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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MATLAB Resource Report Resource Website 10000+ mentions |
MATLAB (RRID:SCR_001622) | MATLAB | programming language, software application, software resource, data processing software, image processing software | Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance. | computing, analyze, visualization, algorithm, plot, vector, matrix |
uses: Functional Network Connectivity (FNC) uses: MVGC Multivariate Granger Causality Matlab Toolbox uses: UltraMegaSort 2000 uses: Elastica2D uses: OSort uses: COMPASS is used by: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) is used by: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) is used by: NiiStat is used by: NeuroElf is used by: MRIcroS is used by: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity is used by: GIMME is used by: GazeReader is used by: Efficient Permutation Testing is used by: APERTURE is used by: Tscratch is used by: PreSurgMapp is used by: SimTracker is used by: ICASSO is used by: TherMos is used by: Mixed Effect Model of Genetic-Set and Environment Interaction is used by: FMAToolbox is used by: BABAM is used by: Soma-Segmentation is used by: SpiSOP is used by: CHIPS is used by: GrowthToolbox is used by: RNAcompete is used by: MicrobeTracker is used by: Sound Analysis Pro is used by: Vocal Inventory Clustering Engine (VoICE) is used by: Automatic Analysis is used by: Measurement Control And Data Analysis Software is used by: Fluorescent Imaging Analysis Software FIMAS is used by: GEMB is used by: IronClust is used by: PAM is used by: calciumImagingAnalysis is used by: TractionsForAll is used by: DeePVP is used by: FieldTrip is used by: Protofilament Bending Models is used by: Toolkit for MIRA LAB Striatal Segmentation is used by: EvaluateMuscleTissueWithElastography is used by: Microscopy_tif_Channel_Quant_MATLAB is used by: CARNet TFA Function is listed by: SoftCite is related to: Spatio- Spectro- Temporal Receptive Field is related to: Extensible MATLAB Medical image Analysis is related to: MultiPhase-SEG is related to: An Open-Source MATLAB-to-Python Compiler is related to: Mastrave modelling library is related to: Libeep EEGLAB plugin is related to: The Bergen fMRI Toolbox Plugin for EEGLab is related to: Electrographic Seizure Analyzer is related to: BVA import/export EEGLAB plugin is related to: ROIs selection with a non-graphical user interface is related to: Reglo ICC control with Matlab is related to: QModeling is related to: MicroFilament Analyzer is related to: Letswave is related to: KiloSort is related to: Suite2P is related to: kCSD-Matlab is related to: nonparametricGGC_toolbox is related to: User Friendly Functional Connectivity - UF²C is related to: Frozen Noise is related to: Microscopy Image Browser is related to: MrDiffusion is related to: rsfMRI_fconn calculation is related to: SPM is related to: Colour maps for brain imaging is related to: Tools for NIfTI and ANALYZE image is related to: PESTO is related to: PPR-Meta is related to: NMF Toolbox is related to: SynapseLocator is related to: SBFSEM-tools is related to: Brain Gene Expression Analysis toolbox is related to: Neural Ideal is related to: Computer Vision System Toolbox is related to: LAN toolbox is related to: hMRI-toolbox is related to: Brainstorm is related to: auto_acpc_reorient is related to: SuperSegger is related to: MNE software is related to: Toolbox for Representational Similarity Analysis is related to: Sandwich Estimator Toolbox is related to: alpha helix coordinate frame simulation is related to: ZebEyeTrack is related to: PottersWheel is related to: Calliope calcium imaging processing package is related to: MVPA Light is related to: Amsterdam Decoding And Modeling is related to: Residue Iteration Decomposition is related to: ObjectFinder is related to: Deep Learning Toolbox is required by: OSort is required by: COMPASS is required by: MicrobeTracker is required by: Wave_clus is required by: Mass Univariate ERP Toolbox is required by: Linear Fascicle Evaluation is required by: PALM works with: CoSMoMVPA works with: Nexus works with: Empirical Gramian Framework works with: OriginPro works with: circular statistics works with: MRspa |
PMID:30609523 PMID:21934110 |
Restricted | nlx_153890 | SCR_001622 | matlab, MATLAB -The Language of Technical Computing, MATLAB, matrix laboratory | 2026-07-31 09:25:07 | 61711 | ||||||
|
Spatio- Spectro- Temporal Receptive Field Resource Report Resource Website 1+ mentions |
Spatio- Spectro- Temporal Receptive Field (RRID:SCR_007995) | software resource | STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation. | matlab, neuroscience, nonlinear, receptive field, response, sensory, signal, spatio, spectro, stimulus, sensory system, temporal |
is related to: MATLAB has parent organization: University of California at Berkeley; Berkeley; USA |
nif-0000-07191 | SCR_007995 | STRFPak | 2026-07-25 12:06:49 | 5 | |||||||||
|
DeePVP Resource Report Resource Website 1+ mentions |
DeePVP (RRID:SCR_022474) | software resource | Software tool for identification and classification of phage virion proteins using deep learning. | Phage virion proteins, proteins identification and classification | uses: MATLAB | DOI:10.1101/2021.10.23.465539 | Free, Available for download, Freely available | SCR_022474 | 2026-07-25 12:10:22 | 1 | |||||||||
|
CHIPS Resource Report Resource Website 100+ mentions |
