ngio 0.5.0a1__tar.gz → 0.5.0a2__tar.gz

{ngio-0.5.0a1 → ngio-0.5.0a2}/.github/workflows/build_docs.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: 🐍 Set up Python

{ngio-0.5.0a1 → ngio-0.5.0a2}/.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     # included in the sdist (unless explicitly excluded)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - run: pipx run check-manifest
 
   test:
@@ -37,7 +37,7 @@ jobs:
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v6
@@ -98,7 +98,7 @@ jobs:
       contents: write
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 

{ngio-0.5.0a1 → ngio-0.5.0a2}/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [v0.5.0]
+
+### Features
+- Add support for OME-NGFF v0.5
+- Move to zarr-python v3
+
+### API Changes
+
+- The `compressor` argument has been renamed to `compressors` in all relevant functions and methods to reflect the support for multiple compressors in zarr v3.
+- The `version` argument has been renamed to `ngff_version` in all relevant functions and methods to specify the OME-NGFF version.
+- Remove the `parallel_safe` argument from all zarr related functions and methods. The locking mechanism is now handled internally and only depends on the 
+`cache`.
+- Remove the unused `parent` argument from `ZarrGroupHandler`.
+## [v0.4.6]
+
+### Bug Fixes
+- Fix channel selection from `wavelength_id`
+- Fix table opening mode to stop wrtiting groups when opening in append mode.
+
+## [v0.4.5]
+
+### Bug Fixes
+- Pin Dask to version <2025.11 to avoid errors when writing zarr pyramids with dask (see https://github.com/dask/dask/issues/12159#issuecomment-3548421833)
+
 ## [v0.4.4]
 
 ### Bug Fixes

{ngio-0.5.0a1 → ngio-0.5.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0a1
+Version: 0.5.0a2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -17,8 +17,8 @@ Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models

{ngio-0.5.0a1 → ngio-0.5.0a2}/pyproject.toml

@@ -41,8 +41,8 @@ dependencies = [
     "pandas>=1.2.0",
     "requests",
     "aiohttp",
-    "dask[array]",
-    "dask[distributed]",
+    "dask[array]<2025.11.0",
+    "dask[distributed]<2025.11.0",
     # "xarray", still not used
     "ome-zarr-models",
     "pooch",

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/common/_pyramid.py

@@ -41,9 +41,19 @@ def _on_disk_dask_zoom(
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
 
-    target_array = target_array.rechunk(target.chunks)  # type: ignore
-    target_array.compute_chunk_sizes()
+    # This is a potential fix for Dask 2025.11
+    # import dask.config
+    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
+    # current_chunk_size = dask.config.get("array.chunk-size")
+    # Increase the chunk size to avoid dask potentially creating
+    # corrupted chunks when writing chunks that are not multiple of the
+    # target chunk size
+    # dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
+    target_array = target_array.rechunk(target.chunks)
+    target_array = target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
+    # Restore previous chunk size
+    # dask.config.set({"array.chunk-size": current_chunk_size})
 
 
 def _on_disk_coarsen(

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/hcs/_plate.py

@@ -40,6 +40,7 @@ from ngio.tables import (
 )
 from ngio.utils import (
     AccessModeLiteral,
+    NgioCache,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
@@ -239,6 +240,12 @@ class OmeZarrPlate:
         self._group_handler = group_handler
         self._meta_handler = find_plate_meta_handler(group_handler)
         self._tables_container = table_container
+        self._wells_cache: NgioCache[OmeZarrWell] = NgioCache(
+            use_cache=self._group_handler.use_cache
+        )
+        self._images_cache: NgioCache[OmeZarrContainer] = NgioCache(
+            use_cache=self._group_handler.use_cache
+        )
 
     def __repr__(self) -> str:
         """Return a string representation of the plate."""
@@ -356,6 +363,24 @@ class OmeZarrPlate:
         well = self.get_well(row=row, column=column)
         return well.get_image_acquisition_id(image_path=image_path)
 
+    def _get_well(self, well_path: str) -> OmeZarrWell:
+        """Get a well from the plate by its path.
+
+        Args:
+            well_path (str): The path of the well.
+
+        Returns:
+            OmeZarrWell: The well.
+
+        """
+        cached_well = self._wells_cache.get(well_path)
+        if cached_well is not None:
+            return cached_well
+
+        group_handler = self._group_handler.derive_handler(well_path)
+        self._wells_cache.set(well_path, OmeZarrWell(group_handler))
+        return OmeZarrWell(group_handler)
+
     def get_well(self, row: str, column: int | str) -> OmeZarrWell:
         """Get a well from the plate.
 
