a tool for interactively viewing & marking multi-channel biosignals
EyeBallGUI: a tool for interactively viewing and marking multi-channel bio-signals for artefacts. The purpose of EyeBallGUI is to facilitate the eyeballing of multi-channel biosignals for the purpose of artefact rejection (or any other binary grouping). EyeBallGUI displays a set of time-series signals in a MATLAB Figure window, allowing the user to visually inspect and interact with the data via the mouse and keyboard in order to mark data as bad/rejected. The tool can be used to visualize a wide range of data types to make any kind of binary decision about segments of data. However, the motivation for the tool is to facilitate the visualization of multi-channel EEG data for the purpose of artefact rejection. EyeBallGUI is based in MATLAB® and works in Microsoft Windows. Proficiency in MATLAB is not required to use EyeBallGUI. It can be used either as a stand-alone MATLAB-based tool or as an EEGLAB plugin. Please cite using: https://doi.org/10.1101/129437
To automatically obtain mosaics of partially overlapping images.
MicroMos is an open-source software tool written in MATLAB (The MathWorks, Inc., Massachusetts, USA), for automatically obtaining mosaics of partially overlapped images, also manually acquired. It was designed for stitching microscopy images, but thanks to the many parameters available it works also for other types of images. For more details, please, read: a) F. Piccinini, M. Pierini, E. Lucarelli, A. Bevilacqua, Semi-quantitative monitoring of confluence of adherent mesenchymal stromal cells on calcium-phosphate granules by using widefield microscopy images. Journal of Materials Science: Materials in Medicine, 25(10):2395-2410, October 2014. 2) F. Piccinini, A. Bevilacqua, E. Lucarelli, Automated image mosaics by non-automated light microscopes: the MicroMos software tool. Journal of Microscopy, 252(3):226-250, December 2013.
slab3d is a real-time virtual acoustic environment.
slab3d is a real-time virtual acoustic environment rendering system. It includes two rendering applications, libraries for spatial auditory display and audio signal processing development, and a set of tools for HRTF analysis and visualization.
Detection of Miniature Inverted Repeat Transposable Elements
detectMITE - a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) in genomes.  Who are we? Please visit website: http://bioinfolab.miamioh.edu  How to cite detectMITE? Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci. Rep. 6, 19688. http://www.nature.com/articles/srep19688 Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. PLoS ONE 9(11): e113349. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349  detectMITE user manual Please visit the Wiki page of this website.  detectMITE Q&A For Q&A, please visit the Blog page of this website.  Update history To see the update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/
Toolbox for processing spinal cord MRI data
The Spinal Cord Toolbox is a comprehensive and open-source library of analysis tools for multi-parametric MRI of the spinal cord. List of contributors can be found here: https://sourceforge.net/p/spinalcordtoolbox/wiki/Home/
All future developments will be implemented in the new MATLAB toolbox SciXMiner, please visit https://sourceforge.net/projects/scixminer/ to download the newest version. The former Matlab toolbox Gait-CAD was designed for the visualization and analysis of time series and features with a special focus to data mining problems including classification, regression, and clustering.
Metagenomic Microbial Interaction Simulator
MetaMIS is the first tool to automatically infer the microbial interactions of microbial community profile in the field of metagenomics. The most distinguished feature of MetaMIS is its ability to retain maximum population of rare species in an ecological interactive network. MetaMIS provides a user-friendly interactive stand-alone graphical interface for scientists without programming skills to investigate the interactions among microorganisms. 2017.03.09 MetaMIS_v1.02: - Create an option to export consensus table. - Decimal time is allowed. 2016.12.16 MetaMIS_v1.01: - fix the memory-out problem for larger abundance table (>500 OTUs). - add three items to constrain the total number of running interaction networks 2016.11.17 MetaMIS_v1
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating the volume of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools for: (a) segmenting z-stacks of fluorescence images; (b) reconstructing the 3D surface of the aggregates and estimating their volume. ReViMS is written in MATLAB (The MathWorks, Inc., Massachusetts, USA). It is an open-source tool and the source code is freely available at: http://sourceforge.net/p/revims Requirements: MATLAB 2015a and Image Processing Toolbox 9.2 or later versions.
