ngio 0.4.8__py3-none-any.whl → 0.5.0__py3-none-any.whl

ngio/images/_image.py

@@ -1,21 +1,21 @@
 """Generic class to handle Image-like data in a OME-NGFF file."""
 
-from collections.abc import Sequence
-from typing import Literal
+import warnings
+from collections.abc import Mapping, Sequence
+from typing import Any, Literal
 
 import dask.array as da
 import numpy as np
 from pydantic import BaseModel, model_validator
-from zarr.types import DIMENSION_SEPARATOR
+from zarr.core.array import CompressorLike
 
 from ngio.common import (
     Dimensions,
     InterpolationOrder,
     Roi,
-    RoiPixels,
 )
-from ngio.images._abstract_image import AbstractImage
-from ngio.images._create import create_empty_image_container
+from ngio.common._pyramid import ChunksLike, ShardsLike
+from ngio.images._abstract_image import AbstractImage, abstract_derive
 from ngio.io_pipes import (
     SlicingInputType,
     TransformProtocol,
@@ -24,19 +24,19 @@ from ngio.ome_zarr_meta import (
     ImageMetaHandler,
     NgioImageMeta,
     PixelSize,
-    find_image_meta_handler,
 )
 from ngio.ome_zarr_meta.ngio_specs import (
     Channel,
     ChannelsMeta,
-    ChannelVisualisation,
     DefaultSpaceUnit,
     DefaultTimeUnit,
+    NgffVersions,
     SpaceUnits,
     TimeUnits,
 )
+from ngio.ome_zarr_meta.ngio_specs._axes import AxesSetup
 from ngio.utils import (
-    NgioValidationError,
+    NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
 )
@@ -47,7 +47,7 @@ class ChannelSelectionModel(BaseModel):
 
     This model is used to select a channel by label, wavelength ID, or index.
 
-    Args:
+    Properties:
         identifier (str): Unique identifier for the channel.
             This can be a channel label, wavelength ID, or index.
         mode (Literal["label", "wavelength_id", "index"]): Specifies how to
@@ -88,7 +88,7 @@ def _check_channel_meta(meta: NgioImageMeta, dimension: Dimensions) -> ChannelsM
         return ChannelsMeta.default_init(labels=c_dim)
 
     if len(meta.channels_meta.channels) != c_dim:
-        raise NgioValidationError(
+        raise NgioValueError(
             "The number of channels does not match the image. "
             f"Expected {len(meta.channels_meta.channels)} channels, got {c_dim}."
         )
@@ -96,7 +96,7 @@ def _check_channel_meta(meta: NgioImageMeta, dimension: Dimensions) -> ChannelsM
     return meta.channels_meta
 
 
-class Image(AbstractImage[ImageMetaHandler]):
+class Image(AbstractImage):
     """A class to handle a single image (or level) in an OME-Zarr image.
 
     This class is meant to be subclassed by specific image types.
@@ -106,7 +106,7 @@ class Image(AbstractImage[ImageMetaHandler]):
         self,
         group_handler: ZarrGroupHandler,
         path: str,
-        meta_handler: ImageMetaHandler | None,
+        meta_handler: ImageMetaHandler,
     ) -> None:
         """Initialize the Image at a single level.
 
@@ -116,16 +116,22 @@ class Image(AbstractImage[ImageMetaHandler]):
             meta_handler: The image metadata handler.
 
         """
-        if meta_handler is None:
-            meta_handler = find_image_meta_handler(group_handler)
         super().__init__(
             group_handler=group_handler, path=path, meta_handler=meta_handler
         )
 
+    @property
+    def meta_handler(self) -> ImageMetaHandler:
+        """Return the metadata handler."""
+        assert isinstance(self._meta_handler, ImageMetaHandler)
+        return self._meta_handler
+
     @property
     def meta(self) -> NgioImageMeta:
         """Return the metadata."""
-        return self._meta_handler.meta
+        meta = self.meta_handler.get_meta()
+        assert isinstance(meta, NgioImageMeta)
+        return meta
 
     @property
     def channels_meta(self) -> ChannelsMeta:
@@ -185,7 +191,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def get_roi_as_numpy(
         self,
-        roi: Roi | RoiPixels,
+        roi: Roi,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -239,7 +245,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def get_roi_as_dask(
         self,
-        roi: Roi | RoiPixels,
+        roi: Roi,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -296,7 +302,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def get_roi(
         self,
-        roi: Roi | RoiPixels,
+        roi: Roi,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
         transforms: Sequence[TransformProtocol] | None = None,
@@ -356,7 +362,7 @@ class Image(AbstractImage[ImageMetaHandler]):
 
     def set_roi(
         self,
-        roi: Roi | RoiPixels,
+        roi: Roi,
         patch: np.ndarray | da.Array,
         channel_selection: ChannelSlicingInputType = None,
         axes_order: Sequence[str] | None = None,
@@ -394,67 +400,135 @@ class Image(AbstractImage[ImageMetaHandler]):
 
 
 class ImagesContainer:
-    """A class to handle the /labels group in an OME-NGFF file."""
+    """A class to handle the /images group in an OME-NGFF file."""
 
