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Error in render_points: cannot reindex on an axis with duplicate labels #545
Description
Calling sdata.pl.render_points("transcripts").pl.show() on a SpatialData object containing Xenium data raises:
ValueError: cannot reindex on an axis with duplicate labels
Observation:
I noticed that the points element index of the SpatialData object is not unique. More generally, when reading the transcripts.parquet file into a Dask DataFrame (Dask 2026.1.1), the resulting index is not globally unique. Instead, indices appear to be enumerated independently within partitions, leading to duplicate labels across the full dataframe.
This may be related to the error above, although I am not certain that this is the index involved in the failing reindex operation.
Activity
LucaMarconato commentedon Mar 10, 2026
CC @melonora in case he has some insights to share.
enric-bazz commentedon Mar 13, 2026
After further checks, the error appears to originate from
spatialdatarather thanspatialdata-plot.The behavior is related to the previously reported issue scverse/spatialdata#1064 and occurs after the fix introduced in scverse/spatialdata#1077.
enric-bazz commentedon Mar 17, 2026
I opened an issue reporting the root cause of this error on the
spatialdatarepository.timtreis commentedon Mar 19, 2026
Thank you for the triage @enric-bazz !