[general help on improving cell extraction]

schnitzer-lab / EXTRACT-public

EXTRACT is a tractable and robust automated cell extraction tool for calcium imaging, which extracts the activities of cells as time series from both one-photon and two-photon calcium imaging movies.

MIT License

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[general help on improving cell extraction] #30

Closed sg-s closed 1 year ago

sg-s commented 1 year ago

Hello, ran EXTRACT on some 1-p data and I am generally unhappy with the cells extracted. some screenshots below. I would greatly appreciate any help in improving cell extraction. I ran this on all defaults. Which parameters should I change to:

get rid of clear non-cells (weird footprints, monotonically decreasing cells)
improve SNR

In my opinion this is the "best" cell in this data, which isn't great:

fatihdinc commented 1 year ago

Would you mind sending over the movie through my email? Happy to give it a look!

sg-s commented 1 year ago

thank you! will send

fatihdinc commented 1 year ago

Let's follow up on the email. It seems the movie is over-processed, so we will try again with the raw, only motion corrected, movie!