-    def __init__(self, group_handler: ZarrGroupHandler) -> None:
-        """Initialize the LabelGroupHandler."""
+    def __init__(
+        self,
+        group_handler: ZarrGroupHandler,
+        axes_setup: AxesSetup | None,
+        version: NgffVersions | None = None,
+        validate_paths: bool = True,
+    ) -> None:
+        """Initialize the ImagesContainer."""
         self._group_handler = group_handler
-        self._meta_handler = find_image_meta_handler(group_handler)
+        self._meta_handler = ImageMetaHandler(
+            group_handler=group_handler, axes_setup=axes_setup, version=version
+        )
+        if validate_paths:
+            for level_path in self._meta_handler.get_meta().paths:
+                self.get(path=level_path)
 
     @property
     def meta(self) -> NgioImageMeta:
         """Return the metadata."""
-        return self._meta_handler.meta
+        return self._meta_handler.get_meta()
+
+    @property
+    def channels_meta(self) -> ChannelsMeta:
+        """Return the channels metadata."""
+        return self.get().channels_meta
+
+    @property
+    def axes_setup(self) -> AxesSetup:
+        """Return the axes setup."""
+        return self.meta.axes_handler.axes_setup
+
+    @property
+    def level_paths(self) -> list[str]:
+        """Return the paths of the levels in the image."""
+        return self.meta.paths
+
+    @property
+    def levels_paths(self) -> list[str]:
+        """Deprecated: use 'level_paths' instead."""
+        warnings.warn(
+            "'levels_paths' is deprecated and will be removed in ngio=0.6. "
+            "Please use 'level_paths' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self.level_paths
 
     @property
     def levels(self) -> int:
         """Return the number of levels in the image."""
-        return self._meta_handler.meta.levels
+        return self.meta.levels
 
     @property
-    def levels_paths(self) -> list[str]:
-        """Return the paths of the levels in the image."""
-        return self._meta_handler.meta.paths
+    def is_3d(self) -> bool:
+        """Return True if the image is 3D."""
+        return self.get().is_3d
 
     @property
-    def num_channels(self) -> int:
-        """Return the number of channels."""
-        image = self.get()
-        return image.num_channels
+    def is_2d(self) -> bool:
+        """Return True if the image is 2D."""
+        return self.get().is_2d
+
+    @property
+    def is_time_series(self) -> bool:
+        """Return True if the image is a time series."""
+        return self.get().is_time_series
+
+    @property
+    def is_2d_time_series(self) -> bool:
+        """Return True if the image is a 2D time series."""
+        return self.get().is_2d_time_series
+
+    @property
+    def is_3d_time_series(self) -> bool:
+        """Return True if the image is a 3D time series."""
+        return self.get().is_3d_time_series
+
+    @property
+    def is_multi_channels(self) -> bool:
+        """Return True if the image is multichannel."""
+        return self.get().is_multi_channels
+
+    @property
+    def space_unit(self) -> str | None:
+        """Return the space unit of the image."""
+        return self.meta.space_unit
+
+    @property
+    def time_unit(self) -> str | None:
+        """Return the time unit of the image."""
+        return self.meta.time_unit
 
     @property
     def channel_labels(self) -> list[str]:
         """Return the channels of the image."""
-        image = self.get()
-        return image.channel_labels
+        return self.get().channel_labels
 
     @property
     def wavelength_ids(self) -> list[str | None]:
-        """Return the wavelength of the image."""
-        image = self.get()
-        return image.wavelength_ids
+        """Return the list of wavelength of the image."""
+        return self.get().wavelength_ids
+
+    @property
+    def num_channels(self) -> int:
+        """Return the number of channels."""
+        return self.get().num_channels
 
     def get_channel_idx(
         self, channel_label: str | None = None, wavelength_id: str | None = None
     ) -> int:
-        """Get the index of a channel by label or wavelength ID.
-
-        Args:
-            channel_label (str | None): The label of the channel.
-                If None a wavelength ID must be provided.
-            wavelength_id (str | None): The wavelength ID of the channel.
-                If None a channel label must be provided.
-
-        Returns:
-            int: The index of the channel.
-
-        """
-        image = self.get()
-        return image.get_channel_idx(
+        """Get the index of a channel by its label or wavelength ID."""
+        return self.channels_meta.get_channel_idx(
             channel_label=channel_label, wavelength_id=wavelength_id
         )
 
