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Images with alpha channel being plotted incorrectly #406
Description
Hey! I've come across an issue when trying to plot some images where one of the channels is an alpha level. This is a visium image that was submitted to cellxgene.
sdata.pl.render_images().pl.show("d551b400-b2e5-454d-b5a9-ece03e6b4739")
As you can see, this looks quite funny. I don't think it's an issue with the image, since plotting it through other routes appears normal:
Plotting with matplotlib
import matplotlib.pyplot as plt
img = sdata.images["d551b400-b2e5-454d-b5a9-ece03e6b4739_library"].compute()
plt.imshow(img.transpose("y", "x", "c"))
Plotting with squidpy
from spatialdata_io.experimental import from_legacy_anndata, to_legacy_anndata
import squidpy as sq
adata = to_legacy_anndata(sdata, include_images=True)
sq.pl.spatial_scatter(adata)
It seems to me like the alpha level is being misinterpreted in spatialdata_plot.
Activity
LucaMarconato commentedon Jan 20, 2025
Thanks for reporting. This is how rgba is dealt with in napari-spatialdata, the issue may be related: https://github.com/scverse/napari-spatialdata/pull/153/files; following the napari-spatialdata approach, the desired implementation may be the following:
r,g,b(a) are the channel names of the image, then interpret it as RGB(A)pl.render_images(), such asrgb=True(defaultfalse)In napari-spatialdata, this approach replaced the previous method, which was based on a heuristic (checking if the channels were 3 or 4 and interpreting the image as RGB(A)).
@timtreis @Sonja-Stockhaus wdyt?
Fix RGBA images being rendered with categorical coloring instead of p…