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fill-in placeholder for github discussion
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src/spatialdata_io/readers/xenium.py

Lines changed: 3 additions & 2 deletions
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@@ -495,12 +495,13 @@ def _get_polygons(
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# cell_id, merging multiple nuclei of multinucleate cells into a single degenerate polygon.
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# The resulting geometry is invalid (two rings concatenated as one), so we skip nucleus
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# boundaries entirely for this format version.
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# See: https://github.com/scverse/spatialdata-io/discussions/XXX
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# See: https://github.com/scverse/spatialdata-io/discussions/387
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warnings.warn(
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"Nucleus boundaries are not supported for this Xenium format version (v2.0.0 early "
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"builds without label_id in the parquet). The parquet merges multinucleate cells into "
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"degenerate polygons. Skipping nucleus boundaries. You can derive nucleus polygons from "
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"the raster labels using spatialdata.to_polygons().",
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"the raster labels using spatialdata.to_polygons(). "
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"See https://github.com/scverse/spatialdata-io/discussions/387 for details.",
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UserWarning,
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stacklevel=3,
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)

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