diff --git a/packages/scratch-core/src/conversion/surface_comparison/cell_registration/coarse.py b/packages/scratch-core/src/conversion/surface_comparison/cell_registration/coarse.py
index b06c72d5..b63f2470 100644
--- a/packages/scratch-core/src/conversion/surface_comparison/cell_registration/coarse.py
+++ b/packages/scratch-core/src/conversion/surface_comparison/cell_registration/coarse.py
@@ -131,6 +131,7 @@ def _find_best_match(
             score_map = _get_score_map(
                 comparison_array=rotated,
                 template=grid_cell.cell_data_filled,
+                template_mask=grid_cell.valid_mask,
             )
             score, x, y = _compute_best_score_from_maps(
                 score_map=score_map, fill_fraction_mask=fill_fraction_mask
@@ -237,7 +238,7 @@ def _compute_best_score_from_maps(
 
 
 def _get_score_map(
-    comparison_array: FloatArray2D, template: FloatArray2D
+    comparison_array: FloatArray2D, template: FloatArray2D, template_mask: BinaryMask
 ) -> FloatArray2D:
     """
     Compute a normalized cross-correlation score map for one reference cell.
@@ -248,6 +249,7 @@ def _get_score_map(
 
     :param comparison_array: NaN-free float32-compatible comparison image, padded by a full cell on each side.
     :param template: Reference grid cell whose ``cell_data`` is used as the template; must contain no NaN values.
+    :param template_mask: Mask with the pixel values that should be matched (i.e. no NaNs).
     :returns: Float64 score map of shape ``(H - cell_height + 1, W - cell_width + 1)`` with values in ``[-1, 1]``.
     """
 
@@ -255,5 +257,6 @@ def _get_score_map(
         image=comparison_array.astype(np.float32),
         templ=template.astype(np.float32),
         method=cv2.TM_CCOEFF_NORMED,
+        mask=template_mask.astype(np.uint8),
     )
     return np.asarray(score_map, dtype=np.float64)
diff --git a/packages/scratch-core/src/conversion/surface_comparison/models.py b/packages/scratch-core/src/conversion/surface_comparison/models.py
index 779f4100..e667032e 100755
--- a/packages/scratch-core/src/conversion/surface_comparison/models.py
+++ b/packages/scratch-core/src/conversion/surface_comparison/models.py
@@ -9,7 +9,7 @@
 
 from scipy.constants import mega
 
-from container_models.base import ConfigBaseModel, FloatArray2D
+from container_models.base import ConfigBaseModel, FloatArray2D, BinaryMask
 from conversion.data_formats import Mark, MarkType
 
 
@@ -246,3 +246,8 @@ def fill_fraction(self) -> float:
     def cell_data_filled(self) -> FloatArray2D:
         """Cell data where NaN values are replaced with the sentinel value."""
         return np.nan_to_num(self.cell_data, nan=self.nan_fill_value, copy=True)
+
+    @cached_property
+    def valid_mask(self) -> BinaryMask:
+        """Mask where the cell data has valid values (i.e. no NaNs)."""
+        return ~np.isnan(self.cell_data)
diff --git a/packages/scratch-core/tests/conversion/surface_comparison/cell_registration/test_coarse.py b/packages/scratch-core/tests/conversion/surface_comparison/cell_registration/test_coarse.py
index f80fdf5e..49cfe88d 100644
--- a/packages/scratch-core/tests/conversion/surface_comparison/cell_registration/test_coarse.py
+++ b/packages/scratch-core/tests/conversion/surface_comparison/cell_registration/test_coarse.py
@@ -136,7 +136,9 @@ def test_get_score_map_self_match_peak_at_cell_top_left(self):
 
         # Act
         score_map = _get_score_map(
-            comparison_array=filled, template=grid_cell.cell_data_filled
+            comparison_array=filled,
+            template=grid_cell.cell_data_filled,
+            template_mask=grid_cell.valid_mask,
         )
 
         # Asserts