ConstensouxAlexis
ConstensouxAlexis
Hi ! Do you have any update on this issue, or a workaround ? Thank you !
Hi, You should inspect your cellpose segmentation and make sure you do not have polygons with less than 4 vertices. If you want to load this Cellpose segmentation anyway, you...
I think this is issue is caused by Xeniumranger import-segmentation and not by spatialdata. When I run xeniumranger with a custom segmentation (Baysor or CellPose), even if I make sure...
I think that it's fine just to remove problematic polygons; this will only impact the vizualisation and not the analysis
Hello @timtreis, thank you for the PR, I will verify with my data. Just to let you know, this polygon issue is caused by xeniumranger software, and they are currently...
Hi ! Thanks for answering (weirdly, using matoplotlib backend seems to fix that issue by the way)
Thank you for your answer ! I will try playing with `--prior-seg-reassignments-prob` parameter on my Xenium data.
Hi, thank you for your answer ! I might be wrong, but I think that if we want to derive the number of micron per pixel from the transformation metadata,...
Ok, thank you very much for explanations !
Hi @ajitjohnson , I saw that you changed matplotlib default params, so this should fix my issue. I just have an incompatibility with the new scimap version: `scimap 2.1.2 requires...