MedSAM Segmentation Extension

[rasakereh]

This module implements MedSAMLite and several of its variant for universal 2D and 3D image segmentation.

New extension

PLUGIN DEVELOPER'S NOTE: The repository has been active for around a year and we have a large number of active users (only ~150 stars at github at the time of submission). As the URL is advertised at numerous places before we become aware of your naming convention, it is not safe for us to rename it. It is MedSAMSlicer instead of SlicerMedSAM. Hopefully it can be admitted the way it is.

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[lassoan]

Thanks a lot for your contribution!

This is very close to be ready to be added to the extensions index, there are just a few items to address:

• Integrate Fix installation issues on Windows and improve GUI/logic separation bowang-lab/MedSAMSlicer#51. I've spent a lot of time with the module, first separating the GUI and logic a bit more cleanly (not perfect, but much better now), and trying to make the module obvious to use (without having to read the documentation), but still allowing adjusting all important options. I'm fairly confident that all the changes are for the better, except the last commit where I removed the optional precomputation of the embedding (always performing it when needed, instead of showing a popup to the user that he should precompute). I decided to do this, because with the popup that was displayed each time made the single segmentation mode so inconvenient that I concluded that probably nobody routinely used that.
• You could consider adding a specific example in the instructions (https://github.com/bowang-lab/MedSAMSlicer?tab=readme-ov-file#usage) about which Sample Data set to use for first testing, and what structure to designate with the ROI. For example, MRBrainTumor1 / tumor; or CTLiver / kidney or liver?
• Update the documentation based on the final implementation.

Extension repository name not starting with Slicer gives us some extra work, but it's OK, we can manage.

Finally, a quick question: is it possible to specify points to include or exclude? That could help fixing segmentations when the segmentation leaks out or incomplete.

[jamesobutler]

PLUGIN DEVELOPER'S NOTE: The repository has been active for around a year and we have a large number of active users (only ~150 stars at github at the time of submission). As the URL is advertised at numerous places before we become aware of your naming convention, it is not safe for us to rename it. It is MedSAMSlicer instead of SlicerMedSAM. Hopefully it can be admitted the way it is.

@rasakereh Changing the repository name wouldn't cause you to lose stars on GitHub. GitHub will actually automatically redirect from say https://github.com/bowang-lab/MedSAMSlicer to https://github.com/bowang-lab/SlicerMedSAM so there wouldn't be concern of the published URL suddenly going broken.
https://docs.github.com/en/repositories/creating-and-managing-repositories/renaming-a-repository

[lassoan]

@rasakereh Let us know if you want to proceed with merging the pull request and addressing the few remaining minor points. We could make the extension available by pointing the Extensions Index to my fork (that contains the required fixes), but it would be nicer if we could use your repository.