ngio 0.5.0a3__py3-none-any.whl → 0.5.0b2__py3-none-any.whl

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/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/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/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/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/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/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",

ngio/ome_zarr_meta/_meta_handlers.py

@@ -7,26 +7,32 @@ from ngio.ome_zarr_meta.ngio_specs import (
     AxesSetup,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
 )
+from ngio.ome_zarr_meta.ngio_specs._ngio_image import NgffVersions
 from ngio.ome_zarr_meta.v04 import (
     ngio_to_v04_image_meta,
     ngio_to_v04_label_meta,
+    ngio_to_v04_labels_group_meta,
     ngio_to_v04_plate_meta,
     ngio_to_v04_well_meta,
     v04_to_ngio_image_meta,
     v04_to_ngio_label_meta,
+    v04_to_ngio_labels_group_meta,
     v04_to_ngio_plate_meta,
     v04_to_ngio_well_meta,
 )
 from ngio.ome_zarr_meta.v05 import (
     ngio_to_v05_image_meta,
     ngio_to_v05_label_meta,
+    ngio_to_v05_labels_group_meta,
     ngio_to_v05_plate_meta,
     ngio_to_v05_well_meta,
     v05_to_ngio_image_meta,
     v05_to_ngio_label_meta,
+    v05_to_ngio_labels_group_meta,
     v05_to_ngio_plate_meta,
     v05_to_ngio_well_meta,
 )
@@ -45,9 +51,22 @@ _plate_encoder_registry = {"0.4": ngio_to_v04_plate_meta, "0.5": ngio_to_v05_pla
 _plate_decoder_registry = {"0.4": v04_to_ngio_plate_meta, "0.5": v05_to_ngio_plate_meta}
 _well_encoder_registry = {"0.4": ngio_to_v04_well_meta, "0.5": ngio_to_v05_well_meta}
 _well_decoder_registry = {"0.4": v04_to_ngio_well_meta, "0.5": v05_to_ngio_well_meta}
+_labels_group_encoder_registry = {
+    "0.4": ngio_to_v04_labels_group_meta,
+    "0.5": ngio_to_v05_labels_group_meta,
+}
+_labels_group_decoder_registry = {
+    "0.4": v04_to_ngio_labels_group_meta,
+    "0.5": v05_to_ngio_labels_group_meta,
+}
 
 _meta_type = TypeVar(
-    "_meta_type", NgioImageMeta, NgioLabelMeta, NgioPlateMeta, NgioWellMeta
+    "_meta_type",
+    NgioImageMeta,
+    NgioLabelMeta,
+    NgioLabelsGroupMeta,
+    NgioPlateMeta,
+    NgioWellMeta,
 )
 
 
@@ -62,6 +81,8 @@ def _find_encoder_registry(
         return _plate_encoder_registry
     elif isinstance(ngio_meta, NgioWellMeta):
         return _well_encoder_registry
+    elif isinstance(ngio_meta, NgioLabelsGroupMeta):
+        return _labels_group_encoder_registry
     else:
         raise NgioValueError(f"Unsupported NGIO metadata type: {type(ngio_meta)}")
 
@@ -97,6 +118,8 @@ def _find_decoder_registry(
         return _plate_decoder_registry
     elif meta_type is NgioWellMeta:
         return _well_decoder_registry
+    elif meta_type is NgioLabelsGroupMeta:
+        return _labels_group_decoder_registry
     else:
         raise NgioValueError(f"Unsupported NGIO metadata type: {meta_type}")
 
