diff --git a/src/cellarr/CellArrDataset.py b/src/cellarr/CellArrDataset.py
index 524963e..2473e17 100644
--- a/src/cellarr/CellArrDataset.py
+++ b/src/cellarr/CellArrDataset.py
@@ -442,7 +442,10 @@ def __getitem__(
     ####
     @property
     def shape(self):
-        return (self._cell_metadata_tdb.shape[0], self._gene_annotation_tdb.shape[0])
+        return (
+            self._cell_metadata_tdb.nonempty_domain()[0][1] + 1,
+            self._gene_annotation_tdb.nonempty_domain()[0][1] + 1,
+        )
 
     def __len__(self):
         return self.shape[0]
diff --git a/src/cellarr/dataloader.py b/src/cellarr/dataloader.py
index 4f99c63..c979bca 100644
--- a/src/cellarr/dataloader.py
+++ b/src/cellarr/dataloader.py
@@ -254,8 +254,8 @@ def __init__(
         )
 
         self.matrix_shape = (
-            self.cell_metadata_tdb.shape[0],
-            self.gene_annotation_tdb.shape[0],
+            self.cell_metadata_tdb.nonempty_domain()[0][1] + 1,
+            self.gene_annotation_tdb.nonempty_domain()[0][1] + 1,
         )
 
         # limit to cells with labels