Scribble-based segmentation

computational-cell-analytics / micro-sam

Segment Anything for Microscopy

https://computational-cell-analytics.github.io/micro-sam/

MIT License

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Scribble-based segmentation #603

Open anwai98 opened 1 month ago

anwai98 commented 1 month ago

This in particular could potentially be a nice feature to segment vessel-like thin (and long) structures using positive scribblles, or eliminate the outside-boundary region in-a-go for parts outside the object using negative scribbles.

constantinpape commented 1 month ago

I agree that this is a good idea. I see two possible ways to implement it:

Derive a mask prompt from the scribbles. This is easy to implement, but I am a bit pessimistic if it will help much. In any case, we can try.
Train a new prompt encoder for it. I think that is in principle more promising, but also more work.

Any other ideas from your end for how to address this?

anwai98 commented 1 month ago

I was thinking in the direction of a simpler version of the first method, however the second one actually sounds more promising.

Also leaving a hint, I think Mehdi has an implementation for scribble-based segmentation with SAM - https://github.com/juglab/napari-sam-labeling-tools