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Fix xenium tutorial#157

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durr1602 wants to merge 5 commits into
scverse:mainfrom
durr1602:fix-xenium-tutorial
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Fix xenium tutorial#157
durr1602 wants to merge 5 commits into
scverse:mainfrom
durr1602:fix-xenium-tutorial

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@durr1602

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Fixes scverse/squidpy#1049

  • changed URL of dataset
  • made the tuto more dataset agnostic
  • added info on dependencies (igraph implemented but optional)

Tested with the following:

Python 3.13.12
--------------
squidpy==1.8.1
spatialdata==0.7.3a2.dev1+gcf91ad57b
zarr==3.1.6
spatialdata-io==0.6.0
spatialdata-plot==0.3.3
napari==0.7.0

Using scverse/spatialdata@cf91ad5 (latest at the time of writing) to have the (yet-to-be-released) fix introduced in scverse/spatialdata@78f75ef. This ensures compatibility with zarr>3

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@selmanozleyen

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hi @timtreis can you have a look at this?

@timtreis timtreis self-requested a review May 26, 2026 14:17
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Incorrect dataset link for Analyze Xenium data tutorial

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