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Segmentation parameter min_size (for discarding small fragments) has no effect #128

Open SilverViking opened 1 year ago

SilverViking commented 1 year ago

Changing the min_size parameter in the segmentation widget in napari-sparrow has no effect whatsoever, no segmentation masks get discarded even when setting min_size to a very large value.

This seems to be due to a bug in Cellpose: internally in Cellpose the min_size parameter is not correctly passed around in all cases. Others have noticed this too, but the corresponding Cellpose issue was closed, even though the bug persists.

TODO: make small test file and re-open issue in Cellpose.

ArneDefauw commented 1 year ago

In sparrow we have thenas.tb.filter_on_size(sdata, min_size=..., ) function, which can filter cells that are too small/big.

So the temporary fix in sparrow could be to remove this min_size parameter from nas.im.segmentation_cellpose, and also from the segmentation widget in the plugin.