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http://www.mathworks.com/products/matlab/
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.
Proper citation: MATLAB (RRID:SCR_001622) Copy
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.
Proper citation: Spatio- Spectro- Temporal Receptive Field (RRID:SCR_007995) Copy
https://github.com/fangzcbio/DeePVP
Software tool for identification and classification of phage virion proteins using deep learning.
Proper citation: DeePVP (RRID:SCR_022474) Copy
https://github.com/EIN-lab/CHIPS
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.
Proper citation: CHIPS (RRID:SCR_015741) Copy
https://github.com/flatironinstitute/ironclust
Spike sorting software for multi day recordings from high channel count probes during electrophysiology experiments.
Proper citation: IronClust (RRID:SCR_018903) Copy
https://github.com/cortex-lab/Kilosort
Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.
Proper citation: KiloSort (RRID:SCR_016422) Copy
https://github.com/automaticanalysis/automaticanalysis
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.
Proper citation: Automatic Analysis (RRID:SCR_003560) Copy
https://www.fieldtriptoolbox.org
Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.
Proper citation: FieldTrip (RRID:SCR_004849) Copy
http://neuroimage.usc.edu/brainstorm/
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.
Proper citation: Brainstorm (RRID:SCR_001761) Copy
http://www.cma.mgh.harvard.edu/iatr/display.php?spec=id&ids=107
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.
Proper citation: Extensible MATLAB Medical image Analysis (RRID:SCR_013499) Copy
http://www.nitrc.org/projects/gazereader/
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.
Proper citation: GazeReader (RRID:SCR_014112) Copy
http://www.nitrc.org/projects/graphvar/
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.
Proper citation: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity (RRID:SCR_014117) Copy
http://www.cse-lab.ethz.ch/index.php?&option=com_content&view=article&id=363
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.
Proper citation: Tscratch (RRID:SCR_014282) Copy
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.
Proper citation: CoSMoMVPA (RRID:SCR_014519) Copy
https://www.vicon.com/products/software/nexus
Data capture software for use with Vicon motion capture system. Its features include MATLAB integration, Python pre-installed, customized workflow, and automated quality assessment.
Proper citation: Nexus (RRID:SCR_015001) Copy
http://www.loni.usc.edu/Software/MultiPhase-SEG
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.
Proper citation: MultiPhase-SEG (RRID:SCR_008275) Copy
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.
Proper citation: MNE software (RRID:SCR_005972) Copy
Software for empirical gramians for model reduction of (nonlinear) input-output systems.
Proper citation: Empirical Gramian Framework (RRID:SCR_015043) Copy
http://mariannebezaire.com/simtracker/
MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.
Proper citation: SimTracker (RRID:SCR_014735) Copy
https://uk.mathworks.com/help/deeplearning/ug/deep-learning-in-matlab.html
Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network.
Proper citation: Deep Learning Toolbox (RRID:SCR_024747) Copy
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