-    def set_channel_meta(
+    def _set_channel_meta(
+        self,
+        channels_meta: ChannelsMeta | None = None,
+    ) -> None:
+        """Set the channels metadata."""
+        if channels_meta is None:
+            channels_meta = ChannelsMeta.default_init(labels=self.num_channels)
+        meta = self.meta
+        meta.set_channels_meta(channels_meta)
+        self._meta_handler.update_meta(meta)
+
+    def _set_channel_meta_legacy(
         self,
         labels: Sequence[str | None] | int | None = None,
         wavelength_id: Sequence[str | None] | None = None,
@@ -490,32 +564,22 @@ class ImagesContainer:
         ref_image = self.get(path=low_res_dataset.path)
 
         if start is not None and end is None:
-            raise NgioValidationError(
-                "If start is provided, end must be provided as well."
-            )
+            raise NgioValueError("If start is provided, end must be provided as well.")
         if end is not None and start is None:
-            raise NgioValidationError(
-                "If end is provided, start must be provided as well."
-            )
+            raise NgioValueError("If end is provided, start must be provided as well.")
 
         if start is not None and percentiles is not None:
-            raise NgioValidationError(
+            raise NgioValueError(
                 "If start and end are provided, percentiles must be None."
             )
 
-        if percentiles is not None:
-            start, end = compute_image_percentile(
-                ref_image,
-                start_percentile=percentiles[0],
-                end_percentile=percentiles[1],
-            )
         elif start is not None and end is not None:
             if len(start) != len(end):
-                raise NgioValidationError(
+                raise NgioValueError(
                     "The start and end lists must have the same length."
                 )
             if len(start) != self.num_channels:
-                raise NgioValidationError(
+                raise NgioValueError(
                     "The start and end lists must have the same length as "
                     "the number of channels."
                 )
@@ -539,44 +603,212 @@ class ImagesContainer:
             data_type=ref_image.dtype,
             **omero_kwargs,
         )
+        self._set_channel_meta(channel_meta)
+        if percentiles is not None:
+            self.set_channel_windows_with_percentiles(percentiles=percentiles)
 
-        meta = self.meta
-        meta.set_channels_meta(channel_meta)
-        self._meta_handler.write_meta(meta)
+    def set_channel_meta(
+        self,
+        channel_meta: ChannelsMeta | None = None,
+        labels: Sequence[str | None] | int | None = None,
+        wavelength_id: Sequence[str | None] | None = None,
+        start: Sequence[float | None] | None = None,
+        end: Sequence[float | None] | None = None,
+        percentiles: tuple[float, float] | None = None,
+        colors: Sequence[str | None] | None = None,
+        active: Sequence[bool | None] | None = None,
+        **omero_kwargs: dict,
+    ) -> None:
+        """Create a ChannelsMeta object with the default unit.
+
+        Args:
+            channel_meta (ChannelsMeta | None): The channels metadata to set.
+                If none, it will fall back to the deprecated parameters.
+            labels(Sequence[str | None] | int): Deprecated. The list of channels names
+                in the image. If an integer is provided, the channels will
+                be named "channel_i".
+            wavelength_id(Sequence[str | None]): Deprecated. The wavelength ID of the
+                channel. If None, the wavelength ID will be the same as
+                the channel name.
+            start(Sequence[float | None]): Deprecated. The start value for each channel.
+                If None, the start value will be computed from the image.
+            end(Sequence[float | None]): Deprecated. The end value for each channel.
+                If None, the end value will be computed from the image.
+            percentiles(tuple[float, float] | None): Deprecated. The start and end
+                percentiles for each channel. If None, the percentiles will
+                not be computed.
+            colors(Sequence[str | None]): Deprecated. The list of colors for the
+                channels. If None, the colors will be random.
+            active (Sequence[bool | None]): Deprecated. Whether the channel should
+                be shown by default.
+            omero_kwargs(dict): Deprecated. Extra fields to store in the omero
+                attributes.
+        """
+        _is_legacy = any(
+            param is not None
+            for param in [
+                labels,
+                wavelength_id,
+                start,
+                end,
+                percentiles,
+                colors,
+                active,
+            ]
+        )
+        if _is_legacy:
+            warnings.warn(
+                "The following parameters are deprecated and will be removed in "
+                "ngio=0.6: labels, wavelength_id, start, end, percentiles, "
+                "colors, active, omero_kwargs. Please use the "
+                "'channel_meta' parameter instead.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            self._set_channel_meta_legacy(
+                labels=labels,
+                wavelength_id=wavelength_id,
+                start=start,
+                end=end,
+                percentiles=percentiles,
+                colors=colors,
+                active=active,
+                **omero_kwargs,
+            )
+            return None
+        self._set_channel_meta(channel_meta)
+
+    def set_channel_labels(
+        self,
+        labels: Sequence[str],
+    ) -> None:
+        """Update the labels of the channels.
+
+        Args:
+            labels (Sequence[str]): The new labels for the channels.
+        """
+        channels_meta = self.channels_meta
+        if len(labels) != len(channels_meta.channels):
+            raise NgioValueError(
+                "The number of labels must match the number of channels."
+            )
+        new_channels = []
+        for label, ch in zip(labels, channels_meta.channels, strict=True):
+            channel = ch.model_copy(update={"label": label})
+            new_channels.append(channel)
+        new_meta = channels_meta.model_copy(update={"channels": new_channels})
+        self._set_channel_meta(new_meta)
+
+    def set_channel_colors(
+        self,
+        colors: Sequence[str],
+    ) -> None:
+        """Update the colors of the channels.
+
+        Args:
+            colors (Sequence[str]): The new colors for the channels.
+        """
+        channel_meta = self.channels_meta
+        if len(colors) != len(channel_meta.channels):
+            raise NgioValueError(
+                "The number of colors must match the number of channels."
+            )
+        new_channels = []
+        for color, ch in zip(colors, channel_meta.channels, strict=True):
+            ch_visualisation = ch.channel_visualisation.model_copy(
+                update={"color": color}
+            )
+            channel = ch.model_copy(update={"channel_visualisation": ch_visualisation})
+            new_channels.append(channel)
+        new_meta = channel_meta.model_copy(update={"channels": new_channels})
+        self._set_channel_meta(new_meta)
 
