diff --git a/src/scportrait/pipeline/extraction.py b/src/scportrait/pipeline/extraction.py
index 505f608..20bfbb7 100644
--- a/src/scportrait/pipeline/extraction.py
+++ b/src/scportrait/pipeline/extraction.py
@@ -732,6 +732,12 @@ def _transfer_tempmmap_to_hdf5(self):
                 dtype=h5py.special_dtype(vlen=str),
             )
 
+            hf.create_dataset(
+                "n_masks",
+                data=self.n_masks,
+                dtype=int,
+            )
+
             self.log("channel information created.")
 
         # cleanup memory