This repository provides an experimental algorithm to remove neuropil signal in calcium signal acquired with 2-photon imaging.

To get started, just download or git clone this repository and add the src folder to your MATLAB path.

Decontamination is done by the fit_ast_model function. You should provide 2 traces (cell ROI and neuropil ROI) and the number of pixels corresponding to each ROI. Use help fit_ast_model or doc fit_ast_model in MATLAB to get a description of all available options.

A description of the probabilistic model is also available online.