@@ -447,3 +470,67 @@ class WellMetaHandler:
             group_handler=self._group_handler,
             ngio_meta=ngio_meta,
         )
+
+
+def get_ngio_labels_group_meta(
+    group_handler: ZarrGroupHandler,
+    version: str | None = None,
+) -> NgioLabelsGroupMeta:
+    """Retrieve the NGIO labels group metadata from the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        version (str | None): Optional NGFF version to use for decoding.
+
+    Returns:
+        NgioLabelsGroupMeta: The NGIO labels group metadata.
+    """
+    return get_ngio_meta(
+        group_handler=group_handler,
+        meta_type=NgioLabelsGroupMeta,
+        version=version,
+    )
+
+
+def update_ngio_labels_group_meta(
+    group_handler: ZarrGroupHandler,
+    ngio_meta: NgioLabelsGroupMeta,
+) -> None:
+    """Update the NGIO labels group metadata in the Zarr group.
+
+    Args:
+        group_handler (ZarrGroupHandler): The Zarr group handler.
+        ngio_meta (NgioLabelsGroupMeta): The new NGIO labels group metadata.
+
+    """
+    update_ngio_meta(
+        group_handler=group_handler,
+        ngio_meta=ngio_meta,
+    )
+
+
+class LabelsGroupMetaHandler:
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        version: NgffVersions | None = None,
+    ):
+        self._group_handler = group_handler
+        self._version = version
+
+        meta = self.get_meta()
+        self._version = meta.version
+
+    def get_meta(self) -> NgioLabelsGroupMeta:
+        """Retrieve the NGIO labels group metadata."""
+        return get_ngio_labels_group_meta(
+            group_handler=self._group_handler,
+            version=self._version,
+        )
+
+    def update_meta(self, ngio_meta: NgioLabelsGroupMeta) -> None:
+        """Update the NGIO labels group metadata."""
+        update_ngio_labels_group_meta(
+            group_handler=self._group_handler,
+            ngio_meta=ngio_meta,
+        )

ngio/ome_zarr_meta/ngio_specs/__init__.py

@@ -40,6 +40,7 @@ from ngio.ome_zarr_meta.ngio_specs._ngio_image import (
     NgioImageLabelMeta,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
 )
 from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
 
@@ -62,6 +63,7 @@ __all__ = [
     "NgioImageLabelMeta",
     "NgioImageMeta",
     "NgioLabelMeta",
+    "NgioLabelsGroupMeta",
     "NgioPlateMeta",
     "NgioWellMeta",
     "PixelSize",

ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py

@@ -62,9 +62,9 @@ class NgioWellMeta(BaseModel):
     @classmethod
     def default_init(
         cls,
-        version: NgffVersions = DefaultNgffVersion,
+        ngff_version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioWellMeta":
-        well = cls(images=[], version=version)
+        well = cls(images=[], version=ngff_version)
         return well
 
     @property
@@ -217,7 +217,7 @@ class NgioPlateMeta(BaseModel):
         cls,
         images: list[ImageInWellPath] | None = None,
         name: str | None = None,
-        version: NgffVersions = DefaultNgffVersion,
+        ngff_version: NgffVersions = DefaultNgffVersion,
     ) -> "NgioPlateMeta":
         plate = cls(
             plate=PlateWithVersion(
@@ -227,9 +227,9 @@ class NgioPlateMeta(BaseModel):
                 wells=[],
                 field_count=None,
                 name=name,
-                version=version,
+                version=ngff_version,
             ),
-            version=version,
+            version=ngff_version,
         )
 
         if images is None:
@@ -503,14 +503,14 @@ class NgioPlateMeta(BaseModel):
     def derive(
         self,
         name: str | None = None,
-        version: NgffVersions | None = None,
+        ngff_version: NgffVersions | None = None,
         keep_acquisitions: bool = False,
     ) -> "NgioPlateMeta":
         """Derive the plate metadata.
 
         Args:
             name (str): The name of the derived plate.
-            version (NgffVersion | None): The version of the derived plate.
+            ngff_version (NgffVersion | None): The version of the derived plate.
                 If None, use the version of the original plate.
             keep_acquisitions (bool): If True, keep the acquisitions in the plate.
         """
@@ -522,8 +522,8 @@ class NgioPlateMeta(BaseModel):
         else:
             acquisitions = None
 
-        if version is None:
-            version = self.version
+        if ngff_version is None:
+            ngff_version = self.version
 
         return NgioPlateMeta(
             plate=PlateWithVersion(
@@ -533,7 +533,7 @@ class NgioPlateMeta(BaseModel):
                 wells=[],
                 field_count=self.plate.field_count,
                 name=name,
-                version=version,
+                version=ngff_version,
             ),
-            version=version,
+            version=ngff_version,
         )

ngio/ome_zarr_meta/ngio_specs/_ngio_image.py

@@ -41,6 +41,13 @@ class ImageLabelSource(BaseModel):
         return cls(version=version, source={"image": "../../"})
 
 
+class NgioLabelsGroupMeta(BaseModel):
+    """Metadata model for the /labels group in OME-NGFF."""
+
+    version: NgffVersions
+    labels: list[str]
+
+
 class AbstractNgioImageMeta:
     """Base class for ImageMeta and LabelMeta."""
 

