README.md

OASIS: Fast online deconvolution of calcium imaging data

Code accompanying the paper "Fast online deconvolution of calcium imaging data".

Python: https://github.com/j-friedrich/OASIS

MATLAB: https://github.com/zhoupc/OASIS_matlab

A brief summary of the FOOPSI approach for denoising & deconvolving calcium imaging

Get Started

Installation

add OASIS function to the search path of MATLAB

>> oasis_setup

Process yoru data

There is also a high-level function deconvolveCa.m for the ease of calling different methods. You only need to specify parameters and then denoise & deconvolve your raw trace. For example

[c, s, options] = deconvolveCa(y, 'foopsi', 'ar1', 'smin', -3, ...'optimize_pars', true, 'optimize_b', true)

In this example, we deconvolve the raw trace $y$ using FOOPSI model and constrain the spike size to be $3\times $ noise levels. The AR coefficients and the baseline were updated automatically.

For more options, check the examples/ folder and see the comments in deconvolveCa.m.

Reproduce figures in the paper

You can reproduce the figures in the paper [3] using the following command (replace * with figure index).

>> run examples/paper/fig*.m

Copyright

Pengcheng Zhou @ Colubmia University 2018