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vanvalenlab / cellSAM

Codebase for "A Foundation Model for Cell Segmentation"
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Getting started... #1

Closed rossbar closed 7 months ago

rossbar commented 7 months ago

Thanks for uploading @rdilip

The first order of business is to define an interface for users. IMO the easiest way to start is with a minimal set of examples in the README.

One component that is obviously necessary to make this usable is the model itself. We can start by ensuring that the current version is available on users.deepcell.org. From perusing the code it looks like these assets are necessary in order to perform inference. Are there others?

ellenemerson commented 7 months ago

I think some of the model setup w/ loading the .pth and setting threshold parameters that is in that main function could be put into a constructor or something similar.

It would also be helpful to make this pip installable at some point.

rossbar commented 7 months ago

There's been a decent amount of progress since this was opened so it's no longer particularly relevant. I'll go ahead and close it and we can focus on specifics moving forward. Thanks @ellenemerson and @rdilip !