR_014226) | web application, software resource | A structure-validation web application which provides an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. MolProbity works best as an active validation tool (used as soon as a model is available and during each rebuild/refine loop) and when used for protein and RNA crystal structures, but it may also work well for DNA, ligands and NMR ensembles. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot. | web application, consultation, macromolecular structure, structure validation, macromolecular crystallography |
is listed by: SoftCite is related to: Phenix is related to: Coot has parent organization: Duke University; North Carolina; USA |
Howard Hughes Medical Institute Predoctoral Fellowship ; NIGMS GM-15000; NIGMS GM-61302 |
DOI:10.1107/S0907444909042073 | Acknowledgement requested, Requires Java and Javascript | https://www.phenix-online.org/documentation/reference/molprobity_tool.html | SCR_014226 | 2026-08-08 12:00:07 | 6711 | |||||||
|
Crystallography and NMR System (CNS) Resource Report Resource Website 1+ mentions |
Crystallography and NMR System (CNS) (RRID:SCR_014223) | CNS | software toolkit, software resource, software application, data visualization software, data processing software | Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website. | structure determination, software suite, macromolecular structure determination, data visualization software, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Yale University; Connecticut; USA |
PMID:9757107 | Available to academic institutions, Request form must be submitted | biotools:cnssolve | https://bio.tools/cnssolve | SCR_014223 | Crystallography and NMR System | 2026-08-08 12:00:07 | 8 | |||||
|
Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | software toolkit, software resource, software application, data analysis software, data processing software | A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR). | matlab, software toolkit, cortical thickness signal, data analysis software |
uses: FreeSurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Wisconsin Partnership Program ; NIA R01AG040396; NIA R01AG021155; NSF RI 1116584; NSF CAREER 1252725; UW ADRC NIA P50 AG033514; UW ICTR NCRR 1UL1RR025011; NIA P30 AG010129; NIA K01 AG030514 |
http://pages.cs.wisc.edu/~wonhwa/code/CTA_toolbox.html, http://pages.cs.wisc.edu/~wonhwa/project/ctdiscrim.html | SCR_014180 | 2026-08-08 12:00:28 | 0 | |||||||||
|
BraTumIA (Brain Tumor Image Analysis) Resource Report Resource Website 10+ mentions |
BraTumIA (Brain Tumor Image Analysis) (RRID:SCR_014184) | segmentation software, image analysis software, software resource, software application, data processing software | Segmentation software for multimodal image analysis of brain tumor studies. It performs volumetric segmentation of healthy and tumor tissues by employing multispectral MRI sequences. Segmented tissues include Gray Matter, White Matter, Cerebrospinal Fluid, necrotic core, edema, non-enhancing tumor and enhancing tumor. | segmentation software, image analysis, brain tumor, volumetric segmentation, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Cancer Imaging Archive (TCIA) |
Free for non-commercial use only | SCR_014184 | BraTumIA | 2026-08-08 12:00:21 | 14 | |||||||||
|
OpenViBE Resource Report Resource Website 100+ mentions |
OpenViBE (RRID:SCR_014156) | software toolkit, data acquisition software, software resource, software application, data visualization software, data processing software | A multi-platform software dedicated to designing, testing and using brain-computer interfaces (BCI). OpenViBE is a software for real-time neurosciences that can be used to acquire, filter, process, classify and visualize brain signals in real time. | software toolkit, multi platform, brain computer interface, real time | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public, Available to the research community | http://openvibe.inria.fr | SCR_014156 | 2026-08-08 12:00:06 | 106 | |||||||||
|
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) Resource Report Resource Website |
Northwestern University Schizophrenia Data and Software Tool (NUSDAST) (RRID:SCR_014153) | NUSDAT | database, data or information resource, image collection | A repository of schizophrenia neuroimaging data collected from over 450 individuals with schizophrenia, healthy controls and their respective siblings, most with 2-year longitudinal follow-up. The data include neuroimaging data, cognitive data, clinical data, and genetic data. | database, neuroimaging, clinical, cognitive, genetic, schizophrenia, longitudinal |
uses: CAWorks is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Northwestern University; Illinois; USA |
Schizophrenia | NIMH 1R01 MH084803; NIMH 1U01 MH097435; NIMH P50 MH071616; NIMH R01 MH056584; NCRR P41 RR15241; NIGMS U24 GM104203; NIH Bio-Informatics Research Network Coordinating Center |
Available to the research community | SCR_014153 | Northwestern University Schizophrenia Data and Software Tool | 2026-08-08 12:00:28 | 0 | ||||||
