ngio 0.5.0a3__tar.gz → 0.5.0b2__tar.gz

{ngio-0.5.0a3 → ngio-0.5.0b2}/CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Features
 - Add support for OME-NGFF v0.5
 - Move to zarr-python v3
+- API to delete labels and tables from OME-Zarr containers and HCS plates.
 
 ### API Breaking Changes
 

{ngio-0.5.0a3 → ngio-0.5.0b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0a3
+Version: 0.5.0b2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/__init__.py

@@ -37,6 +37,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     NgffVersions,
     PixelSize,
 )
+from ngio.utils import NgioSupportedStore, StoreOrGroup
 
 __all__ = [
     "AxesSetup",
@@ -47,12 +48,14 @@ __all__ = [
     "ImageInWellPath",
     "Label",
     "NgffVersions",
+    "NgioSupportedStore",
     "OmeZarrContainer",
     "OmeZarrPlate",
     "OmeZarrWell",
     "PixelSize",
     "Roi",
     "RoiSlice",
+    "StoreOrGroup",
     "create_empty_ome_zarr",
     "create_empty_plate",
     "create_empty_well",

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/hcs/_plate.py

@@ -15,6 +15,7 @@ from ngio.images import (
     list_image_tables_async,
 )
 from ngio.ome_zarr_meta import (
+    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioPlateMeta,
@@ -778,7 +779,8 @@ class OmeZarrPlate:
         self,
         store: StoreOrGroup,
         plate_name: str | None = None,
-        version: NgffVersions = "0.4",
+        version: NgffVersions | None = None,
+        ngff_version: NgffVersions = DefaultNgffVersion,
         keep_acquisitions: bool = False,
         cache: bool = False,
         overwrite: bool = False,
@@ -788,7 +790,8 @@ class OmeZarrPlate:
         Args:
             store (StoreOrGroup): The Zarr store or group that stores the plate.
             plate_name (str | None): The name of the new plate.
-            version (NgffVersion): The version of the new plate.
+            version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
+            ngff_version (NgffVersion): The NGFF version to use for the new 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.
@@ -797,6 +800,7 @@ class OmeZarrPlate:
             ome_zarr_plate=self,
             store=store,
             plate_name=plate_name,
+            ngff_version=ngff_version,
             version=version,
             keep_acquisitions=keep_acquisitions,
             cache=cache,
@@ -955,6 +959,25 @@ class OmeZarrPlate:
             name=name, table=table, backend=backend, overwrite=overwrite
         )
 
+    def delete_table(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a table from the group.
+
+        Args:
+            name (str): The name of the table to delete.
+            missing_ok (bool): If True, do not raise an error if the table does not
+                exist.
+
+        """
+        table_container = self._get_tables_container(create_mode=False)
+        if table_container is None and missing_ok:
+            return
+        if table_container is None:
+            raise NgioValueError(
+                f"No tables found in the image, cannot delete {name}. "
+                "Set missing_ok=True to ignore this error."
+            )
+        table_container.delete(name=name, missing_ok=missing_ok)
+
     def list_image_tables(
         self,
         acquisition: int | None = None,
@@ -1157,7 +1180,6 @@ def open_ome_zarr_plate(
 def _create_empty_plate_from_meta(
     store: StoreOrGroup,
     meta: NgioPlateMeta,
-    version: NgffVersions = "0.4",
     overwrite: bool = False,
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr plate from metadata."""
@@ -1171,7 +1193,8 @@ def create_empty_plate(
     store: StoreOrGroup,
     name: str,
     images: list[ImageInWellPath] | None = None,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrPlate:
@@ -1182,18 +1205,26 @@ def create_empty_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.
+        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
+        ngff_version (NgffVersion): The NGFF version to use for the new plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         overwrite (bool): Whether to overwrite the existing plate.
     """
+    if version is not None:
+        warnings.warn(
+            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
+            "Please use 'ngff_version' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        ngff_version = version
     plate_meta = NgioPlateMeta.default_init(
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
     group_handler = _create_empty_plate_from_meta(
         store=store,
         meta=plate_meta,
-        version=version,
         overwrite=overwrite,
     )
 
