Open Source MATLAB Medical Software
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MATLAB Medical Software
View 203 business solutionsBrowse free open source MATLAB Medical Software and projects below. Use the toggles on the left to filter open source MATLAB Medical Software by OS, license, language, programming language, and project status.
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BioSig is a software library for processing of biomedical signals (EEG, ECG, etc.) with Matlab, Octave, C/C++ and Python. About 50 different data formats are supported.
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Monte Carlo eXtreme (MCX)
Physically accurate and validated GPU ray-tracer
MCX is a GPU-accelerated, general-purpose, physically-accurate and feature-rich 3-D light transport simulator. It is one of the fastest simulators because it can use tens of thousands of GPU threads to simulate photons in parallel. -
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Iso2Mesh - A 3D Mesh Generation Toolbox
A 3D surface and volumetric mesh generator for MATLAB/Octave
A simple yet powerful mesh generator based on MATLAB/GNU Octave language, creating finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows. -
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niftilib
** MAIN SITE IS NOW: https://github.com/NIFTI-Imaging/nifti_clib **
niftilib is a collection of i/o routines for the nifti1 neuroimage data format. C (nifticlib), Java (niftijlib), Matlab (niftimatlib), and Python (pynifti) code is available. For nifti format info see: http://nifti.nimh.nih.gov/ -
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MRiLab
A Numerical MRI Simulation Platform
The MRiLab project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MRiLab/ The MRiLab is a numerical MRI simulation package. It has been developed and optimized to simulate MR signal formation, k-space acquisition and MR image reconstruction. MRiLab provides several dedicated toolboxes to analyze RF pulse, design MR sequence, configure multiple transmitting and receiving coils, investigate magnetic field related properties and evaluate real-time imaging technique. The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961 -
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An evaluation framework for assessing contours generated by segmentation algorithms acting on cardiac magnetic resonance (MR) images. These contours are important for clinical assessment of left ventricular volume and mass.
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ReViSP
ReViSP, a 3D volume rendering MATLAB tool for multicellular spheroids
Reconstruction and Visualization from a Single Projection (ReViSP) tool: a 3D volume rendering method we developed to reconstruct the 3D shape of multicellular spheroids, besides estimating the volume by counting the voxels (3D pixels) fully included in the 3D surface. ReViSP is written in MATLAB (The MathWorks, Inc., Massachusetts, USA) and the source code is freely provided. Requirements for running ReViSP from the source code: MATLAB 2020a and Image Processing Toolbox 11.1 or later versions. Please, when using this software, cite these articles: (a) F. Piccinini, et al., Cancer multicellular spheroids: Volume assessment from a single 2D projection. Computer Methods and Programs in Biomedicine, 118(2):95–106, 2015. (b) F. Piccinini, et al., Single-image based methods used for non-invasive volume estimation of cancer spheroids: a practical assessing approach based on entry-level equipment. Computer Methods and Programs in Biomedicine, 135:51-60, 2016. -
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PsPM
A matlab suite for Psycho-Physiological Modelling
PsPM is a powerful tool for psychophysiological modelling. It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although this website will maintained to provide further releases, there will be no active development on the SVN repository. Thank you for your understanding and for using PsPM. -
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This project will be moving to GitHub. If you want to contribute or get the latest source go to: https://github.com/jramshur/HRVAS HRVAS is a heart rate variability (HRV) analysis tool developed using MATLAB. HRVAS can detrend and filter IBI and can perform time domain, frequency domain, time-frequency, Poincare', and nonlinear HRV analysis. If you use this application or modify this application for your research, please reference the thesis entitled "DESIGN, EVALUATION, AND APPLICAION OF HEART RATE VARIABILITY ANALYSIS SOFTWARE (HRVAS)". The thesis can be found here: http://iweb.dl.sourceforge.net/project/hrvas/Documents/ramshur_thesis.pdf
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DoseLab is a set of software programs for quantitative comparison of measured and computed radiation dose distributions. It is written in the Matlab programming language and is easily extensible to more general applications in radiation physics.
