fix label image dimension mis match

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
     hooks:
     -   id: validate-cff
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.4.0
+    rev: v2.4.1
     hooks:
     -   id: codespell
         exclude: |

src/nviz/image.py

@@ -21,6 +21,7 @@ def image_set_to_arrays(
     label_dir: Optional[str],
     channel_map: Dict[str, str],
     ignore: Optional[List[str]] = ["Merge"],
+    expected_dim: int = 4,
 ) -> Dict[str, Dict[str, np.ndarray]]:
     """
     Read a set of images as an array of images.
@@ -101,7 +102,6 @@ def image_set_to_arrays(
                 key=lambda x: x.name.split("_")[0],
             )
         }
-
     return zstack_arrays
 
 
@@ -234,6 +234,7 @@ def tiff_to_ometiff(  # noqa: PLR0913
     channel_map: Dict[str, str],
     scaling_values: Union[List[int], Tuple[int]],
     ignore: Optional[List[str]],
+    expected_dim: int = 4,
 ) -> str:
     """
     Convert TIFF files to OME-TIFF format.
@@ -286,7 +287,10 @@ def tiff_to_ometiff(  # noqa: PLR0913
     # Collect label data
     if label_dir:
         for compartment_name, stack in frame_zstacks["labels"].items():
-            labels_data.append(stack)
+            if stack.ndim != expected_dim and stack.ndim < expected_dim:
+                labels_data.append(np.expand_dims(stack, axis=0))
+            else:
+                labels_data.append(stack)
             label_names.append(f"{compartment_name} (labels)")
 
     # Stack the images and labels along a new axis for channels

tests/test_image.py

@@ -11,8 +11,14 @@
 import tifffile as tiff
 import zarr
 
-from nviz.image import image_set_to_arrays, tiff_to_ometiff, tiff_to_zarr
-from tests.utils import example_data_for_image_tests
+from nviz.image import (
+    image_set_to_arrays,
+    tiff_to_ometiff,
+    tiff_to_zarr,
+)
+from tests.utils import (
+    example_data_for_image_tests,
+)
 
 
 @pytest.mark.parametrize(