@@ -1218,7 +1249,8 @@ def derive_ome_zarr_plate(
     ome_zarr_plate: OmeZarrPlate,
     store: StoreOrGroup,
     plate_name: str | None = None,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     keep_acquisitions: bool = False,
     cache: bool = False,
     overwrite: bool = False,
@@ -1229,24 +1261,33 @@ def derive_ome_zarr_plate(
         ome_zarr_plate (OmeZarrPlate): The existing OME-Zarr plate.
         store (StoreOrGroup): The Zarr store or group that stores the plate.
         plate_name (str | None): The name of the new plate.
-        version (NgffVersion): The version of the new plate.
+        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
+        ngff_version (NgffVersion): The NGFF version to use for the new 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.
     """
+    if version is not None:
+        warnings.warn(
+            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
+            "Please use 'ngff_version' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        ngff_version = version
+
     if plate_name is None:
         plate_name = ome_zarr_plate.meta.plate.name
 
     new_meta = ome_zarr_plate.meta.derive(
         name=plate_name,
-        version=version,
+        ngff_version=ngff_version,
         keep_acquisitions=keep_acquisitions,
     )
     _ = _create_empty_plate_from_meta(
         store=store,
         meta=new_meta,
         overwrite=overwrite,
-        version=version,
     )
     return open_ome_zarr_plate(
         store=store,
@@ -1277,7 +1318,8 @@ def open_ome_zarr_well(
 
 def create_empty_well(
     store: StoreOrGroup,
-    version: NgffVersions = "0.4",
+    version: NgffVersions | None = None,
+    ngff_version: NgffVersions = DefaultNgffVersion,
     cache: bool = False,
     overwrite: bool = False,
 ) -> OmeZarrWell:
@@ -1285,14 +1327,25 @@ def create_empty_well(
 
     Args:
         store (StoreOrGroup): The Zarr store or group that stores the well.
-        version (NgffVersion): The version of the new well.
+        version (NgffVersion | None): Deprecated. Please use 'ngff_version' instead.
+        ngff_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.
     """
+    if version is not None:
+        warnings.warn(
+            "The 'version' argument is deprecated, and will be removed in ngio=0.3. "
+            "Please use 'ngff_version' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        ngff_version = version
     group_handler = ZarrGroupHandler(
         store=store, cache=True, mode="w" if overwrite else "w-"
     )
-    update_ngio_well_meta(group_handler, NgioWellMeta.default_init())
+    update_ngio_well_meta(
+        group_handler, NgioWellMeta.default_init(ngff_version=ngff_version)
+    )
 
     return open_ome_zarr_well(
         store=store,

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/images/_abstract_image.py

@@ -681,7 +681,7 @@ def _check_chunks_and_shards_compatibility(
 
 def _apply_channel_policy(
     ref_image: AbstractImage,
-    channels_policy: Literal["squeeze", "same"] | int,
+    channels_policy: Literal["squeeze", "same", "singleton"] | int,
     shapes: list[tuple[int, ...]],
     axes: tuple[str, ...],
     chunks: ChunksLike,
@@ -703,6 +703,10 @@ def _apply_channel_policy(
     if channels_policy == "same":
         return shapes, axes, chunks, shards
 
+    if channels_policy == "singleton":
+        # Treat 'singleton' as setting channel size to 1
+        channels_policy = 1
+
     channel_index = ref_image.axes_handler.get_index("c")
     if channel_index is None:
         if channels_policy == "squeeze":
@@ -729,11 +733,6 @@ def _apply_channel_policy(
     elif isinstance(channels_policy, int):
         new_shapes = []
         for shape in shapes:
-            if shape[channel_index] != channels_policy:
-                raise NgioValueError(
-                    f"Cannot apply channel policy {channels_policy=} to an image "
-                    f"with {shape[channel_index]} channels."
-                )
             new_shape = (
                 *shape[:channel_index],
                 channels_policy,
@@ -797,7 +796,7 @@ def abstract_derive(
     z_spacing: float | None = None,
     time_spacing: float | None = None,
     name: str | None = None,
-    channels_policy: Literal["squeeze", "same"] | int = "same",
+    channels_policy: Literal["squeeze", "same", "singleton"] | int = "same",
     channels_meta: Sequence[str | Channel] | None = None,
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
@@ -826,9 +825,11 @@ def abstract_derive(
         time_spacing (float | None): The time spacing of the new image.
         axes_names (Sequence[str] | None): The axes names of the new image.
         name (str | None): The name of the new image.
-        channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+        channels_policy (Literal["squeeze", "same", "singleton"] | int):
+            Possible policies:
             - If "squeeze", the channels axis will be removed (no matter its size).
             - If "same", the channels axis will be kept as is (if it exists).
+            - If "singleton", the channels axis will be set to size 1.
             - If an integer is provided, the channels axis will be changed to have that
                 size.
         channels_meta (Sequence[str | Channel] | None): The channels metadata

