geo_df loc should be after intrisic conversion

Author: quentinblampey

spatialdata_xenium_explorer/converter.py

@@ -95,10 +95,11 @@ def write(
     shapes_key, geo_df = get_element(sdata, "shapes", shapes_key, return_key=True)
 
     if _should_save(mode, "b") and geo_df is not None:
+        geo_df = to_intrinsic(sdata, geo_df, image_key)
+
         if sdata.table is not None:
             geo_df = geo_df.loc[adata.obs[adata.uns["spatialdata_attrs"]["instance_key"]]]
 
-        geo_df = to_intrinsic(sdata, geo_df, image_key)
         write_polygons(path, geo_df.geometry, polygon_max_vertices)
 
     ### Saving transcripts