     def set_channel_percentiles(
         self,
         start_percentile: float = 0.1,
         end_percentile: float = 99.9,
     ) -> None:
-        """Update the percentiles of the channels."""
-        if self.meta._channels_meta is None:
-            raise NgioValidationError("The channels meta is not initialized.")
+        """Deprecated: Update the channel windows using percentiles.
 
-        low_res_dataset = self.meta.get_lowest_resolution_dataset()
-        ref_image = self.get(path=low_res_dataset.path)
-        starts, ends = compute_image_percentile(
-            ref_image, start_percentile=start_percentile, end_percentile=end_percentile
+        Args:
+            start_percentile (float): The start percentile.
+            end_percentile (float): The end percentile.
+        """
+        warnings.warn(
+            "The 'set_channel_percentiles' method is deprecated and will be removed in "
+            "ngio=0.6. Please use 'set_channel_windows_with_percentiles' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        self.set_channel_windows_with_percentiles(
+            percentiles=(start_percentile, end_percentile)
         )
 
-        channels = []
-        for c, channel in enumerate(self.meta._channels_meta.channels):
-            new_v = ChannelVisualisation(
-                start=starts[c],
-                end=ends[c],
-                **channel.channel_visualisation.model_dump(exclude={"start", "end"}),
+    def set_channel_windows(
+        self,
+        starts_ends: Sequence[tuple[float, float]],
+        min_max: Sequence[tuple[float, float]] | None = None,
+    ) -> None:
+        """Update the channel windows.
+
+        These values are used by viewers to set the display
+        range of each channel.
+
+        Args:
+            starts_ends (Sequence[tuple[float, float]]): The start and end values
+                for each channel.
+            min_max (Sequence[tuple[float, float]] | None): The min and max values
+                for each channel. If None, the min and max values will not be updated.
+        """
+        current_channels = self.channels_meta.channels
+        if len(starts_ends) != len(current_channels):
+            raise NgioValueError(
+                "The number of start-end pairs must match the number of channels."
             )
-            new_c = Channel(
-                channel_visualisation=new_v,
-                **channel.model_dump(exclude={"channel_visualisation"}),
+        if min_max is not None and len(min_max) != len(current_channels):
+            raise NgioValueError(
+                "The number of min-max pairs must match the number of channels."
             )
-            channels.append(new_c)
-
+        if min_max is None:
+            min_max_ = [None] * len(current_channels)
+        else:
+            min_max_ = list(min_max)
+        channels = []
+        for se, mm, ch in zip(
+            starts_ends, min_max_, self.channels_meta.channels, strict=True
+        ):
+            updates = {"start": se[0], "end": se[1]}
+            if mm is not None:
+                updates.update({"min": mm[0], "max": mm[1]})
+            channel_visualisation = ch.channel_visualisation.model_copy(update=updates)
+            channel = ch.model_copy(
+                update={"channel_visualisation": channel_visualisation}
+            )
+            channels.append(channel)
         new_meta = ChannelsMeta(channels=channels)
-
         meta = self.meta
         meta.set_channels_meta(new_meta)
-        self._meta_handler.write_meta(meta)
+        self._meta_handler.update_meta(meta)
+
+    def set_channel_windows_with_percentiles(
+        self,
+        percentiles: tuple[float, float] | list[tuple[float, float]] = (0.1, 99.9),
+    ) -> None:
+        """Update the channel windows using percentiles.
+
+        Args:
+            percentiles (tuple[float, float] | list[tuple[float, float]]):
+                The start and end percentiles for each channel.
+                If a single tuple is provided,
+                the same percentiles will be used for all channels.
+        """
+        if self.meta._channels_meta is None:
+            raise NgioValueError("The channels meta is not initialized.")
+
+        low_res_dataset = self.meta.get_lowest_resolution_dataset()
+        ref_image = self.get(path=low_res_dataset.path)
+        starts_ends = compute_image_percentile(ref_image, percentiles=percentiles)
+        self.set_channel_windows(starts_ends=starts_ends)
 