ngio/ome_zarr_meta/v04/__init__.py

@@ -3,10 +3,12 @@
 from ngio.ome_zarr_meta.v04._v04_spec import (
     ngio_to_v04_image_meta,
     ngio_to_v04_label_meta,
+    ngio_to_v04_labels_group_meta,
     ngio_to_v04_plate_meta,
     ngio_to_v04_well_meta,
     v04_to_ngio_image_meta,
     v04_to_ngio_label_meta,
+    v04_to_ngio_labels_group_meta,
     v04_to_ngio_plate_meta,
     v04_to_ngio_well_meta,
 )
@@ -14,10 +16,12 @@ from ngio.ome_zarr_meta.v04._v04_spec import (
 __all__ = [
     "ngio_to_v04_image_meta",
     "ngio_to_v04_label_meta",
+    "ngio_to_v04_labels_group_meta",
     "ngio_to_v04_plate_meta",
     "ngio_to_v04_well_meta",
     "v04_to_ngio_image_meta",
     "v04_to_ngio_label_meta",
+    "v04_to_ngio_labels_group_meta",
     "v04_to_ngio_plate_meta",
     "v04_to_ngio_well_meta",
 ]

ngio/ome_zarr_meta/v04/_v04_spec.py

@@ -16,7 +16,8 @@ from ome_zarr_models.v04.coordinate_transformations import (
 )
 from ome_zarr_models.v04.hcs import HCSAttrs as HCSAttrsV04
 from ome_zarr_models.v04.image import ImageAttrs as ImageAttrsV04
-from ome_zarr_models.v04.image_label import ImageLabelAttrs as LabelAttrsV04
+from ome_zarr_models.v04.image_label import ImageLabelAttrs as ImageLabelAttrsV04
+from ome_zarr_models.v04.labels import LabelsAttrs as LabelsAttrsV04
 from ome_zarr_models.v04.multiscales import Dataset as DatasetV04
 from ome_zarr_models.v04.multiscales import Multiscale as MultiscaleV04
 from ome_zarr_models.v04.multiscales import ValidTransform as ValidTransformV04
@@ -36,6 +37,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     default_channel_name,
@@ -231,7 +233,7 @@ def v04_to_ngio_label_meta(
     Returns:
         NgioImageMeta: The ngio image metadata.
     """
-    v04_label = LabelAttrsV04(**metadata)
+    v04_label = ImageLabelAttrsV04(**metadata)
 
     if len(v04_label.multiscales) > 1:
         raise NotImplementedError(
@@ -381,10 +383,26 @@ def ngio_to_v04_label_meta(metadata: NgioLabelMeta) -> dict:
         "multiscales": [v04_muliscale],
         "image-label": metadata.image_label.model_dump(),
     }
-    v04_label = LabelAttrsV04(**labels_meta)
+    v04_label = ImageLabelAttrsV04(**labels_meta)
     return v04_label.model_dump(exclude_none=True, by_alias=True)
 
 
+def v04_to_ngio_labels_group_meta(
+    metadata: dict,
+) -> NgioLabelsGroupMeta:
+    """Convert a v04 label group metadata to a ngio label group metadata.
+
+    Args:
+        metadata (dict): The v04 label group metadata.
+
+    Returns:
+        NgioLabelGroupMeta: The ngio label group metadata.
+    """
+    v04_label_group = LabelsAttrsV04(**metadata).model_dump()
+    labels = v04_label_group.get("labels", [])
+    return NgioLabelsGroupMeta(labels=labels, version="0.4")
+
+
 def v04_to_ngio_well_meta(
     metadata: dict,
 ) -> NgioWellMeta:
@@ -440,3 +458,16 @@ def ngio_to_v04_plate_meta(metadata: NgioPlateMeta) -> dict:
     """
     v04_plate = HCSAttrsV04(**metadata.model_dump())
     return v04_plate.model_dump(exclude_none=True, by_alias=True)
+
+
+def ngio_to_v04_labels_group_meta(metadata: NgioLabelsGroupMeta) -> dict:
+    """Convert a ngio label group metadata to a v04 label group metadata.
+
+    Args:
+        metadata (NgioLabelsGroupMeta): The ngio label group metadata.
+
+    Returns:
+        dict: The v04 label group metadata.
+    """
+    v04_label_group = LabelsAttrsV04(labels=metadata.labels)
+    return v04_label_group.model_dump(exclude_none=True, by_alias=True)