CHIPS (RRID:SCR_015741) | CHIPS | software resource, software application, image processing software, data processing software | Image processing software designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. CHIPS is a set of classes and functions for MATLAB that integrates a number of algorithms, both novel and existing, into a complete image processing pipeline. | image processing, blood vessel, photon microscopy, matlab, cell, hemodynamic | uses: MATLAB | Open source, Available for download, Runs on Mac OS, Runs on Windows, Runs on Linux | SCR_015741 | Cellular and Hemodynamic Image Processing Suite, CHIPS: an open-source Cellular and Hemodynamic Image Processing Suite | 2026-07-30 09:29:42 | 210 | ||||||||
|
IronClust Resource Report Resource Website 1+ mentions |
IronClust (RRID:SCR_018903) | software resource, software application, image processing software, data processing software | Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments. | Spike sorting, electrophysiology experiment recording, high channel count probe, electrophysiology recording | uses: MATLAB | Free, Available for download, Freely available | SCR_018903 | 2026-07-30 09:30:41 | 7 | ||||||||||
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KiloSort Resource Report Resource Website 100+ mentions |
KiloSort (RRID:SCR_016422) | software resource, software application, data processing software, algorithm resource | Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings. | implement, integrated, template, matching, framework, detect, cluster, spike, multi, channel, electrophysiology, recording, data | is related to: MATLAB | Free, Available for download, Freely available | SCR_016422 | 2026-07-30 09:30:00 | 115 | ||||||||||
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Automatic Analysis Resource Report Resource Website 1+ mentions |
Automatic Analysis (RRID:SCR_003560) | aa | image analysis software, time-series analysis software, software toolkit, workflow software, data analysis software, software application, software resource, data processing software, image processing software | Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps. | Neuroimaging workflows, processing multimodal datasets, brain integrated views, fmri, eeg, meg, dwi, morphometry, parallel-processing, scripting, record-keeping, |
uses: FreeSurfer uses: MATLAB uses: SPM |
NSERC Discovery and the Canada Excellence Research Chair (CERC) in Cognitive Neuroimaging ; NSERC/CIHR CHRP ; NIA R01 AG038490; NIDCD R01 DC013063 |
PMID:25642185 | nlx_157695 | SCR_003560 | automaticanalysis, AutomaticAnalysis | 2026-07-31 09:25:34 | 8 | ||||||
|
FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | software toolkit, data analysis software, software application, software resource, data processing software | Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists. | MEG, EEG, iEEG, analysis, data, time, frequency, source, reconstruction, dipole, beamformers, non parametric, statistical, testing |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Connectome Coordination Facility has parent organization: Radboud University; Nijmegen; The Netherlands works with: CoSMoMVPA works with: SleepTrip works with: EEGLAB works with: SPM |
Human Connectome project ; NIH Blueprint for Neuroscience Research ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-07-31 09:25:57 | 3073 | ||||||
|
Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data visualization software, data analysis software, software application, software resource, data processing software | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB000473; NIBIB R01 EB026299; CNRS ; McGill University |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 | SCR_001761 | brainstorm3 | 2026-07-31 09:25:09 | 558 | ||||
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Extensible MATLAB Medical image Analysis Resource Report Resource Website 1+ mentions |
Extensible MATLAB Medical image Analysis (RRID:SCR_013499) | data visualization software, software toolkit, software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community. | analysis, matlab, medical, neurological, tool, image, toolkit |
is listed by: Internet Analysis Tools Registry is related to: MATLAB is related to: MINC |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33081 | SCR_013499 | MINC-EMMA, EMMA | 2026-07-31 09:27:19 | 7 | |||||||
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GazeReader Resource Report Resource Website 1+ mentions |
GazeReader (RRID:SCR_014112) | software toolkit, data acquisition software, software application, data processing software, software resource | A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment. | software toolkit, data acquisition software, eye tracking, glm analysis, matlab |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
Free for non-commercial use only | http://www.nitrc.org/projects/gazereader | SCR_014112 | 2026-07-31 09:27:24 | 1 | |||||||||
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GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity Resource Report Resource Website 10+ mentions |
GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity (RRID:SCR_014117) | software toolkit, data analysis software, software application, software resource, data processing software | A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results. | software toolbox, data analysis, brain connectivity, graph theoretical analysis, statistical analysis, network construction, network characterization |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:25725332 | Available for download | http://www.rfmri.org/GraphVar | SCR_014117 | GraphVar | 2026-07-31 09:27:26 | 33 | |||||||
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Tscratch Resource Report Resource Website 10+ mentions |
