multiple functional channel from the same ROI

[ghattasb]

First, I would like to thank you for this amazing pipeline.

In my experiment, I have two distinct signals coming from the same ROI (cell), whereas the green channel signals a neurotransmitter's activity and the red channel for a general GCaMP activity. I tried using the Jupyter notebook suggested in issue #77. This has generated two distinct stat.npy files that are then loaded to the classifier GUI, and I was wondering if there is a possible way to generate a combined stat.npy file with the ROIs detected from both the first run of the pipeline (for the green channel) and the second run (for the red channel)? and if there is a way to some how get a similar cell index for the green and the red signals coming from the same ROI?

[mari-sosa]

Hi @ghattasb, if you want a single list of ROI indices, I believe you can just run the extraction once with 'nchannels': 2 and 'functional_chan': 1 (or whichever channel is your calcium indicator, assuming this is the signal you want to use to the define the ROIs), and it should work and give you outputs of 'F' and 'F_chan2' for the same ROIs. Here 'F' will be the calcium indicator and 'F_chan2' will be your other sensor. This has worked for me in the past for a similar goal.