ngio/ome_zarr_meta/v05/__init__.py

@@ -3,10 +3,12 @@
 from ngio.ome_zarr_meta.v05._v05_spec import (
     ngio_to_v05_image_meta,
     ngio_to_v05_label_meta,
+    ngio_to_v05_labels_group_meta,
     ngio_to_v05_plate_meta,
     ngio_to_v05_well_meta,
     v05_to_ngio_image_meta,
     v05_to_ngio_label_meta,
+    v05_to_ngio_labels_group_meta,
     v05_to_ngio_plate_meta,
     v05_to_ngio_well_meta,
 )
@@ -14,10 +16,12 @@ from ngio.ome_zarr_meta.v05._v05_spec import (
 __all__ = [
     "ngio_to_v05_image_meta",
     "ngio_to_v05_label_meta",
+    "ngio_to_v05_labels_group_meta",
     "ngio_to_v05_plate_meta",
     "ngio_to_v05_well_meta",
     "v05_to_ngio_image_meta",
     "v05_to_ngio_label_meta",
+    "v05_to_ngio_labels_group_meta",
     "v05_to_ngio_plate_meta",
     "v05_to_ngio_well_meta",
 ]

ngio/ome_zarr_meta/v05/_v05_spec.py

@@ -19,7 +19,9 @@ from ome_zarr_models.v05.coordinate_transformations import (
 )
 from ome_zarr_models.v05.hcs import HCSAttrs as HCSAttrsV05
 from ome_zarr_models.v05.image import ImageAttrs as ImageAttrsV05
-from ome_zarr_models.v05.image_label import ImageLabelAttrs as LabelAttrsV05
+from ome_zarr_models.v05.image_label import ImageLabelAttrs as ImageLabelAttrsV05
+from ome_zarr_models.v05.labels import Labels as Labels
+from ome_zarr_models.v05.labels import LabelsAttrs as LabelsAttrsV05
 from ome_zarr_models.v05.multiscales import Dataset as DatasetV05
 from ome_zarr_models.v05.multiscales import Multiscale as MultiscaleV05
 from ome_zarr_models.v05.multiscales import ValidTransform as ValidTransformV05
@@ -37,6 +39,7 @@ from ngio.ome_zarr_meta.ngio_specs import (
     ImageLabelSource,
     NgioImageMeta,
     NgioLabelMeta,
+    NgioLabelsGroupMeta,
     NgioPlateMeta,
     NgioWellMeta,
     default_channel_name,
@@ -53,7 +56,7 @@ class ImageV05WithOmero(BaseModel):
 
 
 class ImageLabelV05(BaseModel):
-    ome: LabelAttrsV05
+    ome: ImageLabelAttrsV05
 
 
 def _v05_omero_to_channels(v05_omero: OmeroV05 | None) -> ChannelsMeta | None:
@@ -401,7 +404,7 @@ def ngio_to_v05_label_meta(metadata: NgioLabelMeta) -> dict:
         "multiscales": [v05_muliscale],
         "image-label": metadata.image_label.model_dump(),
     }
-    v05_label = LabelAttrsV05(**labels_meta, version="0.5")
+    v05_label = ImageLabelAttrsV05(**labels_meta, version="0.5")
     v05_label = ImageLabelV05(
         ome=v05_label,
     )
@@ -473,3 +476,36 @@ def ngio_to_v05_plate_meta(metadata: NgioPlateMeta) -> dict:
     v05_plate = HCSAttrsV05(**metadata.model_dump())
     v05_plate = HCSV05(ome=v05_plate)
     return v05_plate.model_dump(exclude_none=True, by_alias=True)
+
+
+class LabelsV05(BaseModel):
+    ome: LabelsAttrsV05
+
+
+def v05_to_ngio_labels_group_meta(
+    metadata: dict,
+) -> NgioLabelsGroupMeta:
+    """Convert a v04 label group metadata to a ngio label group metadata.
+
+    Args:
+        metadata (dict): The v04 label group metadata.
+
+    Returns:
+        NgioLabelGroupMeta: The ngio label group metadata.
+    """
+    v05_label_group = LabelsV05(**metadata)
+    return NgioLabelsGroupMeta(labels=v05_label_group.ome.labels, version="0.5")
+
+
+def ngio_to_v05_labels_group_meta(metadata: NgioLabelsGroupMeta) -> dict:
+    """Convert a ngio label group metadata to a v05 label group metadata.
+
+    Args:
+        metadata (NgioLabelsGroupMeta): The ngio label group metadata.
+
+    Returns:
+        dict: The v05 label group metadata.
+    """
+    v05_labels_attrs = LabelsAttrsV05(labels=metadata.labels, version="0.5")
+    v05_labels_group = LabelsV05(ome=v05_labels_attrs)
+    return v05_labels_group.model_dump(exclude_none=True, by_alias=True)

ngio/tables/_tables_container.py

@@ -311,6 +311,27 @@ class TablesContainer:
             backend=backend,
         )  # type: ignore[return-value]
 