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/images/_image.py

@@ -765,6 +765,7 @@ def derive_image_container(
     z_spacing: float | None = None,
     time_spacing: float | None = None,
     name: str | None = None,
+    channels_policy: Literal["same", "squeeze", "singleton"] | int = "same",
     channels_meta: Sequence[str | Channel] | None = None,
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
@@ -793,6 +794,13 @@ def derive_image_container(
         z_spacing (float | None): The z spacing of the new image.
         time_spacing (float | None): The time spacing of the new image.
         name (str | None): The name of the new image.
+        channels_policy (Literal["squeeze", "same", "singleton"] | int): Possible
+            policies:
+            - If "squeeze", the channels axis will be removed (no matter its size).
+            - If "same", the channels axis will be kept as is (if it exists).
+            - If "singleton", the channels axis will be set to size 1.
+            - If an integer is provided, the channels axis will be changed to have
+                that size.
         channels_meta (Sequence[str | Channel] | None): The channels metadata
             of the new image.
         ngff_version (NgffVersions | None): The NGFF version to use.
@@ -826,7 +834,7 @@ def derive_image_container(
         time_spacing=time_spacing,
         name=name,
         channels_meta=channels_meta,
-        channels_policy="same",
+        channels_policy=channels_policy,
         ngff_version=ngff_version,
         chunks=chunks,
         shards=shards,

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/images/_label.py

@@ -11,8 +11,11 @@ from ngio.images._abstract_image import AbstractImage, abstract_derive
 from ngio.images._image import Image
 from ngio.ome_zarr_meta import (
     LabelMetaHandler,
+    LabelsGroupMetaHandler,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     PixelSize,
+    update_ngio_labels_group_meta,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
     DefaultSpaceUnit,
@@ -112,29 +115,39 @@ class Label(AbstractImage):
 class LabelsContainer:
     """A class to handle the /labels group in an OME-NGFF file."""
 
-    def __init__(self, group_handler: ZarrGroupHandler) -> None:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        ngff_version: NgffVersions | None = None,
+    ) -> None:
         """Initialize the LabelGroupHandler."""
         self._group_handler = group_handler
-        # Validate the group
-        # Either contains a labels attribute or is empty
-        attrs = self._group_handler.load_attrs()
-        if len(attrs) == 0:
-            # It's an empty group
-            pass
-        elif "labels" in attrs and isinstance(attrs["labels"], list):
-            # It's a valid group
-            pass
-        else:
-            raise NgioValidationError(
-                f"Invalid /labels group. "
-                f"Expected a single labels attribute with a list of label names. "
-                f"Found: {attrs}"
+        # If the group is empty, initialize the metadata
+        try:
+            self._meta_handler = LabelsGroupMetaHandler(group_handler)
+        except NgioValidationError:
+            if ngff_version is None:
+                raise NgioValueError(
+                    "The /labels group is missing metadata. "
+                    "Please provide the ngff_version to initialize it."
+                ) from None
+            meta = NgioLabelsGroupMeta(labels=[], version=ngff_version)
+            update_ngio_labels_group_meta(
+                group_handler=group_handler,
+                ngio_meta=meta,
             )
+            self._group_handler = self._group_handler.reopen_handler()
+            self._meta_handler = LabelsGroupMetaHandler(group_handler)
+
+    @property
+    def meta(self) -> NgioLabelsGroupMeta:
+        """Return the metadata."""
+        meta = self._meta_handler.get_meta()
+        return meta
 
     def list(self) -> list[str]:
         """Create the /labels group if it doesn't exist."""
-        attrs = self._group_handler.load_attrs()
-        return attrs.get("labels", [])
+        return self.meta.labels
 
     def get(
         self,
@@ -169,6 +182,31 @@ class LabelsContainer:
         )
         return Label(group_handler, path, label_meta_handler)
 
