diff --git a/biahub/register.py b/biahub/register.py
index 6abe5a84..a48df75f 100644
--- a/biahub/register.py
+++ b/biahub/register.py
@@ -10,6 +10,7 @@
 import submitit
 
 from iohub import open_ome_zarr
+from iohub.ngff.utils import create_empty_plate
 
 from biahub.cli.monitor import monitor_jobs
 from biahub.cli.parsing import (
@@ -24,7 +25,6 @@
 )
 from biahub.cli.utils import (
     copy_n_paste_czyx,
-    create_empty_hcs_zarr,
     estimate_resources,
     process_single_position_v2,
     yaml_to_model,
@@ -498,7 +498,7 @@ def register_cli(
     }
 
     # Create the output zarr mirroring source_position_dirpaths
-    create_empty_hcs_zarr(
+    create_empty_plate(
         store_path=output_dirpath,
         position_keys=[p.parts[-3:] for p in source_position_dirpaths],
         **output_metadata,
diff --git a/biahub/stabilize.py b/biahub/stabilize.py
index 46212a13..e530c0e0 100644
--- a/biahub/stabilize.py
+++ b/biahub/stabilize.py
@@ -7,6 +7,7 @@
 import submitit
 
 from iohub.ngff import open_ome_zarr
+from iohub.ngff.utils import create_empty_plate
 from scipy.linalg import svd
 from scipy.spatial.transform import Rotation as R
 
@@ -23,7 +24,6 @@
 )
 from biahub.cli.utils import (
     copy_n_paste_czyx,
-    create_empty_hcs_zarr,
     estimate_resources,
     process_single_position_v2,
     yaml_to_model,
@@ -214,7 +214,7 @@ def stabilize(
     }
 
     # Create the output zarr mirroring input_position_dirpaths
-    create_empty_hcs_zarr(
+    create_empty_plate(
         store_path=output_dirpath,
         position_keys=[p.parts[-3:] for p in input_position_dirpaths],
         **output_metadata,
diff --git a/biahub/virtual_stain.py b/biahub/virtual_stain.py
index 5e728022..af553b79 100644
--- a/biahub/virtual_stain.py
+++ b/biahub/virtual_stain.py
@@ -10,6 +10,7 @@
 import submitit
 
 from iohub.ngff import open_ome_zarr
+from iohub.ngff.utils import create_empty_plate
 
 from biahub.cli.monitor import monitor_jobs
 from biahub.cli.parsing import (
@@ -22,7 +23,6 @@
     sbatch_filepath_preprocess,
     sbatch_to_submitit,
 )
-from biahub.cli.utils import create_empty_hcs_zarr
 
 
 def run_viscy_preprocess(
@@ -322,7 +322,7 @@ def virtual_stain(
             "dtype": np.float32,
         }
 
-        create_empty_hcs_zarr(
+        create_empty_plate(
             store_path=output_dirpath,
             position_keys=[p.parts[-3:] for p in input_position_dirpaths],
             **output_metadata,