+    def delete(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.
+        """
+        existing_tables = self._get_tables_list()
+        if name not in existing_tables:
+            if missing_ok:
+                return
+            raise NgioValueError(
+                f"Table '{name}' not found in the Tables group. "
+                f"Available tables: {existing_tables}"
+            )
+
+        self._group_handler.delete_group(name)
+        existing_tables.remove(name)
+        self._group_handler.write_attrs({"tables": existing_tables})
+
     def add(
         self,
         name: str,

ngio/tables/backends/_anndata.py

@@ -78,6 +78,7 @@ class AnnDataBackend(AbstractTableBackend):
         copy_group(
             anndata_group,
             self._group_handler._group,
+            suppress_warnings=True,
         )
 
     def write_from_anndata(self, table: AnnData) -> None:

ngio/utils/__init__.py

@@ -17,6 +17,7 @@ from ngio.utils._fractal_fsspec_store import fractal_fsspec_store
 from ngio.utils._zarr_utils import (
     AccessModeLiteral,
     NgioCache,
+    NgioSupportedStore,
     StoreOrGroup,
     ZarrGroupHandler,
     copy_group,
@@ -29,6 +30,7 @@ __all__ = [
     "NgioError",
     "NgioFileExistsError",
     "NgioFileNotFoundError",
+    "NgioSupportedStore",
     "NgioTableValidationError",
     "NgioValidationError",
     "NgioValueError",

ngio/utils/_zarr_utils.py

@@ -3,7 +3,7 @@
 import json
 import warnings
 from pathlib import Path
-from typing import Literal
+from typing import Literal, TypeAlias
 
 import dask.array as da
 import fsspec
@@ -26,17 +26,11 @@ AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
 # but to make sure we can handle the store correctly
 # we need to be more restrictive
-NgioSupportedStore = (
-    str
-    | Path
-    | fsspec.mapping.FSMap
-    | FsspecStore
-    | MemoryStore
-    | LocalStore
-    | ZipStore
+NgioSupportedStore: TypeAlias = (
+    str | Path | fsspec.mapping.FSMap | FsspecStore | MemoryStore | dict | LocalStore
 )
-GenericStore = Store | NgioSupportedStore
-StoreOrGroup = GenericStore | zarr.Group
+GenericStore: TypeAlias = NgioSupportedStore | Store
+StoreOrGroup: TypeAlias = NgioSupportedStore | zarr.Group
 
 
 def _check_store(store) -> NgioSupportedStore:
@@ -398,6 +392,12 @@ class ZarrGroupHandler:
         self._group_cache._cache.pop(path, None)
         self._handlers_cache._cache.pop(path, None)
 
+    def delete_self(self) -> None:
+        """Delete the current group."""
+        if self.group.read_only:
+            raise NgioValueError("Cannot delete a group in read only mode.")
+        self.group.__delitem__("/")
+
     def copy_group(self, dest_group: zarr.Group):
         """Copy the group to a new store."""
         copy_group(self.group, dest_group)
@@ -504,7 +504,9 @@ def _zarr_python_copy(src_group: zarr.Group, dest_group: zarr.Group):
         _zarr_python_copy(subgroup, dest_subgroup)
 
