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The [Squidpy notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/technology_visium_hd.ipynb) shows an error liked to rasterizatation. @Sonja-Stockhaus could you ple…
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Hi, @jlause
There's a issue when using `normalize_pearson_residuals`, it seems that we can't calculated the `log2foldchange` in `rank_genes_groups` will be failed. That's because `np.expm1` …
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### Please make sure these conditions are met
- [x] I have checked that this issue has not already been reported.
- [x] I have confirmed this bug exists on the latest version of anndata.
- [x] (optio…
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Hi,
I am working with a Xenium dataset that includes an H&E image as well as an alignmentmatrix.csv file. I understand that this alignment matrix can be used to transform the image data into the…
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There should be tutorials giving a general introudction to
* spatial anlaysis with squidpy
* how to use spatialdata
grst updated
2 months ago
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We should check all docstring so that they match in the format. Add examples where needed.
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Hi,
I am attemping to add tutorials of ecosystem packages to the scverse-tutorial repo. When trying to merge my pull request, the pre-commit bot gives this error:
`Expected one of commit-msg, manual,…
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https://github.com/scverse/squidpy_notebooks/blob/79257ebbcff71260d752eae9a00a5ea36b8542ee/tutorials/tutorial_xenium.ipynb
I believe `xenium.write(zarr_path)` should be `sdata.write(zarr_path)`. I wa…
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### Please describe your wishes and possible alternatives to achieve the desired result.
Since #504, AnnData supports nullable int and bool columns in `obs`. Support for strings is planned in #679. …
grst updated
3 months ago
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### Please describe your wishes and possible alternatives to achieve the desired result.
I'm thrilled to see that AnnData now supports awkward arrays. This feature has been incredibly useful. I'd l…