Tscratch (RRID:SCR_014282) | image analysis software, data analysis software, software application, software resource, data processing software, standalone software | Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze, wound, scratch, healing, assay, cell, migration, monolayer |
uses: MATLAB has parent organization: ETH Zurich; Zurich; Switzerland |
NCI CA69184; Swiss National Fund ; Austrian Science Foundation ; Cancer League Zurich ; Commission of the European Communities ; NCCR CO-ME |
PMID:19450233 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/cselab/TScratch | SCR_014282 | 2026-07-31 09:27:28 | 45 | |||||||
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CoSMoMVPA Resource Report Resource Website 100+ mentions |
CoSMoMVPA (RRID:SCR_014519) | software toolkit, data analysis software, software application, software resource, data processing software | A multi-modal multivariate pattern analysis of neuroimaging data in Matlab / GNU Octave. Links to examples, exercises, and information for developers are available on the main page. | functional magnetic resonance imaging, magnetoencephalography, multivariate pattern analysis, neuroscience, weill cornell, software toolkit, data analysis software |
is related to: PyMVPA works with: MATLAB works with: GNU Octave works with: FieldTrip |
Autonomous Province of Trento ; Call Grandi Progetti 2012 ; project Characterizing and improving brain mechanisms of attention - ATTEND |
DOI:10.1101/047118 | Available for download | https://github.com/CoSMoMVPA/CoSMoMVPA | SCR_014519 | 2026-07-31 09:27:35 | 179 | |||||||
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Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | data acquisition software, software application, data processing software, software resource | Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment. | biomechanics, motion capture |
is listed by: SoftCite works with: MATLAB works with: Bodybuilder |
Available for download | https://www.vicon.com/downloads/core-software/nexus | SCR_015001 | Nexus 2, Nexus 1.8.5, Nexus 2.5.0, Nexus 2.4.0 | 2026-07-31 09:27:37 | 373 | ||||||||
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MultiPhase-SEG Resource Report Resource Website |
MultiPhase-SEG (RRID:SCR_008275) | image analysis software, segmentation software, software application, software resource, data processing software | A segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Its features include: segmentation of three-dimensional brain volumes into two or more regions (for example, regions could be WM, GM, and CSF), visualization of surfaces representing boundaries of different brain regions, and being written in Matlab with the ability to run on any platform with Matlab installed. | segementation, visualization, 3D, software |
is related to: Laboratory of Neuro Imaging is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23319 | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 | SCR_008275 | 2026-07-31 09:26:38 | 0 | |||||||
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MNE software Resource Report Resource Website 50+ mentions |
MNE software (RRID:SCR_005972) | MNE | data visualization software, software toolkit, data analysis software, software application, software resource, data processing software | Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. | Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MNE-BIDS is related to: MATLAB is related to: NumPy is related to: SciPy is related to: Matplotlib is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project is related to: NiBabel |
NIBIB R01 EB009048; NIBIB P41 EB015896; NCRR P41 RR014075; NIDCD F32DC012456; NSF 0958669; NSF 1042134; European Research Council (ERC) StG-263584 |
PMID:24161808 PMID:24431986 |
Free, Available for download, Freely available | nlx_151346 | https://sources.debian.org/src/python3-mne/, http://www.nitrc.org/projects/mne, http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html, https://github.com/mne-tools/, https://mne.tools/ | SCR_005972 | Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python | 2026-07-31 09:26:19 | 97 | ||||
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Empirical Gramian Framework Resource Report Resource Website |
Empirical Gramian Framework (RRID:SCR_015043) | emgr | software resource, software application | Software for empirical gramians for model reduction of (nonlinear) input-output systems. | model reduction, model order reduction, empirical gramian, empirical cross gramian matrix, combined reduction |
works with: MATLAB works with: GNU Octave |
DOI:10.5281/zenodo.2530021 | Runs on Windows, Runs on Linux, Open source, Demo available | https://github.com/gramian/emgr | SCR_015043 | emgr - EMpirical GRamian framework, Empirical Gramian Framework (EMGR) | 2026-07-30 09:29:30 | 0 | ||||||
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SimTracker Resource Report Resource Website 1+ mentions |
SimTracker (RRID:SCR_014735) | software resource, software application, standalone software | MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility. | matlab, simulation, neuron, neuron network model, model design, model organization, model execution, model analysis, model reproducibility |
uses: MATLAB works with: NEURON |
DOI:10.1101/081927 | Available for download | SCR_014735 | 2026-07-30 09:29:26 | 1 | |||||||||
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Deep Learning Toolbox Resource Report Resource Website 1+ mentions |
Deep Learning Toolbox (RRID:SCR_024747) | software resource, software application | Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network. | simple MATLAB commands, creating and interconnecting layers of deep neural network, | is related to: MATLAB | Restricted | SCR_024747 | 2026-07-30 09:32:00 | 2 |
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