Fix radius

scverse · Aug 7, 2023 · 790ac13 · 790ac13
1 parent 8a61442
commit 790ac13
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/src/spatialdata_io/_constants/_constants.py b/src/spatialdata_io/_constants/_constants.py
@@ -171,6 +171,7 @@ class StereoseqKeys(ModeEnum):
     EXPRESSION = "expression"
     EXON = "exon"
     # cells
+    CELL_AREA = "area"
     CELL_ID = "id"
     GENECOUNT = "geneCount"
     DNBCOUNT = "dnbCount"

diff --git a/src/spatialdata_io/readers/stereoseq.py b/src/spatialdata_io/readers/stereoseq.py
@@ -201,9 +201,11 @@ def stereoseq(
         region_key=StereoseqKeys.REGION_KEY,
         instance_key=StereoseqKeys.INSTANCE_KEY,
     )
+
+    radii = np.sqrt(adata.obs[StereoseqKeys.CELL_AREA].to_numpy() / np.pi)
     shapes = {
         StereoseqKeys.REGION_KEY: ShapesModel.parse(
-            adata.obsm[StereoseqKeys.SPATIAL_KEY], geometry=0, radius=1, index=adata.obs[StereoseqKeys.INSTANCE_KEY]
+            adata.obsm[StereoseqKeys.SPATIAL_KEY], geometry=0, radius=radii, index=adata.obs[StereoseqKeys.INSTANCE_KEY]
         )
     }
     sdata = SpatialData(images=images, labels=labels, table=table, points=points, shapes=shapes)