treat2p 0.1.1

Treatment pipeline for suite2p extracted fluorescent traces over time.

Treat2p

Made to be used with suite2p, to extend it's capabilities with treatment one, on top of the nice extraction features of suite2p.

Made after the matlab developments of Pierre Marie Gardères.

Getting started

To install this package, you simply need to hop into your own virtual / anaconda environment and run :

pip install git+https://gitlab.pasteur.fr/haisslab/analysis-packages/treat2p.git

It is as simple as that.

In case there is some messages telling you about import errors when you import treat2p, (please don't hesitate to report problems with the issues tracker) the necessary packages to install by yourself are :

• numpy
• joblib (a famous library to parallelize processings easily in python, usedc by scipy)
• scipy
• tqdm (a famous progress tracker, used by pandas)

How to use :

In short, to run on a suite2p plane/channel :

import treat2p
suite2p_path = r"C:\Users\yourname\Desktop\suite2p"
outputs, stats, ops = treat2p.run_treat2p(suite2p_path, plane = 0, chan = 1)

For a bit more explanations, please see the jupyter notebook tutorial here.