mehta-lab / VisCy

computer vision models for single-cell phenotyping
https://pypi.org/project/viscy/
BSD 3-Clause "New" or "Revised" License
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Keep segmentation task for U-Nets? #11

Closed ziw-liu closed 10 months ago

ziw-liu commented 1 year ago

In microDL, using U-Nets for segmentation was explored, leaving branching code paths for both regression (virtual staining) and segmentation tasks (e.g. in preprocessing and model architecture).

@mattersoflight Given the strategy to use virtual staining models with off-the-shelf segmentation tools such as CellPose, is it still useful to keep these under-tested code?

mattersoflight commented 1 year ago

@ziw-liu our strategy is to work towards generalization. Approaches such as CellPose and StarDist generalize a lot better than vanilla U-Net. Having said the above, @edyoshikun will drive the segmentation of zebrafish organs, which may require a U-Net. Let's discuss this offline today.

mattersoflight commented 1 year ago

As we discussed, let's remove segmentation-related code.