Software

Selection of open-source software contributed by members of the project.

Oscillator decomposition of time series data (OSC-DECOMP)

This is the MATLAB code for OSC-DECOMP, a statistical method for extracting oscillators from univariate or multivariate time series data.

As an example related to brain study, this code has been used to investigate oscillatory activity in functional near-infrared spectroscopy (fNIRS) data. (The fNIRS can detect hemodynamic responses in the brain, where collected data are bivariate time series of oxygenated and deoxygenated hemoglobin, see PLOS Computational Biology, 2022 for details about this specific application).

Contributor: Takeru Matsuda, Statistical Mathematics Unit

MATLAB Oscillator decomposition fNIRS

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Vector Auto-Regressive Deep Neural Network (VARDNN) toolbox

VARDNN is a powerful tool of data-driven analysis technique to estimate directed FC (Functional Connectivity). Based on VARDNN framework, two types of directed FC are defined, such as VARDNN-DI and VARDNN-GC to measure causal relation among multiple time-series data.

This toolbox includes several functional connectome measures, such as VARDNN-DI, VARDNN-GC, VARLSTM-GC, multivariate Granger Causality (GC), pairwise GC, multivariate Principal Component (PC)-GC, multivariate Partial Least Squares (PLS)-GC, multivariate Elastic Net (EN)-GC, linear Transfer Entropy, Functional Connectivity (Correlation), Partial Correlation, PC-PC, PLS-PC, EN-PC and Wavelet Coherence to estimate conectivity from multiple node signals.

Contributor: Connectome Analysis Unit

MATLAB Deep Neural Network

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ZAViewer - Zooming Atlas Viewer

ZAViewer is a web 2D image viewer that was primarily designed to explore the Brain/MINDS Marmoset Reference Atlas.
It can display up to 3 sets of multimodal, regularly interspaced, large image slices along the 3 standard orthogonal axes (Axial, Coronal, Sagittal). Each slice view may contains several raster images layers, and Atlas regions (represented by aligned vector images, SVG) displayed as an overlay over the raster images.

Contributor: Connectome Analysis Unit

webApp slice-viewer ReactJs

see more on github...