Py-oopsi: the python implementation of the fast-oopsi algorithm

TL;DR

This paper provides a Python implementation of the fast-oopsi algorithm for extracting neuron spike activities from calcium signals, including corrections to the original method, making it more accessible and accurate for researchers.

Contribution

It introduces a detailed Python version of fast-oopsi with corrections, enhancing usability and precision over the original implementation.

Findings

Python implementation of fast-oopsi available

Corrections improve algorithm accuracy

Facilitates wider adoption in neuroscience research

Abstract

Fast-oopsi was developed by Joshua Vogelstein in 2009, which is now widely used to extract neuron spike activities from calcium fluorescence signals. Here, we propose detailed implementation of the fast-oopsi algorithm in python programming language. Some corrections are also made to the original fast-oopsi paper.