 
-def copy_group(src_group: zarr.Group, dest_group: zarr.Group):
+def copy_group(
+    src_group: zarr.Group, dest_group: zarr.Group, suppress_warnings: bool = False
+):
     if src_group.metadata.zarr_format != dest_group.metadata.zarr_format:
         raise NgioValueError(
             "Different Zarr format versions between source and destination, "
@@ -521,11 +523,12 @@ def copy_group(src_group: zarr.Group, dest_group: zarr.Group):
     ):
         _fsspec_copy(src_group.store, src_group.path, dest_group.store, dest_group.path)
         return
-    warnings.warn(
-        "Fsspec copy not possible, falling back to Zarr Python API for the copy. "
-        "This will preserve some tabular data non-zarr native (parquet, and csv), "
-        "and it will be slower for large datasets.",
-        UserWarning,
-        stacklevel=2,
-    )
+    if not suppress_warnings:
+        warnings.warn(
+            "Fsspec copy not possible, falling back to Zarr Python API for the copy. "
+            "This will preserve some tabular data non-zarr native (parquet, and csv), "
+            "and it will be slower for large datasets.",
+            UserWarning,
+            stacklevel=2,
+        )
     _zarr_python_copy(src_group, dest_group)

{ngio-0.5.0a3.dist-info → ngio-0.5.0b2.dist-info}/METADATA

@@ -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.dist-info → ngio-0.5.0b2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-ngio/__init__.py,sha256=A7o63AVFPNbhOpePPOb-BZvszc52tNqp2NW277h3rAo,1433
+ngio/__init__.py,sha256=kyInohhWrBs4qkbMYFIQeAiy1CDpvbSOtXB4buFocbw,1535
 ngio/common/__init__.py,sha256=F3zAHQIhwig1xUA-SpmFVRtMeOrEj926-nHWhj-wS6c,684
 ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
 ngio/common/_masking_roi.py,sha256=YSEZ5nv3-TqMrQ04cI70U9NGx3LSy7Z1_cbw_NE-78k,4831
@@ -15,15 +15,15 @@ ngio/experimental/iterators/_mappers.py,sha256=VVVsjems57wJUnWeufUFcgqa23k7VPeFL
 ngio/experimental/iterators/_rois_utils.py,sha256=5foGjt3qrACNrO29LlvSUbJ4yfI0z6MhU2oVCzEU214,4363
 ngio/experimental/iterators/_segmentation.py,sha256=xzotGvTn04HPeMeXZ_URnQqWco6d2lH6Ng6vkCUh9NM,9153
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
-ngio/hcs/_plate.py,sha256=-8Ffx07s73jKTDKBj11yrJTtfNfwBP0DwUbzJQKPCWM,43503
+ngio/hcs/_plate.py,sha256=l2a2ZMniutxRzZ88HOYwajug-svr6OanREG5mTy39x0,45773
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
-ngio/images/_abstract_image.py,sha256=xCpI--oe9B81s3A99JGSYNiZzN-DaYheUJoP19n9Uwg,31915
+ngio/images/_abstract_image.py,sha256=PyginvViqjKNsnUBF8yX7pUI2fHDJq4QthjeQzJWzDU,31906
 ngio/images/_create_synt_container.py,sha256=Cvg_J0KSxK0PH8IBzlKLIcCwH2vRTuBj-nZo5uOKXXk,5182
 ngio/images/_create_utils.py,sha256=hXVbFM8D_0mZTfBAhcZiuGX2lLXSJCep8THuxpH4d4E,14374
-ngio/images/_image.py,sha256=YSO6dzEKdrgh4AE-cE4j_hxsU4QBpxUc_j6-Xpq5YqM,33664
-ngio/images/_label.py,sha256=Y7Y0yLgoRUJtRzqgNPWc1yZ3HgDu4bbXbwhQJlnPKA8,14047
+ngio/images/_image.py,sha256=TiKQXnzm0Mhxx6zmS4CVThcIJLV_guwjbVx7ZOd_0IU,34197
