Tim Treis comments

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                                            Tim Treis

Catch-all: XYZ doesn't work with `SpatialData`

Essentially tried following the [Squidpy Xenium tutorial](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_xenium.html) but using a `spatialdata` object. Failed when I tried to color my plot by Leiden colors.

Catch-all: XYZ doesn't work with `SpatialData`

No, this one seems to basically just extract the `adata` and then does normal things that were possible before. I think the goal should be to directly pass either the...

Coloring by AnnData in `render_labels` is insanely slow

There's no reason why this should be so slow

`render_points` for categorical columns assumes there is always a table

Is this still open? Works locally for me?

`render_points` for categorical columns assumes there is always a table

@LucaMarconato is this still broken?

Can't specify single color for `render_label` by a color string

We're currently working on homogenising the color handling in https://github.com/scverse/spatialdata-plot/pull/497, but in the meantime you can just substitute `color` for `na_color` and it'll work

Git history is getting huge due to Jupyter Notebooks

I don't think that having these extra 500 MB on disk is the issue (mildly inconvenient at best), but realistically this history will very quickly grow even larger in size...

fix table name and add unit test for colors passed via .uns

Closed in favour of https://github.com/scverse/spatialdata-plot/pull/492 Thank you for the work @ArneDefauw! Only closing this one because I couldn't rebase your fork on the current main branch

Transformations with flipped y-axis

@LucaMarconato any thoughts on this? Our current best guess is "do what matplotlib is doing" so we don't change all plots created to date with the library 😅

Expected `width` to be in interval error `im.calculate_image_features`

Hey @mjakobs, we're currently in the process of migrating `Squidpy` to make use of `SpatialData` instead of the old AnnData-based way. Therefore, we won't be updating this function as it...