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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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More tutorials #47

Closed stevevanhooser closed 7 months ago

stevevanhooser commented 9 months ago

This adds two more Livescript versions of tutorials:

In addition, it fixes two small bugs in cell_check/get_movie and view_movie.

This adds in much of the material that is in https://github.com/appasamy-sc/extract-wip/blob/live-scripts/tutorials/tutorials.mlx but in smaller pieces.

On my machine, the output of "understanding hyperparameters" isn't so good; many cells are found okay but then there are some large cells. Not sure if something has changed in the optimization procedure or if there's some other issue (this is R2023b on a Mac Silicon).

Best Steve

vijayiyer05 commented 7 months ago

Hi @fatihdinc, have you had a chance to take a look at this? (it's 1a from the work plan Steve at WDS is working from)

fatihdinc commented 7 months ago

Hi! The understanding the hyperparameter tutorial is left as an exercise with a provided starter code. Indeed, those are not optimal at all. Otherwise, happy to accept this!