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Add Xenium tutorial using spatialdata
An updated Xenium tutorial for analysis using Squidpy, but instead of only working with anndata, spatialdata is used.
@LucaMarconato please let me know if things should be added. So far I just reproduced the original Xenium tutorial with spatialdata.
Check out this pull request on 
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Extra thing: @giovp after the code that you wrote in the latest hackathon on graph support for squidpy, is there anything additional to add? If not needed, after the (quick) changes above, we can merge 😊
Extra thing: @giovp after the code that you wrote in the latest hackathon on graph support for squidpy, is there anything additional to add? If not needed, after the (quick) changes above, we can merge 😊
yes I think we could be using the new gr.spatial_neighbors that support directly spatialdata, but for that I think we'd first need to merge the PR/do release
super nice! I just reviewed it and there are few aesthetics that should be modified, for the rest it looks great! I would merge after the points in the review have been addressed
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giovp commented on 2024-08-23T15:38:30Z ----------------------------------------------------------------
Line above I would remove, it appears elsewhere in the nb
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giovp commented on 2024-08-23T15:38:30Z ----------------------------------------------------------------
also here and above
LLehner commented on 2024-08-27T08:07:22Z ----------------------------------------------------------------
Shouldn't some titles remain so people find certain sections more easily?
giovp commented on 2024-08-30T21:10:37Z ----------------------------------------------------------------
yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?
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giovp commented on 2024-08-23T15:38:31Z ----------------------------------------------------------------
would be nice maybe a screenshot to add here of the napari plugin open?
Shouldn't some titles remain so people find certain sections more easily?
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yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense?
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see the diffs here regarding the misunderstanding between lines and titles
or
please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra
e.g. see what I mean here, the title is in both, and the text should stay, but there is the line --- which is unclear why is it there