Units for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal, S and Matlab.
An open source controller for Scalextric community
Open source controller for Scalextric community. Scalextric Controller is composed by a custom hand controller, used to drive the Scalextric slots cars, and Android application used to communicate with the hand controller via Bluethoot low power (BLE). This project repository contains the PCB project, the micro embedded software, the Android App and the 3D CAD design of the cricital mechanical parts.
A MATLAB toolbox for relating neural signals to continuous stimuli
mTRF Toolbox is a MATLAB toolbox that permits the fast computation of the linear stimulus-response mapping of any sensory system in the forward or backward direction. It is suitable for analysing EEG, MEG, ECoG and EMG data. The forward model, or temporal response function (TRF), can be interpreted using conventional analysis techniques such as time-frequency and source analysis. The TRF can also be used to predict future responses of the system given a new stimulus signal. Similarly, the backward model can be used to reconstruct spectrotemporal stimulus information given new response data. mTRF Toolbox facilitates the use of continuous stimuli in electrophysiological studies as opposed to time-locked averaging techniques which require discrete stimuli. This enables examination of how neural systems process more natural and ecologically valid stimuli such as speech, music, motion and contrast. Support documentation: http://dx.doi.org/10.3389/fnhum.2016.00604
A Matlab software routine to perform Principal Component Analysis using Covariance, Correlation or Comedian as the criterion. Though, initially developed for experiments related to fretting wear but can be effectively used to interpret experimental data from any field. The attached files contain source code as well as a sample MATLAB (.mat) data file of 13 variables. It could be replaced to the data file of your choice. The code is open source but you are requested to give credits if used. Additionally, it also has some useful functions for exporting and generating publication quality figures for different kind of figures in MATLAB
Hysteresis of ellipsoidal single domain ferromagnetic particle.
Sample code for Ocean Optics OmniDriver spectrometer device driver
Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more.
Version 1.1 is no longer supported.
Version 1.1 is no longer supported. Please see the new version at https://usc-imi.github.io/aeo-light/ Description for 1.1 continues below: AEO-Light 1.1 is an open-source software application that takes a digital scan of motion picture film with optical sound tracks and directly reproduces the audio, producing as a result a synchronized sound film file. Funded by a grant from the National Endowment for the Humanities and by the University of South Carolina.
Spatially Oriented Format for Acoustics
In this project we work on the (S)patially (O)riented (F)ormat for (A)coustics: SOFA. The file format is intended for reading, saving, and describing spatially oriented data of acoustic systems. Examples of data we consider are head-related transfer functions (HRTFs), binaural room impulse responses (BRIRs), multichannel measurements such as done with microphone arrays, or directionality data of loudspeakers. The format specifications are the major issue, but we also aim in providing APIs for reading and writing the data in SOFA.
SparesPOP is a MATLAB implementation of a sparse semidefinite programming (SDP) relaxation method proposed for polynomial optimization problems (POPs). Please send a message to firstname.lastname@example.org if you have any question and/or request. We also release SparsePOPC++ and SparsePOPC++-windows. Both implementations are SparsePOP which does not use MATLAB, but only C++. In particular, SparsePOPC++-windows contains a binary file which works on Windows, and does not require to compile.
A tool able to simulate gene-environment and gene-gene interactions.
Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface.
Development of new data assimilation techniques for ocean models
The mfBox is a Matlab toolbox for performing model-free analysis of multivariate data sets. It also plugs into SPM used for the analysis of multivariate brain recordings such as fMRI, SPECT and PET data sets.
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.
Advanced acoustic detection, classification and localization
Advanced detection, classification and localization (DCL) of marine mammals and passive acoustic monitoring (PAM). Code is being developed as Matlab routines, interfaces for Ishmael (http://www.bioacoustics.us/ishmael.html), and in other formats.
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. Enclosed in this package is also an archive of different Bioinformatics matrices.
A simple yet powerful mesh generator based on matlab/octave language, making finite-element mesh from surfaces or arbitrary 3D volumetric images (such as MRI/CT scans) with fully automatic workflows.
A Numerical MRI Simulation Platform
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 MRiLab v1.3 is available now, with supports for generalized multicomponent tissue model.