From 53ce5fad1b762435cc3b2ae2a2c36f4a3ce564a8 Mon Sep 17 00:00:00 2001 From: Luca Marconato Date: Thu, 1 Aug 2024 23:06:26 +0200 Subject: [PATCH] xenium fix area circles --- src/spatialdata_io/readers/xenium.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py index b9d0e50..b14e80a 100644 --- 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,