diff --git a/scenvi/utils.py b/scenvi/utils.py
index 0d1fd93..843f755 100644
--- a/scenvi/utils.py
+++ b/scenvi/utils.py
@@ -181,7 +181,10 @@ def CalcCovMats(spatial_data, kNN, genes, spatial_key="spatial", batch_key=-1):
     :meta private:
     """
 
-    ExpData = np.log(spatial_data[:, genes].X + 1)
+    if isinstance(spatial_data.X, np.ndarray):
+        ExpData = np.log(spatial_data[:, genes].X + 1)
+    else:
+        ExpData = np.log(np.asarray(spatial_data[:, genes].X.todense()) + 1)
 
     if batch_key == -1:
         kNNGraph = sklearn.neighbors.kneighbors_graph(