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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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Instructions for the Use of the config.crop_circular Parameter #58

Open 1re2turn1 opened 12 hours ago

1re2turn1 commented 12 hours ago

Hi EXTRACT team,

Thank you very much for developing such an excellent program like EXTRACT!

I'd like to ask if there is any instruction on the use of the parameter config.crop_circular (When I run extractor(M, config) with the default parameters, the circular field of view boundary is often wrongly extracted as a cell. I think this parameter might help solve this problem). However, after I set config.crop_circular = 1 and run the program, Matlab reported an error (as shown in the figure below). Screenshot 2024-11-23 123903 image

Thank you in advance for the help.

fatihdinc commented 9 hours ago

Hello! Thank you for reaching out. I realized there was a small bug with the code. Could you please pull and try again? Thank you!