@@ -367,8 +392,7 @@ class OmeZarrPlate:
             OmeZarrWell: The well.
         """
         well_path = self._well_path(row=row, column=column)
-        group_handler = self._group_handler.derive_handler(well_path)
-        return OmeZarrWell(group_handler)
+        return self._get_well(well_path=well_path)
 
     async def get_wells_async(self) -> dict[str, OmeZarrWell]:
         """Get all wells in the plate asynchronously.
@@ -380,26 +404,17 @@ class OmeZarrPlate:
             dict[str, OmeZarrWell]: A dictionary of wells, where the key is the well
                 path and the value is the well object.
         """
-        wells = self._group_handler.get_from_cache("wells")
-        if wells is not None:
-            assert isinstance(wells, dict)
-            return wells
-
-        def process_well(well_path):
-            group_handler = self._group_handler.derive_handler(well_path)
-            well = OmeZarrWell(group_handler)
-            return well_path, well
-
         wells, tasks = {}, []
         for well_path in self.wells_paths():
-            task = asyncio.to_thread(process_well, well_path)
+            task = asyncio.to_thread(
+                lambda well_path: (well_path, self._get_well(well_path)), well_path
+            )
             tasks.append(task)
 
         results = await asyncio.gather(*tasks)
         for well_path, well in results:
             wells[well_path] = well
 
-        self._group_handler.add_to_cache("wells", wells)
         return wells
 
     def get_wells(self) -> dict[str, OmeZarrWell]:
@@ -409,24 +424,25 @@ class OmeZarrPlate:
             dict[str, OmeZarrWell]: A dictionary of wells, where the key is the well
                 path and the value is the well object.
         """
-        wells = self._group_handler.get_from_cache("wells")
-        if wells is not None:
-            assert isinstance(wells, dict)
-            return wells
-
-        def process_well(well_path):
-            group_handler = self._group_handler.derive_handler(well_path)
-            well = OmeZarrWell(group_handler)
-            return well_path, well
-
         wells = {}
         for well_path in self.wells_paths():
-            _, well = process_well(well_path)
-            wells[well_path] = well
-
-        self._group_handler.add_to_cache("wells", wells)
+            wells[well_path] = self._get_well(well_path)
         return wells
 
+    def _get_image(self, image_path: str) -> OmeZarrContainer:
+        """Get an image from the plate by its path.
+
+        Args:
+            image_path (str): The path of the image.
+        """
+        cached_image = self._images_cache.get(image_path)
+        if cached_image is not None:
+            return cached_image
+        img_group_handler = self._group_handler.derive_handler(image_path)
+        image = OmeZarrContainer(img_group_handler)
+        self._images_cache.set(image_path, image)
+        return image
+
     async def get_images_async(
         self, acquisition: int | None = None
     ) -> dict[str, OmeZarrContainer]:
@@ -442,30 +458,19 @@ class OmeZarrPlate:
             dict[str, OmeZarrContainer]: A dictionary of images, where the key is the
                 image path and the value is the image object.
         """
-        images = self._group_handler.get_from_cache("images")
-        if images is not None:
-            assert isinstance(images, dict)
-            return images
-
         paths = await self.images_paths_async(acquisition=acquisition)
 
-        def process_image(image_path):
-            """Process a single image and return the image path and image object."""
-            img_group_handler = self._group_handler.derive_handler(image_path)
-            image = OmeZarrContainer(img_group_handler)
-            return image_path, image
-
         images, tasks = {}, []
         for image_path in paths:
-            task = asyncio.to_thread(process_image, image_path)
+            task = asyncio.to_thread(
+                lambda image_path: (image_path, self._get_image(image_path)), image_path
+            )
             tasks.append(task)
 
         results = await asyncio.gather(*tasks)
 
         for image_path, image in results:
             images[image_path] = image
-
-        self._group_handler.add_to_cache("images", images)
         return images
 
     def get_images(self, acquisition: int | None = None) -> dict[str, OmeZarrContainer]:
@@ -474,24 +479,11 @@ class OmeZarrPlate:
         Args:
             acquisition: The acquisition id to filter the images.
         """
-        images = self._group_handler.get_from_cache("images")
-        if images is not None:
-            assert isinstance(images, dict)
-            return images
         paths = self.images_paths(acquisition=acquisition)
-
-        def process_image(image_path):
-            """Process a single image and return the image path and image object."""
-            img_group_handler = self._group_handler.derive_handler(image_path)
-            image = OmeZarrContainer(img_group_handler)
-            return image_path, image
-
         images = {}
         for image_path in paths:
-            _, image = process_image(image_path)
-            images[image_path] = image
+            images[image_path] = self._get_image(image_path)
 
