Force separation of masks

[CristiSoitu]

Hello,

First of all great resource!

Is there a way to force cellpose to produce separated masks when cells are close together or overlapping rather than a continuous one? I've tried decreasing the diameter, but it get into a region where it picks up things way too small to be cells.

Thanks, Cristian

[carsen-stringer]

do you have an image you can post as an example? I'd recommend maybe retraining the model if cellpose is merging your masks. you can alternatively use a decreased diameter then use the min_size input to model.eval to filter out objects which are too small (min_size is in pixels)

[carsen-stringer]

closing due to inactivity