🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata

tests/test_wsireader.py

@@ -2034,11 +2034,11 @@ def test_ngff_empty_datasets_mpp(tmp_path):
     assert wsi.info.mpp is None
 
 
-def test_nff_no_scale_transforms_mpp(tmp_path):
+def test_ngff_no_scale_transforms_mpp(tmp_path):
     """Test that mpp is None if no scale transforms are present."""
     sample = _fetch_remote_sample("ngff-1")
     # Create a copy of the sample with no axes
-    sample_copy = tmp_path / "ngff-1"
+    sample_copy = tmp_path / "ngff-1.zarr"
     shutil.copytree(sample, sample_copy)
     with open(sample_copy / ".zattrs", "r") as fh:
         zattrs = json.load(fh)
@@ -2051,6 +2051,36 @@ def test_nff_no_scale_transforms_mpp(tmp_path):
     assert wsi.info.mpp is None
 
 
+def test_ngff_missing_omero_version(tmp_path):
+    """Test that the reader can handle missing omero version."""
+    sample = _fetch_remote_sample("ngff-1")
+    # Create a copy of the sample
+    sample_copy = tmp_path / "ngff-1.zarr"
+    shutil.copytree(sample, sample_copy)
+    with open(sample_copy / ".zattrs", "r") as fh:
+        zattrs = json.load(fh)
+    # Remove the omero version
+    del zattrs["omero"]["version"]
+    with open(sample_copy / ".zattrs", "w") as fh:
+        json.dump(zattrs, fh, indent=2)
+    wsireader.WSIReader.open(sample_copy)
+
+
+def test_ngff_non_numeric_version(tmp_path):
+    """Test that the reader can handle non-numeric omero versions."""
+    sample = _fetch_remote_sample("ngff-1")
+    # Create a copy of the sample
+    sample_copy = tmp_path / "ngff-1.zarr"
+    shutil.copytree(sample, sample_copy)
+    with open(sample_copy / ".zattrs", "r") as fh:
+        zattrs = json.load(fh)
+    # Set the omero version to a non-numeric string
+    zattrs["omero"]["version"] = "0.5-dev"
+    with open(sample_copy / ".zattrs", "w") as fh:
+        json.dump(zattrs, fh, indent=2)
+    wsireader.WSIReader.open(sample_copy)
+
+
 class TestReader:
     scenarios = [
         (

tiatoolbox/wsicore/wsireader.py

@@ -136,11 +136,14 @@ def is_ngff(path: pathlib.Path, min_version: Tuple[int, ...] = (0, 4)) -> bool:
         tuple(int(part) for part in scale.get("version", "").split("."))
         for scale in multiscales
     )
-    omero_version = tuple(int(part) for part in omero.get("version", "").split("."))
+    omero_version = omero.get("verion")
+    if omero_version:
+        omero_version = tuple(omero_version.split("."))
+        if omero_version < min_version:
+            return False
     if any(version < min_version for version in multiscales_versions):
         return False
-    if omero_version < min_version:
-        return False
+
     return is_zarr(path)
 
 

whitelist.txt

@@ -41,6 +41,7 @@ Nx4
 NxM
 NxN
 OME
+Omero
 Omnyx
 OpenCV
 Otsu's