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SCRalyze
A matlab environment for model-based psychophysiology
SCRalyze is a powerful tool for model-based analysis of psychophysiological signals, using linear convolution models and dynamic causal modelling. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM (formerly SCRalyze) has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although this website will maintained to provide further releases, there will be no active development on the SVN repository. Thank you for your understanding and for using PsPM. -
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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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MatrixUser
A Multi-functional GUI-based Program for Image Processing and Analysis
The MatrixUser project is moving to GitHub, the latest version can be obtained from https://leoliuf.github.io/MatrixUser/ Most of the medical images (e.g. CT, MRI, PET, etc.) comprises multiple frames which represent slices, phases, timing etc. from the same imaging object. Those images can be saved as multidimensional matrices in Matlab thanks to Matlab's powerful support of multidimensional data representation. However, within Matlab, most of image manipulation functions are limited or tailored for processing two-dimensional matrix. The MatrixUser is a software package which features functions designed and optimized specifically for manipulating multidimensional real or complex data matrix. MatrixUser provides a nice graphical environment for easily performing image analysis tasks including multidimensional image display, matrix (image stack) processing and rendering etc. MatrixUser is a great lightweight tool for users who are working in image processing field under Matlab. -
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While resting-state fMRI is drawing more and more attention, there has not been a software for its data analysis. Based on MATLAB, we developed a package named REST. Currently REST has three main functions: function connectivity, ReHo and ALFF.
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GoIFISH
for the semi-automated analysis of IFISH images
GoIFISH has been developed for the analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection. Users can manually edit segmentation results, perform background adjustments, construct heatmaps, topology maps, and perform cell classification. All results can be exported for further analysis. GoIFISH has been developed in MATLAB, however binaries are provided to run the program outside of the MATLAB environment. Source code is also available for download. To cite this software: "GoIFISH: A system for the quantification of single cell heterogeneity from IFISH images" Trinh A, Rye IH, Almendro V, Helland A, Russness HG, Markowetz F May 2014 -
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This project will use 3D Human Emulation using sensors to pickup human movements and displaying them on GUI for analysis.
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ARIA
Retinal vessel detection using MATLAB
NOTE: This project is now hosted at GitHub. Please follow the link below to visit its new home. -
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Adaptative thresholding for fMRI
Matlab scripts to perform cluster FDR adaptative thresholding
Matlab plug-in for SPM allowing to obtain a threshold for cluster FDR - the method fits a Gamma-Gaussian mixture model to the SPM-T and finds the optimal threshold (crossing between noise and activation). Optionally write the thresholded maps. -
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AnalyzeNNLS
MRI Multiple Echo T2 Analysis
Users load multiecho MRI data and draw ROIs. AnalyzeNNLS creates a T2 distribution from the averaged decay data. Regional fractions and geometric T2 times can be determined. Please reference: Bjarnason TA, Mitchell JR. JMR 206:200-4 (2010). Temporal Phase Correction included in version 2.5. If you use this functionality, please reference: Bjarnason TA, Laule C, Bluman J, Kozlowski P. JMR 232:22-31 (2013). -
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Brain imaging software produced by the Brain Research Imaging Centre of The University of Edinburgh.
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Matlab tool for plotting multi-channel biomedical signals. It is designed for researchers on both engineering and medicine who have to collaborate to visualize and analyze signals. It is the ideal tool to plot electroencephalogram (EEG), Foetal Heart Rate (FHR) and many other signals with the standard tools used in clinical routine.
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The Biopsychology Nonlinear Toolbox is a MATLAB toolbox that combines established analysis routines in one easy to use graphical user interface.
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BrOxy is an open-source program used to analyse haemodynamic brain oxygenation from near-infrared spectroscopy data. It covers data import/export, filtering, correlation and multi-variate regression analysis, visualisation...