+ngio/images/_label.py,sha256=MYmYIikKyf2nDqrFd8xZ3nYR-JKe-JneUNuE1jEPHdA,15682
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
-ngio/images/_ome_zarr_container.py,sha256=_fI23IHb1iuhgLUqWdVvOwbFKtFpLY3J6y_k_i6mkjA,46044
+ngio/images/_ome_zarr_container.py,sha256=aa8l8wfZ8p0YpsdBd8ixvrdgVcdZs6RnSOpUWPE1ixU,48247
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
 ngio/io_pipes/__init__.py,sha256=arW_7GWzZs82kPNKdm_6B1sIDFV0lWwp-ZaORr9Q1FQ,2412
 ngio/io_pipes/_io_pipes.py,sha256=l85mmjj1l0uYU3qzsSHg9l8cMIEevInm_MTD-8MlXgw,10603
@@ -36,21 +36,21 @@ ngio/io_pipes/_ops_slices.py,sha256=hHMIOQ_niUSK9uFl8P2-10dP_K4GX3Do6vivN4fGRE0,
 ngio/io_pipes/_ops_slices_utils.py,sha256=mps_I0eTI4gdBVM9MCKsd8rCyefdo9bIK9fEmqwr23E,6633
 ngio/io_pipes/_ops_transforms.py,sha256=uITs6v6sZ7DQ_Hpw3JdX8MuPOzir-bihvGzY84Qn4wY,2934
 ngio/io_pipes/_zoom_transform.py,sha256=WBY1tO6_Qhf8FaDujfTdipuuqFf7PSi204wx5VKKs88,6884
-ngio/ome_zarr_meta/__init__.py,sha256=3_QbSt-Ta8MXL8R_tGmgrYMGePgawI96Hc5msrbZCgM,1139
-ngio/ome_zarr_meta/_meta_handlers.py,sha256=70R0waA1BNX7yNOZnvVuNBeIIxkzGQN6xEKebFpYFx0,13673
-ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=U2FqZR91Ob2N6CqKdyw-_Ll-wMgmGuPZGVRCr6wuRFY,1698
+ngio/ome_zarr_meta/__init__.py,sha256=0VVB0r5CTjVqOsC8pa_Jf9H8ctPzTLRmC6LJqWWAs7Q,1371
+ngio/ome_zarr_meta/_meta_handlers.py,sha256=M8bHeWUjSgPCg-JTvnbwoL5sTPyGrWb2j8d-3r0Ua6Q,16172
+ngio/ome_zarr_meta/ngio_specs/__init__.py,sha256=sYGlV2-0-z-a1gDFlk_pCjgcdRsgbwBf72vM2ZAVTtQ,1750
 ngio/ome_zarr_meta/ngio_specs/_axes.py,sha256=CY63mWf7_ALoi7o_1QDVK1lAG56xN0gvgwfcuNRmMIg,16446
 ngio/ome_zarr_meta/ngio_specs/_channels.py,sha256=TDxIy-yVc2YaWPIFJRYnYwZbA8O5Ee_OiWppHYrEdpU,16647
 ngio/ome_zarr_meta/ngio_specs/_dataset.py,sha256=5YdAplk90koX3vjoIJimms-CJYxt095rJ9YagZSQg88,2872
-ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=_KM9Ql-sBL1zV_OLhDiFBj9QhEjwVcW8W5sMUA7xtzM,16944
-ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=kjlC2Otz7z__ojrSHYsFJaQW_OKNQoevVlAn1cZYNJs,14442
+ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py,sha256=-YOC39YXDk5ojFkpvj8Vup6A3tAtHotV9e8QNZ0l_Cs,16999
+ngio/ome_zarr_meta/ngio_specs/_ngio_image.py,sha256=g32ytm4jxDR5duHyO6_kU0MrcE2NzI8V4EWCYanuIrI,14591
 ngio/ome_zarr_meta/ngio_specs/_pixel_size.py,sha256=4VF1djY9T5tp6GCJXppFrUJwALI1XgIm0imoM5rNvdE,3876
-ngio/ome_zarr_meta/v04/__init__.py,sha256=WHT8RFLxqx9QBtm8wwg8tZ_EBuC1l8PG_JxwFl02Tk4,577
+ngio/ome_zarr_meta/v04/__init__.py,sha256=tRt3zGelL948EoLfy_gW-LKvJcBbSkbT9kwIgU0hQV8,721
 ngio/ome_zarr_meta/v04/_custom_models.py,sha256=5GxiDERvLuvq4QvApcA6EiKLS6hLFX1R0R_9rSaa85A,530
-ngio/ome_zarr_meta/v04/_v04_spec.py,sha256=qmp9xAfA2z9UErrs4xvS0qmO5G8Dli-CenAL3rO4TFo,14348
-ngio/ome_zarr_meta/v05/__init__.py,sha256=zGWjeVCXQX7ezs4hEmmLrgOcQNhR6nZJ4LXKpj1oCfE,577
+ngio/ome_zarr_meta/v04/_v04_spec.py,sha256=PRkxNeIDCCxG4J5HD3hQPrV-iPW_KAs4HyjyrT4i_NI,15362
+ngio/ome_zarr_meta/v05/__init__.py,sha256=B6VIUkrm5W4lcrvy4R7c7NZ6dEx-0a1AhqhZ7snCnCo,721