+    def delete(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a label from the group.
+
+        Args:
+            name (str): The name of the label to delete.
+            missing_ok (bool): If True, do not raise an error if the label does not
+                exist.
+
+        """
+        existing_labels = self.list()
+        if name not in existing_labels:
+            if missing_ok:
+                return
+            raise NgioValueError(
+                f"Label '{name}' not found in the Labels group. "
+                f"Available labels: {existing_labels}"
+            )
+
+        self._group_handler.delete_group(name)
+        existing_labels.remove(name)
+        update_meta = NgioLabelsGroupMeta(
+            labels=existing_labels, version=self.meta.version
+        )
+        self._meta_handler.update_meta(update_meta)
+
     def derive(
         self,
         name: str,
@@ -178,7 +216,7 @@ class LabelsContainer:
         pixelsize: float | tuple[float, float] | None = None,
         z_spacing: float | None = None,
         time_spacing: float | None = None,
-        channels_policy: Literal["same", "squeeze"] | int = "squeeze",
+        channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
         chunks: ChunksLike = "auto",
@@ -210,9 +248,11 @@ class LabelsContainer:
             name (str | None): The name of the new image.
             channels_meta (Sequence[str | Channel] | None): The channels metadata
                 of the new image.
-            channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+            channels_policy (Literal["squeeze", "same", "singleton"] | int):
+                Possible policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
+                - If "singleton", the channels axis will be set to size 1.
                 - If an integer is provided, the channels axis will be changed to have
                     that size.
             ngff_version (NgffVersions | None): The NGFF version to use.
@@ -267,8 +307,11 @@ class LabelsContainer:
 
         if name not in existing_labels:
             existing_labels.append(name)
-            self._group_handler.write_attrs({"labels": existing_labels})
 
+        update_meta = NgioLabelsGroupMeta(
+            labels=existing_labels, version=self.meta.version
+        )
+        self._meta_handler.update_meta(update_meta)
         return self.get(name)
 
 
@@ -282,7 +325,7 @@ def derive_label(
     z_spacing: float | None = None,
     time_spacing: float | None = None,
     name: str | None = None,
-    channels_policy: Literal["same", "squeeze"] | int = "squeeze",
+    channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
     ngff_version: NgffVersions | None = None,
     # Zarr Array parameters
     chunks: ChunksLike = "auto",
@@ -308,9 +351,11 @@ def derive_label(
         z_spacing (float | None): The z spacing of the new label.
         time_spacing (float | None): The time spacing of the new label.
         name (str | None): The name of the new label.
-        channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+        channels_policy (Literal["squeeze", "same", "singleton"] | int): Possible
+            policies:
             - If "squeeze", the channels axis will be removed (no matter its size).
             - If "same", the channels axis will be kept as is (if it exists).
+            - If "singleton", the channels axis will be set to size 1.
             - If an integer is provided, the channels axis will be changed to have that
                 size.
         ngff_version (NgffVersions | None): The NGFF version to use.

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/images/_ome_zarr_container.py

@@ -61,13 +61,13 @@ def _try_get_table_container(
 
 
 def _try_get_label_container(
-    handler: ZarrGroupHandler, create_mode: bool = True
+    handler: ZarrGroupHandler, ngff_version: NgffVersions, create_mode: bool = True
 ) -> LabelsContainer | None:
     """Return a default label container."""
     try:
         label_handler = handler.get_handler("labels", create_mode=create_mode)
-        return LabelsContainer(label_handler)
-    except NgioError:
+        return LabelsContainer(label_handler, ngff_version=ngff_version)
+    except FileNotFoundError:
         return None
 
 
@@ -149,7 +149,9 @@ class OmeZarrContainer:
             return self._labels_container
 
         _labels_container = _try_get_label_container(
-            self._group_handler, create_mode=create_mode
+            self._group_handler,
+            create_mode=create_mode,
+            ngff_version=self.image_meta.version,
         )
         self._labels_container = _labels_container
         return self._labels_container
@@ -428,6 +430,7 @@ class OmeZarrContainer:
         z_spacing: float | None = None,
         time_spacing: float | None = None,
         name: str | None = None,
+        channels_policy: Literal["squeeze", "same", "singleton"] | int = "same",
         channels_meta: Sequence[str | Channel] | None = None,
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
@@ -459,6 +462,12 @@ class OmeZarrContainer:
             z_spacing (float | None): The z spacing of the new image.
             time_spacing (float | None): The time spacing of the new image.
             name (str | None): The name of the new image.
+            channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+                - If "squeeze", the channels axis will be removed (no matter its size).
+                - If "same", the channels axis will be kept as is (if it exists).
+                - If "singleton", the channels axis will be set to size 1.
+                - If an integer is provided, the channels axis will be changed to have
+                    that size.
             channels_meta (Sequence[str | Channel] | None): The channels metadata
                 of the new image.
             ngff_version (NgffVersions | None): The NGFF version to use.
@@ -665,6 +674,25 @@ class OmeZarrContainer:
             name=name, table=table, backend=backend, overwrite=overwrite
         )
 
