Tim Treis
Tim Treis
The codebase of `spatialdata-plot` started out as some chimera between Squidpy's plotting and a prototype from Harald, but has matured a lot since. So we're essentially maintaining duplicate code. Ideally,...
related: https://github.com/scverse/spatialdata-plot/pull/451
Hey @lucas-diedrich, if I'm not mistaken, SpatialData has an .attrs level at the highest level, so not directly associated with the individual elements, that is persistent (see https://github.com/scverse/spatialdata/pull/711). Until we...
Hey @liuyang2006, that's probably because your table doesn't annotate the `cell_labels` object but only the `cell_circles` object. That's currently the default for Xenium. You can find a tutorial on how...
> @timtreis any idea? > > @Yifan-debug thanks for reporting, I'd suggest using this PR from `spatialdata-plot`: [scverse/spatialdata-plot#309](https://github.com/scverse/spatialdata-plot/pull/309) which fixes many recent bugs (but which is not merged yet). >...
Hey @Lem-P and @ConstensouxAlexis, I linked a PR to this issue which should fix the issue. Could you verify with your data? @LucaMarconato I'm filtering out the polygons and remove...
Hm, thanks for the extra info! I think given that we are seeing datasets with this issue in the wild now, we know they exist and will cause errors for...
Great to hear @LoganAMorrison! However, I think we should still merge that PR since there might be datasets out there generated with the faulty versions. The current implementations tells users...
Would something like this help for your usecase? ``` import numpy as np import matplotlib.pyplot as plt from matplotlib.colors import Normalize # pick channels and compute per-channel percentiles from the...