Open Source MATLAB Medical Software

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.

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.

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.

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

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

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.

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/

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.

Toolboxes for SPM (http://www.fil.ion.ucl.ac.uk/spm/) developed at Freiburg Brain Imaging (http://fbi.uniklinik-freiburg.de/)

NOTE: This project is now hosted at GitHub. Please follow the link below to visit its new home.

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.

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.

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.

SPKtool is a toolbox developed on MATLAB which enables a user to perform spike (action potential of neurons) detection, spike sorting (manually or automatically) and spike train analysis.

This project will use 3D Human Emulation using sensors to pickup human movements and displaying them on GUI for analysis.

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.

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).

Brain imaging software produced by the Brain Research Imaging Centre of The University of Edinburgh.

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.

The Biopsychology Nonlinear Toolbox is a MATLAB toolbox that combines established analysis routines in one easy to use graphical user interface.

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...

CCA-fMRI is a SPM-toolbox (http://www.fil.ion.ucl.ac.uk/spm/) for detecting brain activity pattern using functional magnetic resonance imaging (fMRI) in combination with canonical correlation analysis.

A tool to register and superpose CTF MEG SAM(g2) result and MRI image into one gray-level image.

There is the toolbox of implementing a mehod for consistent group indepent component analysis for functional magnetic resonance imaging.

DAT_Analyzer (DANA) is fully automated tool for analyzing dopamine transporter PET. DANA utilizes coregistration and spatial normalization functions in SPM8 and therefore requires MATLAB 7.1 (or higher) and SPM8 in 64bit environment with more than 8 GB RAM. MAC OSX OS is recommended. It includes various custom templates for conventional MR, DARTEL MR, two type of CT, and ligand specific PET and also includes various types of striatal subregional VOI templates. It supports five types of spatial normalization methods. (This project will be uploaded soon. It's now under construction.)