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Getting started

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

Made following the matlab developments of Pierre Marie Gardères

Installation

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

pip install treat2p

uv add treat2p

How to use

In short, to treat some plane/channel data that suite2p extracted already:

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

Takes all the arguments that goes into the various stages of the pipeline, registers, them, and stores them in the ops.npy file under the treat2p key.

The stages of treat2p pipeline are (for each roi):

notebook tutorial

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