[BUG]: Outliers in cell segmentation points (both for ['mask'] and ['outlines'])

[postnubilaphoebus]

Describe the bug
The outlines as given by Cellpose vary in density, sometimes producing outliers.
This becomes problematic when approximating the shape of the cell using the outlines.
Is this behaviour intended, and what could it signify when outliers are present in the segmentation?
For now, I assume rejecting these outliers is best practice.

Screenshots

[carsen-stringer]

sorry I'm not sure I understand, we use cv2 to make the outlines but they might not be perfect. but there are also mask outliers? this is with do_3D=True or with stitching?

[postnubilaphoebus]

Hello, my apologies for the late reply.
I used python -m cellpose --Zstack to run a fine-tuned 3d model.
So I assume it has to do with 3D=True. But I can investigate this further if you like. I did not question this observation, because my thinking was that it is inherently difficult to model boundary conditions with heat diffusion (especially in 3d, or by combining 2d heat diffusion outputs in 3d like cellpose does). If you have a different intuition, please let me know.

[carsen-stringer]

for the outlier mask points you could run connected components and use that to create the mesh: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.label.html, we can also add this as an optional post-processing step