-        self._group_handler.add_to_cache("images", images)
         return images
 
     def get_image(
@@ -508,8 +500,7 @@ class OmeZarrPlate:
             OmeZarrContainer: The image.
         """
         image_path = self._image_path(row=row, column=column, path=image_path)
-        group_handler = self._group_handler.derive_handler(image_path)
-        return OmeZarrContainer(group_handler)
+        return self._get_image(image_path)
 
     def get_image_store(
         self, row: str, column: int | str, image_path: str
@@ -785,7 +776,6 @@ class OmeZarrPlate:
         keep_acquisitions: bool = False,
         cache: bool = False,
         overwrite: bool = False,
-        parallel_safe: bool = True,
     ) -> "OmeZarrPlate":
         """Derive a new OME-Zarr plate from an existing one.
 
@@ -796,7 +786,6 @@ class OmeZarrPlate:
             keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
             cache (bool): Whether to use a cache for the zarr group metadata.
             overwrite (bool): Whether to overwrite the existing plate.
-            parallel_safe (bool): Whether the group handler is parallel safe.
         """
         return derive_ome_zarr_plate(
             ome_zarr_plate=self,
@@ -806,7 +795,6 @@ class OmeZarrPlate:
             keep_acquisitions=keep_acquisitions,
             cache=cache,
             overwrite=overwrite,
-            parallel_safe=parallel_safe,
         )
 
     def _get_tables_container(self) -> TablesContainer | None:
@@ -1143,7 +1131,6 @@ def open_ome_zarr_plate(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
     """Open an OME-Zarr plate.
 
@@ -1152,11 +1139,8 @@ def open_ome_zarr_plate(
         cache (bool): Whether to use a cache for the zarr group metadata.
         mode (AccessModeLiteral): The
             access mode for the image. Defaults to "r+".
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
-    group_handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
+    group_handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     return OmeZarrPlate(group_handler)
 
 
@@ -1168,9 +1152,7 @@ def _create_empty_plate_from_meta(
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr plate from metadata."""
     mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, cache=True, mode=mode, parallel_safe=False
-    )
+    group_handler = ZarrGroupHandler(store=store, cache=True, mode=mode)
     meta_handler = get_plate_meta_handler(group_handler, version=version)
     meta_handler.write_meta(meta)
     return group_handler
@@ -1183,9 +1165,18 @@ def create_empty_plate(
     version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
-    """Initialize and create an empty OME-Zarr plate."""
+    """Initialize and create an empty OME-Zarr plate.
+
+    Args:
+        store (StoreOrGroup): The Zarr store or group that stores the plate.
+        name (str): The name of the plate.
+        images (list[ImageInWellPath] | None): A list of images to add to the plate.
+            If None, no images are added. Defaults to None.
+        version (NgffVersion): The version of the new plate.
+        cache (bool): Whether to use a cache for the zarr group metadata.
+        overwrite (bool): Whether to overwrite the existing plate.
+    """
     plate_meta = NgioPlateMeta.default_init(
         name=name,
         version=version,
@@ -1211,7 +1202,6 @@ def create_empty_plate(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )
 
 
@@ -1223,7 +1213,6 @@ def derive_ome_zarr_plate(
     keep_acquisitions: bool = False,
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
     """Derive a new OME-Zarr plate from an existing one.
 
@@ -1235,7 +1224,6 @@ def derive_ome_zarr_plate(
         keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         overwrite (bool): Whether to overwrite the existing plate.
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     if plate_name is None:
         plate_name = ome_zarr_plate.meta.plate.name
@@ -1255,7 +1243,6 @@ def derive_ome_zarr_plate(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )
 
 
@@ -1263,7 +1250,6 @@ def open_ome_zarr_well(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
-    parallel_safe: bool = True,
 ) -> OmeZarrWell:
     """Open an OME-Zarr well.
 
@@ -1271,10 +1257,11 @@ def open_ome_zarr_well(
         store (StoreOrGroup): The Zarr store or group that stores the plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         mode (AccessModeLiteral): The access mode for the image. Defaults to "r+".
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     group_handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
+        store=store,
+        cache=cache,
+        mode=mode,
     )
     return OmeZarrWell(group_handler)
 
@@ -1284,7 +1271,6 @@ def create_empty_well(
     version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrWell:
     """Create an empty OME-Zarr well.
 