     def set_axes_unit(
         self,
@@ -589,61 +821,127 @@ class ImagesContainer:
             space_unit (SpaceUnits): The space unit of the image.
             time_unit (TimeUnits): The time unit of the image.
         """
-        meta = self.meta
-        meta = meta.to_units(space_unit=space_unit, time_unit=time_unit)
-        self._meta_handler.write_meta(meta)
+        self.get().set_axes_unit(space_unit=space_unit, time_unit=time_unit)
+
+    def set_axes_names(
+        self,
+        axes_names: Sequence[str],
+    ) -> None:
+        """Set the axes names of the image.
+
+        Args:
+            axes_names (Sequence[str]): The axes names of the image.
+        """
+        image = self.get()
+        image.set_axes_names(axes_names=axes_names)
+        self._meta_handler._axes_setup = image.meta.axes_handler.axes_setup
+
+    def set_name(
+        self,
+        name: str,
+    ) -> None:
+        """Set the name of the image in the metadata.
+
+        This does not change the group name or any paths.
+
+        Args:
+            name (str): The name of the image.
+        """
+        self.get().set_name(name=name)
 
     def derive(
         self,
         store: StoreOrGroup,
         ref_path: str | None = None,
+        # Metadata parameters
         shape: Sequence[int] | None = None,
-        labels: Sequence[str] | None = None,
-        pixel_size: PixelSize | None = None,
-        axes_names: Sequence[str] | None = None,
+        pixelsize: float | tuple[float, float] | None = None,
+        z_spacing: float | None = None,
+        time_spacing: float | None = None,
         name: str | None = None,
-        chunks: Sequence[int] | None = None,
-        dtype: str | None = None,
-        dimension_separator: DIMENSION_SEPARATOR | None = None,
-        compressor: str | None = None,
+        translation: Sequence[float] | None = None,
+        channels_meta: Sequence[str | Channel] | None = None,
+        channels_policy: Literal["same", "squeeze", "singleton"] | int = "same",
+        ngff_version: NgffVersions | None = None,
+        # Zarr Array parameters
+        chunks: ChunksLike | None = None,
+        shards: ShardsLike | None = None,
+        dtype: str = "uint16",
+        dimension_separator: Literal[".", "/"] = "/",
+        compressors: CompressorLike = "auto",
+        extra_array_kwargs: Mapping[str, Any] | None = None,
         overwrite: bool = False,
+        # Deprecated arguments
+        labels: Sequence[str] | None = None,
+        pixel_size: PixelSize | None = None,
     ) -> "ImagesContainer":
         """Create an empty OME-Zarr image from an existing image.
 
