Proseg v3.1.0 SpatialData points: Xenium qv column dropped + coordinate naming is confusing for cropping #136
Description
In Proseg v3.1.0, the produced SpatialData object appears to drop the Xenium transcript qv column in the points table. It would be great if qv could be preserved, since it is useful for downstream transcript-level quality control.
Additionally, the coordinate naming in points is potentially confusing: the repositioned coordinates are stored as "x", "y", "z", while the raw/observed coordinates are renamed to "observed_x", "observed_y", "observed_z". I would recommend keeping the raw coordinates as "x", "y", "z" and instead naming the repositioned ones "repositioned_x", "repositioned_y", "repositioned_z".
Reason: spatialdata.query.bounding_box uses "x", "y", "z" for cropping, which can be problematic if users assume these correspond to the raw Xenium coordinates.