|
OpenWalnut Resource Report Resource Website |
OpenWalnut (RRID:SCR_014157) | software resource, software application, data visualization software, data processing software | Open source tool for multi-modal medical and brain data visualization. It is a tool for the scientific user and a powerful framework for the visualization researcher. It is written in Standard C++ and uses a number of portable libraries (e.g. Qt, Boost and OpenSceneGraph). It runs on common GNU/Linux operating systems, Mac OSX and Windows. | open source, data visualization software, brain data, medical tool |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian |
Free, Available for download, Freely available | http://www.openwalnut.org, https://sources.debian.org/src/openwalnut-qt4/ | SCR_014157 | 2026-08-08 12:00:20 | 0 | |||||||||
|
Orientation Distribution Function in Constant Solid Angle (CSA-ODF) Resource Report Resource Website |
Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (RRID:SCR_014158) | CSA ODF | software toolkit, software resource, software application, data visualization software, data processing software | A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI. | matlab, toolbox, imaging orientation, diffusion weighted mri, image reconstruction, modeling |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
Available to the research community | SCR_014158 | Orientation Distribution Function in Constant Solid Angle | 2026-08-08 12:00:28 | 0 | ||||||||
|
NiiStat Resource Report Resource Website 50+ mentions |
NiiStat (RRID:SCR_014152) | software resource, software application, source code, data analysis software, data processing software | A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data. | matlab script, source code, data analysis, neuroimaging data, clinical population |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
Available to the research community | http://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage | SCR_014152 | 2026-08-08 12:00:20 | 88 | |||||||||
|
MassLynx Resource Report Resource Website 5000+ mentions |
MassLynx (RRID:SCR_014271) | data acquisition software, software resource, software application, data management software, data analysis software, data processing software | Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data acquisition software, data analysis software, data management software, mass spectrometry | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014271 | MassLynx MS Software | 2026-08-08 12:00:22 | 5809 | |||||||||
|
Ruby NIfTI Resource Report Resource Website |
Ruby NIfTI (RRID:SCR_014164) | software library, software resource, software toolkit | A library for handling NIfTI data in the Ruby programming language. Ruby NIfTI supports basic read and write access to NIfTI files, including basic and extended header information and image information. It doesn't attempt to touch the image data but it does provide access to qform and sform orientation matrices. It also provides a nice interface to get at NIfTI info from within Ruby. | nifti library, ruby, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard University; Cambridge; United States |
https://github.com/brainmap/nifti | SCR_014164 | 2026-08-08 12:00:28 | 0 | ||||||||||
|
SCORE Resource Report Resource Website 100+ mentions |
SCORE (RRID:SCR_014165) | data or information resource, narrative resource, experimental protocol | A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. | experiment protocol, method, different image algorithm, quantitative score |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NLM HHSN276201000584P; NIBIB 1R41 EB011796 |
SCR_014165 | 2026-08-08 12:00:06 | 481 | ||||||||||
|
Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data Resource Report Resource Website |
Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data (RRID:SCR_014163) | image analysis software, software resource, software application, data analysis software, data processing software | An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class. | pca algorithm, shape analysis, data analysis software, scalar data set, vector data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
Available to the research community | SCR_014163 | 2026-08-08 12:00:20 | 0 | ||||||||||
|
PsyGeNET Resource Report Resource Website 10+ mentions |
PsyGeNET (RRID:SCR_014406) | data or information resource, software resource, software application, database, data analysis software, data processing software | Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts. | psychiatric disease, associated gene, database, analysis tool, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools |
Psychiatric disorder | DOI:10.1093/bioinformatics/btv301 | Available for the research community | biotools:psygenet2r | https://bio.tools/psygenet2r | SCR_014406 | Psychiatric disorders Gene association NETwork, Psychiatric disorders Gene association Network | 2026-08-08 12:00:10 | 11 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
