Python and MATLAB code for Granger causality analysis on empirically observed calcium transients in zebrafish neuronal populations, and on synthetic dynamics generated on toy networks.

A repository of neural manifold techniques described and compared in "Neural manifold analysis of brain circuit dynamics in health and disease"

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

This python code estimates conditional mutual information (CMI) and mutual information (MI) for discrete and/or continuous variables using a nearest neighbors approach.

Matplotlib styles for scientific plotting

ChatGPT Plus 共享方案。ChatGPT Plus / OpenAI API sharing solution.

Python implementation of the Mantel test, a significance test of the correlation between two distance matrices

InMoose is the INtegrated Multi Omic Open Source Environment. It is a collection of tools for the analysis of omic data.

Analysis package for miniscope data

Decoding behavior from calcium imaging data

A table containing imaging analysis tools for biology, with a focus on calcium imaging.

Python exercises accompanying the book "Neuronal Dynamics"

A MATLAB toolbox for performing information theory analyses of neuroscience data

Python package for information theory.

Registration of cells across sessions.

Platform for Calcium Imaging analysis. DEPRECATED.

Analysis for spatially modulated spiking activity, e.g. place cells, grid cells

CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnal…

Device for injecting gradient-refractive index (GRIN) lens probes into animals.

Software for streaming and controlling neural and behavioral data from freely behaving animals