xenium fix area circles

scverse · Aug 1, 2024 · 53ce5fa · 53ce5fa
1 parent 8387b91
commit 53ce5fa
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
@@ -533,7 +533,7 @@ def _get_tables_and_circles(
     table = TableModel.parse(adata, region=specs["region"], region_key="region", instance_key=str(XeniumKeys.CELL_ID))
     if cells_as_circles:
         transform = Scale([1.0 / specs["pixel_size"], 1.0 / specs["pixel_size"]], axes=("x", "y"))
-        radii = np.sqrt(adata.obs[XeniumKeys.CELL_NUCLEUS_AREA].to_numpy() / np.pi)
+        radii = np.sqrt(adata.obs[XeniumKeys.CELL_AREA].to_numpy() / np.pi)
         circles = ShapesModel.parse(
             circ,
             geometry=0,