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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 | data processing software, image processing software, programming language, software application, software resource | 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 works with: shiTools |
PMID:30609523 PMID:21934110 |
Restricted | nlx_153890 | SCR_001622 | matlab, MATLAB -The Language of Technical Computing, MATLAB, matrix laboratory | 2026-09-19 12:55:04 | 66533 | ||||||
|
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 | 2026-09-19 12:51:33 | 6 | |||||||||
|
MultiPhase-SEG Resource Report Resource Website |
MultiPhase-SEG (RRID:SCR_008275) | data processing software, image analysis software, segmentation software, software application, software resource | 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 | 2026-09-19 12:51:37 | 0 | |||||||
|
Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data analysis software, data processing software, data visualization software, software application, software resource | 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 |
CNRS ; McGill University ; NIBIB R01 EB000473; NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB026299 |
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 | 2026-09-19 12:49:46 | 622 | ||||
|
MNE software Resource Report Resource Website 100+ mentions |
MNE software (RRID:SCR_005972) | MNE | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 |
European Research Council (ERC) StG-263584; NCRR P41 RR014075; NIBIB P41 EB015896; NIBIB R01 EB009048; NIDCD F32DC012456; NSF 0958669; NSF 1042134 |
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 | 2026-09-19 12:51:02 | 114 | ||||
|
Extensible MATLAB Medical image Analysis Resource Report Resource Website 1+ mentions |
Extensible MATLAB Medical image Analysis (RRID:SCR_013499) | data processing software, data visualization software, software application, software resource, software toolkit | 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 | 2026-09-19 12:52:43 | 7 | |||||||
|
FieldTrip Resource Report Resource Website 1000+ mentions |
FieldTrip (RRID:SCR_004849) | data analysis software, data processing software, software application, software resource, software toolkit | 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 ; Netherlands Ministry of Economic Affairs ; Netherlands Ministry of Education Culture and Science ; NIH Blueprint for Neuroscience Research |
PMID:21253357 | Free, Available for download, Freely available, Tutorial available | nlx_143928 | http://www.nitrc.org/projects/fieldtrip | SCR_004849 | 2026-09-19 12:50:43 | 3297 | ||||||
|
Automatic Analysis Resource Report Resource Website 1+ mentions |
Automatic Analysis (RRID:SCR_003560) | aa | data analysis software, data processing software, image analysis software, image processing software, software application, software resource, software toolkit, time-series analysis software, workflow 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 |
NIA R01 AG038490; NIDCD R01 DC013063; NSERC Discovery and the Canada Excellence Research Chair (CERC) in Cognitive Neuroimaging ; NSERC/CIHR CHRP |
PMID:25642185 | nlx_157695 | SCR_003560 | automaticanalysis, AutomaticAnalysis | 2026-09-19 12:50:22 | 8 | ||||||
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GazeReader Resource Report Resource Website 1+ mentions |
GazeReader (RRID:SCR_014112) | data acquisition software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-19 12:52:52 | 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) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-19 12:52:52 | 34 | |||||||
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Tscratch Resource Report Resource Website 10+ mentions |
Tscratch (RRID:SCR_014282) | data analysis software, data processing software, image analysis software, software application, software resource, 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 |
Austrian Science Foundation ; Cancer League Zurich ; Commission of the European Communities ; NCCR CO-ME ; NCI CA69184; Swiss National Fund |
PMID:19450233 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/cselab/TScratch | SCR_014282 | 2026-09-19 12:52:54 | 48 | |||||||
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CoSMoMVPA Resource Report Resource Website 100+ mentions |
CoSMoMVPA (RRID:SCR_014519) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-19 12:52:58 | 193 | |||||||
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Tools for NIfTI and ANALYZE image Resource Report Resource Website 1+ mentions |
Tools for NIfTI and ANALYZE image (RRID:SCR_016895) | data analysis software, data processing software, image analysis software, service resource, software application, software resource, software toolkit | Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform. | neuroimaging, data, program, analysis, image |