 ngio/ome_zarr_meta/v05/_custom_models.py,sha256=ZN3bE9nwx4y3tElhsYafI4S2zp_WzdkQKcyuuBiaXXo,530
-ngio/ome_zarr_meta/v05/_v05_spec.py,sha256=JBZrm3BRZVbxHB29UFsfo3tuedhpMdy8KuWf4vDL3_g,15134
+ngio/ome_zarr_meta/v05/_v05_spec.py,sha256=qjSRSkz20jQwd47tzHjeX5ECYBbZoU6q8lnALFeAZts,16285
 ngio/resources/__init__.py,sha256=4E4TXTNYEgRHt26C1XcC4pPobJJsmZRYm1Ml4uAuAkE,1664
 ngio/resources/resource_model.py,sha256=eE1m0dyk-2psPC4X8Ifyan524QHUOd52TEQdvoU0m8I,861
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/mask.png,sha256=g3QmxQdmeciAtBe5cTCRfR6yw3keG9cBYfjizMo6EGo,11890
@@ -58,10 +58,10 @@ ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png,sha
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg,sha256=82lejQAIokj5w9g-qqhysDTWpHtNvJTkdURG_BjqIxQ,37743
 ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
 ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
-ngio/tables/_tables_container.py,sha256=DV_uX_bf3kCcmWLFKjY9FhKX8iBewbHkZSECqKjsCIw,12333
+ngio/tables/_tables_container.py,sha256=1HXIfofOtwJr6XQ_ILM8-rr7Cxq1XmV4BzL5Q2g2tLk,13097
 ngio/tables/backends/__init__.py,sha256=MwSRXNF1rWQBFOTDA_vT3oGoNZpviVgytsL5Txnu08I,1619
 ngio/tables/backends/_abstract_backend.py,sha256=M1ogsBpWBiQMV65YweZhA845PAtkzG2BsZCPN_7Xp8U,7613
-ngio/tables/backends/_anndata.py,sha256=brJaTZCBe_ipexWbGQgFM2-B30sRKI1kxNLuSTcY2uE,4546
+ngio/tables/backends/_anndata.py,sha256=T67N-SPNO4eqe7-VGAUfgtwaSy_o2DqCvZgE2yRH5jE,4582
 ngio/tables/backends/_anndata_utils.py,sha256=PoHiLkGeDhBgPsEMJi9QH-NejHmfrfILcwj1CYubyCM,3095
 ngio/tables/backends/_csv.py,sha256=iZJNLHOXYysV_2iq6Lmekq0XXYsVE7OYrKz2HP2TU9w,479
 ngio/tables/backends/_json.py,sha256=A4iaKOIc5Q_XKDOm321QNqAN4DAOuA-dEinnfTlk1Fk,3091
@@ -76,13 +76,13 @@ ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUed
 ngio/tables/v1/_roi_table.py,sha256=DuKJlDmtQtLOfL0g4CSdncfm4hBsKWG6F6fkMUpt4Nk,17821
 ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,113
 ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
-ngio/utils/__init__.py,sha256=1eIInpFEEWQtMeGaRhAyVjqSKWUCuksMkx2cqg9D9nI,987
+ngio/utils/__init__.py,sha256=d2OHQGMFPpf8-_ipuqquxtqCNGJpX5yXt34A65nScUU,1037
 ngio/utils/_cache.py,sha256=Ey9fgc_BTdMyqg6c80C0CuGDhOafln8-3e_1MQ0MFzw,1283
 ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
-ngio/utils/_zarr_utils.py,sha256=asAmD4FSFspyAfIDB8ISwHLCZYctsKENyCCAQHEfubA,17817
-ngio-0.5.0a3.dist-info/METADATA,sha256=yvzf4IseuuNv8cAvtQLnrWwrdbZYVl422KnEjnQpyQc,6294
-ngio-0.5.0a3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-ngio-0.5.0a3.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.5.0a3.dist-info/RECORD,,
+ngio/utils/_zarr_utils.py,sha256=MVbW-a0S3iuzMaknqkliJa_lp8i6mEO4Q2YN2XxmeDw,18158
+ngio-0.5.0b2.dist-info/METADATA,sha256=r1un40xipjI7Kctjt0Gj9-B28PjO5pBSPWxOyoQjXCc,6294
+ngio-0.5.0b2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+ngio-0.5.0b2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0b2.dist-info/RECORD,,