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Analysis of conditional colocalization relationships and hierarchies from three-color microscopy images.

+microstate is a MATLAB toolbox for performing microstate analysis in sensor- or source-reconstructed EEG or MEG data. +microstate can be used for individual- or group-level analyses, and applied to both resting-state or task-evoked data. As well as microstate analysis, +microstate includes functions for calculating microstate statistics and microstate-segmented functional connectivity, visualisation, and simulation of data.

a computer-aided scoring tool for resting-state M/EEG epochs. scorEpochs: a computer aided scoring tool for resting-state M/EEG epochs. Scorepochs aims to represent a simple tool for automatic scoring of resting-state M/EEG epochs to provide an accurate yet objective method to aid M/EEG experts during epoch selection procedure.

A real-coded genetic algorithm software for parameter estimation of kinetic models. RCGAToolbox is a MATLAB toolbox that contains two real-coded genetic algorithms (RCGAs): the unimodal normal distribution crossover with minimal generation gap (UNDX/MGG) and the real-coded ensemble crossover star with just generation gap (REXstar/JGG). The stochastic ranking method is implemented to efficiently handle constrained optimization problems. RCGAToolbox not only provides access to RCGAs but also several useful features for parameter estimation in systems biology. For demonstrations, run scripts in RCGAToolbox/doc/demo. For usage, type "help function_name" in the MATLAB Command Window.

Analyzing engineered point spread functions using phasor-based single-molecule localization microscopy.

MVPAlab is a MATLAB-based and very flexible decoding toolbox for multidimensional electroencephalography and magnetoencephalography data. The MVPAlab Toolbox implements several machine learning algorithms to compute multivariate pattern analyses, cross-classification, temporal generalization matrices and feature and frequency contribution analyses. This toolbox has been designed to include an easy-to-use and very intuitive graphic user interface and data representation software, which makes MVPAlab a very convenient tool for those users with few or no previous coding experience. However, MVPAlab is not for beginners only, as it implements several high and low-level routines allowing more experienced users to design their own projects in a highly flexible manner.

Flexible Matlab toolbox for fNIRS data analysis.

A Standardized Processing Pipeline for Event-Related Potential Analyses.

A tool for determining a Pareto front of growth-coupled cell factory designs.

CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems.

The Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED).

Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit.

EZcalcium is a flexible, user-friendly toolbox for analysis of calcium imaging data, controlled by a set of intuitive graphical user interfaces (GUI) based on MATLAB.

DRUIDom (DRUg Interacting Domain prediction): a computational method for predicting new drug/compound - target protein interactions for drug discovery and repurposing, via mapping ligands to structural domains.

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.