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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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APERTURE Resource Report Resource Website 1+ mentions |
APERTURE (RRID:SCR_014082) | data analysis software, data processing software, software application, software toolkit, workflow software, software resource | A MATLAB-based toolbox for analysis of EEG, MEG, and ECoG data. APERTURE allows flexible multivariate analysis of ERPs and oscillatory activity and supports mass-univariate analysis with advanced statistical tests. Computations are accelerated using parallel computing supported through the MATLAB distributed computing toolbox. Examination of large, high-dimensional datasets is made simple through data visualization tools, including advanced plotting routines and generation of PDF reports with many figures. | matlab, software toolkit, workflow software, toolbox, multivariate analysis, data analysis |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Vanderbilt University; Tennessee; USA |
SCR_014082 | Analysis of Patterns in Electrophysiological Recordings Toolbox with Utilities for REsearch | 2026-08-13 09:29:08 | 3 | ||||||||||
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SoftMax Pro Data Acquisition and Analysis Software Resource Report Resource Website 50+ mentions |
SoftMax Pro Data Acquisition and Analysis Software (RRID:SCR_014240) | data analysis software, data processing software, software resource, software application | A software package for microplate reader control and microplate data analysis. It includes analysis templates for a variety of assays run on Molecular Devices microplate readers. | data analysis software, assay analysis, microplate reader control, microplate data analysis | Pay for product | SCR_014240 | SoftMax Pro Software | 2026-08-13 09:29:01 | 88 | ||||||||||
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FluoView FV10-ASW software Resource Report Resource Website 100+ mentions |
FluoView FV10-ASW software (RRID:SCR_014215) | image processing software, data processing software, software resource, software application | 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 | 2026-08-13 09:28:58 | 295 | ||||||||
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Phaser Resource Report Resource Website 1000+ mentions |
Phaser (RRID:SCR_014219) | data processing software, software application, image analysis software, image reconstruction software, data acquisition software, software resource | 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 | 2026-08-13 09:29:09 | 2664 | ||||||||
|
iMosflm Resource Report Resource Website 100+ mentions |
iMosflm (RRID:SCR_014217) | image processing software, data processing software, software resource, software application | 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 | 2026-08-13 09:29:00 | 332 | |||||||||||
|
Coot Resource Report Resource Website 10000+ mentions |
Coot (RRID:SCR_014222) | COOT | data or information resource, simulation software, software application, software toolkit, model, software resource | 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 | 2026-08-13 09:29:09 | 15682 | |||||
|
SHELX Resource Report Resource Website 500+ mentions |
SHELX (RRID:SCR_014220) | data processing software, software application, image analysis software, image reconstruction software, standalone software, software resource | 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 | 2026-08-13 09:28:58 | 523 | |||||||
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Crystallography and NMR System (CNS) Resource Report Resource Website 1+ mentions |
Crystallography and NMR System (CNS) (RRID:SCR_014223) | CNS | data processing software, software application, software toolkit, data visualization software, software resource | 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 | 2026-08-13 09:28:58 | 8 | |||||
|
Wisconsin Cortical Thickness Analysis (CTA) Toolbox Resource Report Resource Website |
Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) | data analysis software, data processing software, software application, software toolkit, software resource | 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 | 2026-08-13 09:29:08 | 0 | |||||||||
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BraTumIA (Brain Tumor Image Analysis) Resource Report Resource Website 10+ mentions |
BraTumIA (Brain Tumor Image Analysis) (RRID:SCR_014184) | segmentation software, data processing software, software application, image analysis software, software resource | 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 | 2026-08-13 09:28:59 | 14 | |||||||||
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KWIPPED Resource Report Resource Website |
KWIPPED (RRID:SCR_014061) | service resource, access service resource | An online rental equipment marketplace which connects renters to instrument suppliers from various industries. Renters can rent directly from suppliers or request quotes from different suppliers. | lab equipment, rentals, marketplace, instrument supplier | Avaialble to the academic community, Available to industry | SCR_014061 | 2026-08-13 09:29:08 | 0 | |||||||||||
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Emerald Cloud Lab Resource Report Resource Website 1+ mentions |
Emerald Cloud Lab (RRID:SCR_013976) | data processing software, data management software, software application, data acquisition software, software resource | A production service resource which allows researchers to conduct experimental procedures through the cloud. Researchers can ship samples for an experiment to Emerald, then design the experiment(s) over the web using ECL software. Emerald then conducts the experiment(s) in an automated lab as specified, organizing the data into a database in the cloud. Samples are then shipped back to the lab (within a metter of days) and results can be analyze ECL's data analysis suite. Standard experiment types include but are not limited to: analytical balance readings, light microscopy, solid phase extraction, flourescence thermodynamics, RNA extraction/cDNA prep, and Western blot. Additional experiment types may be contributed. | production service resource, automated experiment, cloud |
is listed by: Connected Researchers is related to: Connected Researchers |
Charge by experiment on a per sample basis with no minimum transaction size, The community can contribute to this resource | SCR_013976 | 2026-08-13 09:29:07 | 3 | ||||||||||
|
OpenViBE Resource Report Resource Website 100+ mentions |
OpenViBE (RRID:SCR_014156) | data processing software, software application, software toolkit, data visualization software, data acquisition software, software resource | 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 | 2026-08-13 09:29:08 | 106 | |||||||||
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OpenWalnut Resource Report Resource Website |
OpenWalnut (RRID:SCR_014157) | data processing software, software resource, data visualization software, software application | 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 | 2026-08-13 09:28:57 | 0 | |||||||||
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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 | data processing software, software application, software toolkit, data visualization software, software resource | 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 | 2026-08-13 09:28:59 | 0 | ||||||||
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NiiStat Resource Report Resource Website 50+ mentions |
NiiStat (RRID:SCR_014152) | data analysis software, data processing software, software application, source code, software resource | 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 | 2026-08-13 09:29:08 | 88 | |||||||||
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Cytobank Resource Report Resource Website 1000+ mentions |
Cytobank (RRID:SCR_014043) | web application, training service resource, service resource, software resource | A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow. | single-cell biology, data, platform, cytometry, analyze, visualize, graphic, training service |
is related to: FLOWRepository is related to: FLOWRepository |
Free, Price varies for different options, Available to the research community, Available to industry | SCR_014043 | Cytobank Inc. | 2026-08-13 09:29:08 | 1326 | |||||||||
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Ruby NIfTI Resource Report Resource Website |
Ruby NIfTI (RRID:SCR_014164) | software toolkit, software resource, software library | 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 | 2026-08-13 09:28:59 | 0 | ||||||||||
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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) | data analysis software, data processing software, software application, image analysis software, software resource | 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 | 2026-08-13 09:28:57 | 0 | ||||||||||
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PsyGeNET Resource Report Resource Website 10+ mentions |
PsyGeNET (RRID:SCR_014406) | data or information resource, data processing software, data analysis software, software application, database, software resource | 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 | 2026-08-13 09:29:02 | 11 |
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