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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 |
PMID:30609523 PMID:21934110 |
Restricted | nlx_153890 | SCR_001622 | matlab, MATLAB -The Language of Technical Computing, MATLAB, matrix laboratory | 2026-08-21 12:36:26 | 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 | 2026-08-15 11:23:39 | 6 | |||||||||
|
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 | 2026-08-15 11:27:23 | 1 | |||||||||
|
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) | 2026-08-20 09:29:14 | 0 | ||||||
|
CARNet TFA Function Resource Report Resource Website 1+ mentions |
CARNet TFA Function (RRID:SCR_027022) | software application, software resource | Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report. | Cerebral Autoregulation Research Network, Transfer Function Analysis, Matlab TFA function, | uses: MATLAB | DOI:10.1177/0271678X15626425 | Free, Freely available, | SCR_027022 | , Matlab TFA function, Cerebral Autoregulation Research Network Transfer Function Analysis Function | 2026-08-20 09:32:03 | 3 | ||||||||
|
Deep Learning Toolbox Resource Report Resource Website 1+ mentions |
Deep Learning Toolbox (RRID:SCR_024747) | software application, software resource | 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 | 2026-08-20 09:31:26 | 2 | ||||||||||
|
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 | 2026-08-21 12:37:08 | 8 | ||||||
|
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 | 2026-08-21 12:37:39 | 3297 | ||||||
|
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 | 2026-08-21 12:37:40 | 114 | ||||
|
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 | 2026-08-21 12:36:29 | 622 | ||||
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Nexus Resource Report Resource Website 100+ mentions |
Nexus (RRID:SCR_015001) | data acquisition software, data processing software, software application, 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 | 2026-08-21 12:40:10 | 397 | ||||||||
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CHIPS Resource Report Resource Website 100+ mentions |
CHIPS (RRID:SCR_015741) | CHIPS | data processing software, image processing software, software application, software resource | 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 | 2026-08-21 12:40:58 | 213 | ||||||||
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BABAM Resource Report Resource Website |
BABAM (RRID:SCR_015632) | data analysis resource, data processing software, data visualization software, software application, software resource | Graphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection. | drosophila melanogaster, correlation hypothesis, neural activity, thermogenetic neural activation screen | uses: MATLAB | Free, Available for download | SCR_015632 | Browsable Atlas of Behavior-Anatomy Maps, Browsable Atlas of Behavior-Anatomy Maps (BABAM) | 2026-08-21 12:40:57 | 0 | |||||||||
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SpiSOP Resource Report Resource Website 10+ mentions |
SpiSOP (RRID:SCR_015673) | data processing resource, software resource, software toolkit, source code | Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel. | spindle, slow oscillation, frequency band, sleep, eeg, meg, emg artifact detection, matlab, sleep scoring, file conversion |
uses: MATLAB is related to: COsleep is related to: SleepTrip has parent organization: University of Tubingen; Tubingen; Germany has parent organization: Institute of Medical Psychology and Behavioral Neurobiology, University of Tbingen |
Open Source, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | https://github.com/Frederik-D-Weber/spisop | SCR_015673 | Spindles Slow Oscillation and Power-spectral-density | 2026-08-21 12:40:57 | 31 | ||||||||
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FMAToolbox Resource Report Resource Website 50+ mentions |
FMAToolbox (RRID:SCR_015533) | data analysis software, data processing software, software application, software resource | Matlab toolbox used to help analyze electrophysiological and behavioral data recorded from freely moving animals. | electrophysiology software, behavioral software, freely moving animal, matlab |
uses: MATLAB is listed by: SourceForge |
Available for download, Acknowledgement requested | http://www.buzsakilab.com/content/PDFs/HasanJNeuroscMeth2006.pdf | SCR_015533 | FMA Toolbox, Freely Moving Animal Toolbox | 2026-08-21 12:40:53 | 65 | ||||||||
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OSort Resource Report Resource Website 10+ mentions |
OSort (RRID:SCR_015869) | algorithm resource, data analysis software, data processing software, data visualization software, software application, software resource | Framework for spike sorting that includes tools for pre-processing, spike detection, spike sorting, and sorting quality evaluation. It is principally designed for sorting of single-wire microwire recordings in humans, but is being used for other types of recordings as well. | spike sorting, spike detection, single-wire microwire recording, neuroimaging, neuron recording |
is used by: MATLAB requires: MATLAB |
Cedars-Sinai Medical Center ; Gimbel Discovery Fund ; Howard Hughes Medical Institute |
PMID:16488479 | Open source, Available for download, Tutorial available | SCR_015869 | OSort: spike sorting package | 2026-08-21 12:40:59 | 13 | |||||||
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Sound Analysis Pro Resource Report Resource Website 10+ mentions |
Sound Analysis Pro (RRID:SCR_016003) | SAP | data analysis software, data processing software, software application, software resource | Software for birdsong analysis that performs automated recording and analysis of animal vocalization. It can record, analyze and manage sound data over prolonged periods. | matlab, bird, birdsong, avian, auditory, animal, communication, record, auditory analysis | uses: MATLAB | NIDCD | Free, Available for download | SCR_016003 | 2026-08-21 12:40:32 | 28 | ||||||||
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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 | 2026-08-21 12:40:45 | 1 | ||||||||||
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MRIcroS Resource Report Resource Website 1+ mentions |
MRIcroS (RRID:SCR_014142) | data analysis software, data processing software, data visualization software, software application, software resource | A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap. | data visualization software, data analysis software, surface mesh visualization, matlab |
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 | SCR_014142 | 2026-08-21 12:40:16 | 3 | ||||||||||
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GIMME Resource Report Resource Website 1+ mentions |
GIMME (RRID:SCR_014115) | GIMME | data analysis software, data processing software, software application, software resource, software toolkit | Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. | Functional, connectivity, analysis, fMRI, BOLD, signal, predefined, region, pattern, BRAIN Initiative |
uses: MATLAB is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NIBIB EB022904; NIBIB R21 EB015573; NSF 0852147 |
PMID:22732562 | Free, Available for download, Freely available | SCR_014115 | Group Iterative Multiple Model Estimation | 2026-08-21 12:40:11 | 2 |
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