@@ -1293,10 +1279,9 @@ def create_empty_well(
         version (NgffVersion): The version of the new well.
         cache (bool): Whether to use a cache for the zarr group metadata.
         overwrite (bool): Whether to overwrite the existing well.
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     group_handler = ZarrGroupHandler(
-        store=store, cache=True, mode="w" if overwrite else "w-", parallel_safe=False
+        store=store, cache=True, mode="w" if overwrite else "w-"
     )
     meta_handler = get_well_meta_handler(group_handler, version=version)
     meta = NgioWellMeta.default_init()
@@ -1306,5 +1291,4 @@ def create_empty_well(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/images/_create.py

@@ -40,7 +40,7 @@ def _init_generic_meta(
     space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
     name: str | None = None,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> tuple[_image_or_label_meta, list[float]]:
     """Initialize the metadata for an image or label."""
     scaling_factors = []
@@ -75,7 +75,7 @@ def _init_generic_meta(
         axes_names=axes_names,
         pixel_size=pixel_sizes,
         scaling_factors=scaling_factors,
-        version=version,
+        version=ngff_version,
     )
     return meta, scaling_factors
 
@@ -98,7 +98,7 @@ def create_empty_label_container(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty label with the given shape and metadata.
 
@@ -130,7 +130,7 @@ def create_empty_label_container(
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultVersion.
 
     """
@@ -155,14 +155,16 @@ def create_empty_label_container(
         time_unit=time_unit,
         axes_names=axes_names,
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     mode = "w" if overwrite else "w-"
     group_handler = ZarrGroupHandler(
         store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
     )
-    image_handler = get_label_meta_handler(version=version, group_handler=group_handler)
+    image_handler = get_label_meta_handler(
+        version=ngff_version, group_handler=group_handler
+    )
     image_handler.write_meta(meta)
 
     init_empty_pyramid(
@@ -199,7 +201,7 @@ def create_empty_image_container(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -231,7 +233,7 @@ def create_empty_image_container(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultVersion.
 
     """
@@ -256,13 +258,15 @@ def create_empty_image_container(
         time_unit=time_unit,
         axes_names=axes_names,
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
     mode = "w" if overwrite else "w-"
     group_handler = ZarrGroupHandler(
         store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
     )
-    image_handler = get_image_meta_handler(version=version, group_handler=group_handler)
+    image_handler = get_image_meta_handler(
+        version=ngff_version, group_handler=group_handler
+    )
     image_handler.write_meta(meta)
 
     init_empty_pyramid(

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/images/_create_synt_container.py

@@ -40,7 +40,7 @@ def create_synthetic_ome_zarr(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -72,7 +72,7 @@ def create_synthetic_ome_zarr(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (NgffVersion, optional): The version of the OME-Zarr specification.
+        ngff_version (NgffVersion, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     if isinstance(reference_sample, str):
@@ -105,7 +105,7 @@ def create_synthetic_ome_zarr(
         overwrite=overwrite,
         dimension_separator=dimension_separator,
         compressors=compressors,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     image = ome_zarr.get_image()

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/images/_image.py

@@ -823,7 +823,7 @@ def derive_image_container(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=ngff_version,
+        ngff_version=ngff_version,
     )
     image_container = ImagesContainer(handler)
 
@@ -885,7 +885,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "wavelength_id":
             return image.get_channel_idx(
-                channel_label=str(channel_selection.identifier)
+                wavelength_id=str(channel_selection.identifier)
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/images/_label.py

@@ -329,7 +329,7 @@ def derive_label(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=ref_meta.version,
+        ngff_version=ref_meta.version,
         name=name,
     )
     return None

{ngio-0.5.0a1 → ngio-0.5.0a2}/src/ngio/images/_ome_zarr_container.py

@@ -845,7 +845,7 @@ def create_empty_ome_zarr(
     channel_colors: Sequence[str] | None = None,
     channel_active: Sequence[bool] | None = None,
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -885,7 +885,7 @@ def create_empty_ome_zarr(
             active. Defaults to None.
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (NgffVersion, optional): The version of the OME-Zarr specification.
+        ngff_version (NgffVersion, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     handler = create_empty_image_container(
@@ -906,7 +906,7 @@ def create_empty_ome_zarr(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     ome_zarr = OmeZarrContainer(group_handler=handler)
@@ -942,7 +942,7 @@ def create_ome_zarr_from_array(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an OME-Zarr image from a numpy array.
 
@@ -983,7 +983,7 @@ def create_ome_zarr_from_array(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     handler = create_empty_image_container(
@@ -1004,7 +1004,7 @@ def create_ome_zarr_from_array(
         overwrite=overwrite,
         dimension_separator=dimension_separator,
         compressors=compressors,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     ome_zarr = OmeZarrContainer(group_handler=handler)