+        If a kwarg is not provided, the value from the reference image will be used.
+
         Args:
             store (StoreOrGroup): The Zarr store or group to create the image in.
-            ref_path (str | None): The path to the reference image in
-                the image container.
+            ref_path (str | None): The path to the reference image in the image
+                container.
             shape (Sequence[int] | None): The shape of the new image.
-            labels (Sequence[str] | None): The labels of the new image.
-            pixel_size (PixelSize | None): The pixel size of the new image.
-            axes_names (Sequence[str] | None): The axes names of the new image.
+            pixelsize (float | tuple[float, float] | None): The pixel size of the new
+                image.
+            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.
-            chunks (Sequence[int] | None): The chunk shape of the new image.
-            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
-                dimensions. If None it will use the same as the reference image.
-            compressor (str | None): The compressor to use. If None it will use
-                the same as the reference image.
+            translation (Sequence[float] | None): The translation for each axis
+                at the highest resolution level. Defaults to None.
+            channels_meta (Sequence[str | Channel] | None): The channels metadata
+                of the new image.
+            channels_policy (Literal["same", "squeeze", "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.
+            chunks (ChunksLike | None): The chunk shape of the new image.
+            shards (ShardsLike | None): The shard shape of the new image.
             dtype (str | None): The data type of the new image.
+            dimension_separator (Literal[".", "/"] | None): The separator to use for
+                dimensions.
+            compressors (CompressorLike | None): The compressors to use.
+            extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to
+                the zarr array creation.
             overwrite (bool): Whether to overwrite an existing image.
+            labels (Sequence[str] | None): The labels of the new image.
+                This argument is deprecated please use channels_meta instead.
+            pixel_size (PixelSize | None): The pixel size of the new image.
+                This argument is deprecated please use pixelsize, z_spacing,
+                and time_spacing instead.
 
         Returns:
-            ImagesContainer: The new image
+            ImagesContainer: The new derived image.
+
         """
         return derive_image_container(
             image_container=self,
             store=store,
             ref_path=ref_path,
             shape=shape,
-            labels=labels,
-            pixel_size=pixel_size,
-            axes_names=axes_names,
+            pixelsize=pixelsize,
+            z_spacing=z_spacing,
+            time_spacing=time_spacing,
             name=name,
+            translation=translation,
+            channels_meta=channels_meta,
+            channels_policy=channels_policy,
+            ngff_version=ngff_version,
             chunks=chunks,
+            shards=shards,
             dtype=dtype,
             dimension_separator=dimension_separator,
-            compressor=compressor,
+            compressors=compressors,
+            extra_array_kwargs=extra_array_kwargs,
             overwrite=overwrite,
+            labels=labels,
+            pixel_size=pixel_size,
         )
 
     def get(
@@ -662,7 +960,7 @@ class ImagesContainer:
                 closest pixel size level will be returned.
 
         """
-        dataset = self._meta_handler.meta.get_dataset(
+        dataset = self._meta_handler.get_meta().get_dataset(
             path=path, pixel_size=pixel_size, strict=strict
         )
         return Image(
@@ -674,34 +972,53 @@ class ImagesContainer:
 
 def compute_image_percentile(
     image: Image,
-    start_percentile: float = 0.1,
-    end_percentile: float = 99.9,
-) -> tuple[list[float], list[float]]:
+    percentiles: tuple[float, float] | list[tuple[float, float]] = (0.1, 99.9),
+) -> list[tuple[float, float]]:
     """Compute the start and end percentiles for each channel of an image.
 
     Args:
         image: The image to compute the percentiles for.
-        start_percentile: The start percentile to compute.
-        end_percentile: The end percentile to compute.
+        percentiles: The start and end percentiles for each channel.
+            If a single tuple is provided, the same percentiles will be used
+            for all channels.
 
     Returns:
         A tuple containing the start and end percentiles for each channel.
     """
-    starts, ends = [], []
-    for c in range(image.num_channels):
-        if image.num_channels == 1:
-            data = image.get_as_dask()
-        else:
-            data = image.get_as_dask(c=c)
+    num_channels = image.num_channels
+    # handle the case where a single tuple is provided
+    if isinstance(percentiles, tuple):
+        if len(percentiles) != 2:
+            raise NgioValueError(
+                "Percentiles must be a tuple of two floats: "
+                "(start_percentile, end_percentile) or "
+                "a list of such tuples with length equal to the number of channels."
+            )
+        if not isinstance(percentiles[0], float) or not isinstance(
+            percentiles[1], float
+        ):
+            raise NgioValueError(
+                "Percentiles must be a tuple of two floats: "
+                "(start_percentile, end_percentile) or "
+                "a list of such tuples with length equal to the number of channels."
+            )
+        percentiles = [percentiles] * num_channels
 
+    if len(percentiles) != num_channels:
+        raise NgioValueError(
+            "If a list of percentiles is provided, its length must be equal "
+            "to the number of channels."
+        )
+    starts_and_ends = []
+    for c_idx, (start_percentile, end_percentile) in enumerate(percentiles):
+        data = image.get_as_dask(c=c_idx)
         data = da.ravel(data)
         # remove all the zeros
         mask = data > 1e-16
         data = data[mask]
         _data = data.compute()
         if _data.size == 0:
-            starts.append(0.0)
-            ends.append(0.0)
+            starts_and_ends.append((0.0, 0.0))
             continue
 