is related to: NIfTI Data Format Working Group is related to: MATLAB |
Free, Available for download, Freely available | https://perso.telecom-paristech.fr/bloch/P6Image/Projets/Nez2/NIfTI_matlab_tools/NIfTI_tools.pdf | SCR_016895 | Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data | 2026-09-19 12:53:30 | 1 | ||||||||
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PESTO Resource Report Resource Website 10+ mentions |
PESTO (RRID:SCR_016891) | PESTO | data analysis software, data processing software, software application, software resource, software toolkit | Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions. | parameter, estimation, MATLAB, algorithm, optimization, uncertainty, identifiability, analysis | is related to: MATLAB | European Union‘s Horizon ; German Federal Ministry of Education and Research ; German Research Foundation via the Graduate School of Quantitative Biosciences Munich |
PMID:29069312 | Free, Available for download, Freely available | https://zenodo.org/record/579890#.XDZvSlxKiM9 | SCR_016891 | Parameter EStimation TOolbox, PESTO | 2026-09-19 12:53:30 | 11 | |||||
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PPR-Meta Resource Report Resource Website 1+ mentions |
PPR-Meta (RRID:SCR_016915) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, metagenomic, sequence, phage, chromosome, plasmid, fragment, machine, learning |
is related to: Python Programming Language is related to: MATLAB is related to: tensorflow |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/zhenchengfang/PPR-Meta | SCR_016915 | 2026-09-19 12:53:30 | 4 | |||||||||
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PALM Resource Report Resource Website 50+ mentions |
PALM (RRID:SCR_017029) | PALM | data analysis software, data processing software, software application, software resource | Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools. | statistics, permutation, bootstrap, non parametric, combination, inference |
requires: MATLAB is a plug in for: FSL |
Brazilian National Research Council ; GlaxoSmithKline ; Marie Curie ITN ; Medical Research Council ; MRC G0900908; NIBIB R01 EB015611; Wellcome Trust |
PMID:24530839 PMID:26074200 DOI:10.1002/hbm.23115 PMID:27288322 |
Free, Available for download, Freely available | https://github.com/andersonwinkler/PALM | SCR_017029 | PALM, Permutation Analysis of Linear Models | 2026-09-19 12:53:32 | 58 | |||||
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SBFSEM-tools Resource Report Resource Website 10+ mentions |
SBFSEM-tools (RRID:SCR_017350) | 3d visualization software, data analysis software, data processing software, data visualization software, software application, software resource | Data analysis and 3D visualization for connectomics and serial electron microscopy. This toolbox provides missing 3D visualization and analysis tools for cylinder-based annotations. Integration with contour, skeleton based annotations and common morphology file formats is also supported. | Data analysis, 3D visualization, connectomics, serial electron microscopy, annotation, morphology |
is related to: MATLAB has parent organization: University of Washington; Seattle; USA |
NEI EY001730; NEI EY027859; NEI EY07031; NINDS NS099578 |
DOI:10.1101/667204 | Free, Available for download, Freely available | https://github.com/neitzlab/SBFSEM-tools | SCR_017350 | 2026-09-19 12:53:39 | 11 | |||||||
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MRspa Resource Report Resource Website 10+ mentions |
MRspa (RRID:SCR_017292) | data analysis software, data processing software, software application, software resource | Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab. | post, process, magnetic, resonance, spectroscopy, data, analysis |
has parent organization: University of Minnesota Twin Cities; Minnesota; USA works with: MATLAB |
Restricted | SCR_017292 | Magnetic Resonance signal processing and analysis | 2026-09-19 12:53:38 | 19 | |||||||||
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Reglo ICC control with Matlab Resource Report Resource Website 1+ mentions |
Reglo ICC control with Matlab (RRID:SCR_016353) | application programming interface, data access protocol, software resource | A Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec. | adapter, class, user, interfce, control, Reglo ICC, peristaltic, pump, Ismatec | is related to: MATLAB | Free, Available for download, Freely available | SCR_016353 | 2026-09-19 12:57:35 | 1 | ||||||||||
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Empirical Gramian Framework Resource Report Resource Website |
Empirical Gramian Framework (RRID:SCR_015043) | emgr | software application, software resource | 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) | 2026-09-19 12:58:13 | 0 |
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