Open pakiessling opened 2 weeks ago
Hi @pakiessling,
Thanks for sending these detailed images. It seems the segmentation here is pretty difficult (is it DAPI staining?), so I think the results are less consistent than expected between the different patches, leading to these artifacts.
What would be a good solution for you? I wanted to work on a new resolve method to avoid these overlaps (split the overlapping region between the two cells). Would that be something interesting here?
I'm planning to add a new resolve_method
argument, which would be a string to decide on the resolve method to use (with, by default, the one that is currently used).
Hi Quentin, we talked a little bit about this in Munich. I think this might be more noticeble in our samples as we are working with big cells:
You can see the lines where I assume the shapes from different runs were stitched. Even more apparent with my trained cellpose model:
I find the overlaps especially concerning as the transcripts / intensities will be counted twice.
I am also experimenting with porting the polygon resolution from VPT:
In this case it leads to the removal of many cells, but there are no more overlaps.
I have uploaded the sdata and my code here: https://github.com/pakiessling/sopa_poly_experiment
Let me know what you think. I would be happy to try and help in improving this