troutpy.pp.xenium_converter

troutpy.pp.xenium_converter#

troutpy.pp.xenium_converter(sdata, copy=False, unassigned_tag='UNASSIGNED')#

Convert a 10x Xenium SpatialData object’s transcripts and table to the troutpy-expected format.

Renames/derives columns on sdata.points["transcripts"] (gene, control_probe, transcript_id, overlaps_cell, …) and adds a "raw" layer to sdata.table.

Parameters:

  • sdata (spatialdata.SpatialData) – A SpatialData object with attributes such as Images, Points, and Tables, conforming to the structure detailed in the SpatialData documentation.

  • copy (bool, optional) – If True, return the modified SpatialData object. Otherwise modify sdata in place and return None.

  • unassigned_tag (str, optional) – Value of cell_id used to mark transcripts that are not assigned to any cell.

Returns:

spatialdata.SpatialData or None The converted SpatialData object if copy=True; otherwise None.

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