Reader does not support cell segmentation of visium hd got after using latest spaceranger version 4

[rahmaqadeer]

I am using the visiumhd data from the latest spaceranger pipeline that also contain segmented outputs but the reader doesnot support it unfortunately. It just work with bins Is there any possibility to read the segmented outputs through the reader?

        sdata = visium_hd(
            path=full_path,
            dataset_id=sample_name,
            bin_size=8
        )

[SizhaoLu]

I haven't tried this. But spaceranger v4 creates a folder named "segmented_outputs". In it, there are some ".geojson" files that can be parsed into shapes.

https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/models2.html#polygons-multipolygons

[SizhaoLu]

I just realized it can be parses easily sd_io.geojson({path_to_geojson}, coordinate_system={sample_id})

[NadineBestard]

Further discussed in https://github.com/scverse/spatialdata-io/issues/310