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Using cmap
s fails when rendering multiscale images
#354
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Hey @gdurif, currently at a conference so I'll try to have a deeper look later. But my first assumption is that the channel is a string and not a number? Could you maybe try "0" instead of 0? Also, in this notebook (https://github.com/PMBio/spatialdata-workshops/blob/main/notebooks/nb2_static_plotting.ipynb) we're showing how you can use a modified cmap that has true 0s as transparent - maybe that could also help you |
Hey @timtreis no problem, it is not urgent. I tried with And thanks for the modified cmap with 0s as transparent, that is exactly what I was aiming for. Saddly, I got the same error but I'll keep that for later. |
cmap
s fails when rendering multiscale images
Hey @gdurif, I was able to reproduce your bug. I took the liberty of renaming your issue to better reflect the actual error. Will put it on the todo-list 👍 You'll get automatically notified when I merge a PR that addresses it :) |
No problem. Thanks! |
Hi,
I want to render a specific channel in a Xenium data image using
.pl.render_images()
.If I don't specified a colormap (i.e. input argument
cmap=None
by default), it works, however if I specify a colormap usingcmap = "xxx"
, I get the error below.Note: I would really like to change the colormap because the default one with the black color corresponding to 0 is not suited to visualize that kind of image (it works on small crops but not on the full image).
MWE using
spatialdata
documentation tutorial on Xenium data:Note: Data can be downloaded with this script and transformed to
zarr
format with this one. It is also possible to directly works with Xenium data (c.f. below).Error:
Here is the code to directly read Xenium data:
Note: I use the following to get possible colormaps (and see here for the corresponding visualization of the colormaps):
FYI, using a totally different dataset, I do not get the error:
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