+    def delete_table(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a table from the group.
+
+        Args:
+            name (str): The name of the table to delete.
+            missing_ok (bool): If True, do not raise an error if the table does not
+                exist.
+
+        """
+        table_container = self._get_tables_container(create_mode=False)
+        if table_container is None and missing_ok:
+            return
+        if table_container is None:
+            raise NgioValueError(
+                f"No tables found in the image, cannot delete {name}. "
+                "Set missing_ok=True to ignore this error."
+            )
+        table_container.delete(name=name, missing_ok=missing_ok)
+
     def list_labels(self) -> list[str]:
         """List all labels in the image."""
         label_container = self._get_labels_container(create_mode=False)
@@ -730,6 +758,25 @@ class OmeZarrContainer:
             masking_roi_table=masking_table,
         )
 
+    def delete_label(self, name: str, missing_ok: bool = False) -> None:
+        """Delete a label from the group.
+
+        Args:
+            name (str): The name of the label to delete.
+            missing_ok (bool): If True, do not raise an error if the label does not
+                exist.
+
+        """
+        label_container = self._get_labels_container(create_mode=False)
+        if label_container is None and missing_ok:
+            return
+        if label_container is None:
+            raise NgioValueError(
+                f"No labels found in the image, cannot delete {name}. "
+                "Set missing_ok=True to ignore this error."
+            )
+        label_container.delete(name=name, missing_ok=missing_ok)
+
     def derive_label(
         self,
         name: str,
@@ -739,7 +786,7 @@ class OmeZarrContainer:
         pixelsize: float | tuple[float, float] | None = None,
         z_spacing: float | None = None,
         time_spacing: float | None = None,
-        channels_policy: Literal["same", "squeeze"] | int = "squeeze",
+        channels_policy: Literal["same", "squeeze", "singleton"] | int = "squeeze",
         ngff_version: NgffVersions | None = None,
         # Zarr Array parameters
         chunks: ChunksLike = "auto",
@@ -769,6 +816,7 @@ class OmeZarrContainer:
             channels_policy (Literal["same", "squeeze"] | int): Possible policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
+                - If "singleton", the channels axis will be set to size 1.
                 - If an integer is provided, the channels axis will be changed to have
                     that size.
                 Defaults to "squeeze".

{ngio-0.5.0a3 → ngio-0.5.0b2}/src/ngio/ome_zarr_meta/__init__.py

@@ -3,10 +3,12 @@
 from ngio.ome_zarr_meta._meta_handlers import (
     ImageMetaHandler,
     LabelMetaHandler,
+    LabelsGroupMetaHandler,
     PlateMetaHandler,
     WellMetaHandler,
     update_ngio_image_meta,
     update_ngio_label_meta,
+    update_ngio_labels_group_meta,
     update_ngio_meta,
     update_ngio_plate_meta,
     update_ngio_well_meta,
@@ -14,10 +16,12 @@ from ngio.ome_zarr_meta._meta_handlers import (
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
     Dataset,
+    DefaultNgffVersion,
     ImageInWellPath,
     NgffVersions,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     PixelSize,
@@ -28,13 +32,16 @@ from ngio.ome_zarr_meta.ngio_specs import (
 __all__ = [
     "AxesHandler",
     "Dataset",
+    "DefaultNgffVersion",
     "ImageInWellPath",
     "ImageMetaHandler",
     "LabelMetaHandler",
+    "LabelsGroupMetaHandler",
     "NgffVersions",
     "NgffVersions",
     "NgioImageMeta",
     "NgioLabelMeta",
+    "NgioLabelsGroupMeta",
     "NgioPlateMeta",
     "NgioWellMeta",
     "PixelSize",
@@ -45,6 +52,7 @@ __all__ = [
     "path_in_well_validation",
     "update_ngio_image_meta",
     "update_ngio_label_meta",
+    "update_ngio_labels_group_meta",
     "update_ngio_meta",
     "update_ngio_plate_meta",
     "update_ngio_well_meta",