diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 51d3b3b..8883aea 100644
--- a/.pre-commit-config.yaml
+++ b/.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: |
diff --git a/docs/src/_static/coverage-badge.svg b/docs/src/_static/coverage-badge.svg
index ad88956..8a9b8bd 100644
--- a/docs/src/_static/coverage-badge.svg
+++ b/docs/src/_static/coverage-badge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="114" height="20" role="img" aria-label="coverage: 97.33%"><title>coverage: 97.33%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="114" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="61" height="20" fill="#555"/><rect x="61" width="53" height="20" fill="#4c1"/><rect width="114" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="315" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="510">coverage</text><text x="315" y="140" transform="scale(.1)" fill="#fff" textLength="510">coverage</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">97.33%</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="430">97.33%</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="114" height="20" role="img" aria-label="coverage: 59.47%"><title>coverage: 59.47%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="114" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="61" height="20" fill="#555"/><rect x="61" width="53" height="20" fill="#fe7d37"/><rect width="114" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="315" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="510">coverage</text><text x="315" y="140" transform="scale(.1)" fill="#fff" textLength="510">coverage</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">59.47%</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="430">59.47%</text></g></svg>
\ No newline at end of file
diff --git a/src/nviz/image.py b/src/nviz/image.py
index 8cd8c29..5ec6c3a 100644
--- a/src/nviz/image.py
+++ b/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
diff --git a/tests/test_image.py b/tests/test_image.py
index c13e97e..1f9d4a9 100644
--- a/tests/test_image.py
+++ b/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(