         # compute the percentiles
@@ -709,148 +1026,107 @@ def compute_image_percentile(
             data, [start_percentile, end_percentile], method="nearest"
         ).compute()  # type: ignore (return type is a tuple of floats)
 
-        starts.append(float(_s_perc))
-        ends.append(float(_e_perc))
-    return starts, ends
+        starts_and_ends.append((float(_s_perc), float(_e_perc)))
+    return starts_and_ends
 
 
 def derive_image_container(
+    *,
     image_container: ImagesContainer,
     store: StoreOrGroup,
     ref_path: str | None = None,
+    # Metadata parameters
     shape: Sequence[int] | None = None,
-    labels: Sequence[str] | None = None,
-    pixel_size: PixelSize | None = None,
-    axes_names: Sequence[str] | None = None,
+    pixelsize: float | tuple[float, float] | None = None,
+    z_spacing: float | None = None,
+    time_spacing: float | None = None,
     name: str | None = None,
-    chunks: Sequence[int] | None = None,
+    translation: Sequence[float] | 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
+    chunks: ChunksLike | None = None,
+    shards: ShardsLike | None = None,
     dtype: str | None = None,
-    dimension_separator: DIMENSION_SEPARATOR | None = None,
-    compressor=None,
+    dimension_separator: Literal[".", "/"] | None = None,
+    compressors: CompressorLike | None = None,
+    extra_array_kwargs: Mapping[str, Any] | None = None,
     overwrite: bool = False,
+    # Deprecated arguments
+    labels: Sequence[str] | None = None,
+    pixel_size: PixelSize | None = None,
 ) -> ImagesContainer:
-    """Create an empty OME-Zarr image from an existing image.
+    """Derive a new OME-Zarr image container from an existing image.
+
+    If a kwarg is not provided, the value from the reference image will be used.
 
     Args:
-        image_container (ImagesContainer): The image container to derive the new image.
+        image_container (ImagesContainer): The image container to derive the new image
+            from.
         store (StoreOrGroup): The Zarr store or group to create the image in.
         ref_path (str | None): The path to the reference image in the image container.
         shape (Sequence[int] | None): The shape of the new image.
-        labels (Sequence[str] | None): The labels of the new image.
-        pixel_size (PixelSize | None): The pixel size of the new image.
-        axes_names (Sequence[str] | None): The axes names of the new image.
+        pixelsize (float | tuple[float, float] | None): The pixel size of the new image.
+        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.
-        chunks (Sequence[int] | None): The chunk shape of the new image.
-        dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
-            dimensions. If None it will use the same as the reference image.
-        compressor: The compressor to use. If None it will use
-            the same as the reference image.
+        translation (Sequence[float] | None): The translation for each axis
+            at the highest resolution level. Defaults to None.
+        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.
+        chunks (ChunksLike | None): The chunk shape of the new image.
+        shards (ShardsLike | None): The shard shape of the new image.
         dtype (str | None): The data type of the new image.
-        overwrite (bool): Whether to overwrite an existing image.
+        dimension_separator (Literal[".", "/"] | None): The separator to use for
+            dimensions.
+        compressors (CompressorLike | None): The compressors to use.
+        extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to
+            the zarr array creation.
+        overwrite (bool): Whether to overwrite an existing image. Defaults to False.
+        labels (Sequence[str] | None): Deprecated. This argument is deprecated,
+            please use channels_meta instead.
+        pixel_size (PixelSize | None): Deprecated. The pixel size of the new image.
+            This argument is deprecated, please use pixelsize, z_spacing,
+            and time_spacing instead.
 
     Returns:
-        ImagesContainer: The new image
+        ImagesContainer: The new derived image container.
 
