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Writes a transcript-assignment CSV with the headers xeniumranger expects (transcript_id/cell_id/overlaps_nucleus/feature_name/x_location/y_location/ z_location/qv), joining transcript_id/qv/overlaps_nucleus back from the raw Xenium transcripts via -i since segger's own output drops them. Cell boundaries are written as GeoJSON instead of parquet. Prints the exact xeniumranger import-segmentation command to run afterward. Fixes #88
Fix .not() -> .not_() (not is a reserved keyword, invalid as an attribute name).
assigned drops the filtered column, so building is_noise off it crashed with ColumnNotFoundError. tx already carries filtered, and already went through load_transcripts' legacy join if the segmentation predates it, so reuse that instead of joining again.
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Adds a
xeniumrangerelement tosegger export:-i/--source-path(just for suggesting the path thoughxenium_transcript_assignment.csv: the transcript-assignment CSVxeniumranger import-segmentationexpects, with headerstranscript_id,cell,is_noise.cell_idis reassigned to segger's calls; unassigned transcripts are dropped.xenium_cell_boundaries.geojson: the same boundary computation assegger export boundaries, written as GeoJSON instead of parquet.xeniumranger import-segmentationcommand to run against these two files.Example
Closes #88