Open SilverViking opened 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.
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.