     """
-    if ref_path is None:
-        ref_image = image_container.get()
-    else:
-        ref_image = image_container.get(path=ref_path)
-
-    ref_meta = ref_image.meta
-
-    if shape is None:
-        shape = ref_image.shape
-
-    if pixel_size is None:
-        pixel_size = ref_image.pixel_size
-
-    if axes_names is None:
-        axes_names = ref_meta.axes_handler.axes_names
-
-    if len(axes_names) != len(shape):
-        raise NgioValidationError(
-            "The axes names of the new image does not match the reference image."
-            f"Got {axes_names} for shape {shape}."
-        )
-
-    if chunks is None:
-        chunks = ref_image.chunks
-
-    if len(chunks) != len(shape):
-        raise NgioValidationError(
-            "The chunks of the new image does not match the reference image."
-            f"Got {chunks} for shape {shape}."
-        )
-
-    if name is None:
-        name = ref_meta.name
-
-    if dtype is None:
-        dtype = ref_image.dtype
-
-    if dimension_separator is None:
-        dimension_separator = ref_image.zarr_array._dimension_separator  # type: ignore
-
-    if compressor is None:
-        compressor = ref_image.zarr_array.compressor  # type: ignore
-
-    handler = create_empty_image_container(
+    ref_image = image_container.get(path=ref_path)
+    group_handler, axes_setup = abstract_derive(
+        ref_image=ref_image,
+        meta_type=NgioImageMeta,
         store=store,
         shape=shape,
-        pixelsize=pixel_size.x,
-        z_spacing=pixel_size.z,
-        time_spacing=pixel_size.t,
-        levels=ref_meta.paths,
-        yx_scaling_factor=ref_meta.yx_scaling(),
-        z_scaling_factor=ref_meta.z_scaling(),
-        time_unit=pixel_size.time_unit,
-        space_unit=pixel_size.space_unit,
-        axes_names=axes_names,
+        pixelsize=pixelsize,
+        z_spacing=z_spacing,
+        time_spacing=time_spacing,
         name=name,
+        translation=translation,
+        channels_meta=channels_meta,
+        channels_policy=channels_policy,
+        ngff_version=ngff_version,
         chunks=chunks,
+        shards=shards,
         dtype=dtype,
-        dimension_separator=dimension_separator,  # type: ignore
-        compressor=compressor,  # type: ignore
+        dimension_separator=dimension_separator,
+        compressors=compressors,
+        extra_array_kwargs=extra_array_kwargs,
         overwrite=overwrite,
-        version=ref_meta.version,
-    )
-    image_container = ImagesContainer(handler)
-
-    if ref_image.num_channels == image_container.num_channels:
-        _labels = ref_image.channel_labels
-        wavelength_id = ref_image.wavelength_ids
-
-        channel_meta = ref_image.channels_meta
-        colors = [c.channel_visualisation.color for c in channel_meta.channels]
-        active = [c.channel_visualisation.active for c in channel_meta.channels]
-        start = [c.channel_visualisation.start for c in channel_meta.channels]
-        end = [c.channel_visualisation.end for c in channel_meta.channels]
-    else:
-        _labels = None
-        wavelength_id = None
-        colors = None
-        active = None
-        start = None
-        end = None
-
-    if labels is not None:
-        if len(labels) != image_container.num_channels:
-            raise NgioValidationError(
-                "The number of labels does not match the number of channels."
-            )
-        _labels = labels
-
-    image_container.set_channel_meta(
-        labels=_labels,
-        wavelength_id=wavelength_id,
-        percentiles=None,
-        colors=colors,
-        active=active,
-        start=start,
-        end=end,
+        labels=labels,
+        pixel_size=pixel_size,
     )
-    return image_container
+    return ImagesContainer(group_handler=group_handler, axes_setup=axes_setup)
 
 
 def _parse_str_or_model(
@@ -859,9 +1135,9 @@ def _parse_str_or_model(
     """Parse a string or ChannelSelectionModel to an integer channel index."""
     if isinstance(channel_selection, int):
         if channel_selection < 0:
-            raise NgioValidationError("Channel index must be a non-negative integer.")
+            raise NgioValueError("Channel index must be a non-negative integer.")
         if channel_selection >= image.num_channels:
-            raise NgioValidationError(
+            raise NgioValueError(
                 "Channel index must be less than the number "
                 f"of channels ({image.num_channels})."
             )
@@ -879,7 +1155,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)
-    raise NgioValidationError(
+    raise NgioValueError(
         "Invalid channel selection type. "
         f"{channel_selection} is of type {type(channel_selection)} ",
         "supported types are str, ChannelSelectionModel, and int.",
@@ -898,7 +1174,7 @@ def _parse_channel_selection(
     elif isinstance(channel_selection, Sequence):
         _sequence = [_parse_str_or_model(image, cs) for cs in channel_selection]
         return {"c": _sequence}
-    raise NgioValidationError(
+    raise NgioValueError(
         f"Invalid channel selection type {type(channel_selection)}. "
         "Supported types are int, str, ChannelSelectionModel, and Sequence."
     )
@@ -912,7 +1188,7 @@ def add_channel_selection_to_slicing_dict(
     """Add channel selection information to the slicing dictionary."""
     channel_info = _parse_channel_selection(image, channel_selection)
     if "c" in slicing_dict and channel_info:
-        raise NgioValidationError(
+        raise NgioValueError(
             "Both channel_selection and 'c' in slicing_kwargs are provided. "
             "Which channel selection should be used is ambiguous. "
             "Please provide only one."