ngio 0.3.0a1__tar.gz → 0.3.2__tar.gz

ngio-0.3.2/.github/pull_request_template.md

@@ -0,0 +1,3 @@
+
+## Checklist before merging
+- [ ] I added an appropriate entry to `CHANGELOG.md`

ngio-0.3.2/CHANGELOG.md

@@ -0,0 +1,12 @@
+# Changelog
+
+## [v0.3.2]
+
+### API Changes
+
+- change table backend default to `anndata_v1` for backward compatibility. This will be chaanged again when ngio `v0.2.x` is no longer supported.
+
+### Bug Fixes
+
+- fix [#13](https://github.com/fractal-analytics-platform/fractal-converters-tools/issues/13) (converters tools)
+- fix [#88](https://github.com/fractal-analytics-platform/ngio/issues/88)

{ngio-0.3.0a1 → ngio-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.3.0a1
+Version: 0.3.2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/fractal-analytics-platform/ngio
 Project-URL: repository, https://github.com/fractal-analytics-platform/ngio
@@ -63,7 +63,7 @@ Requires-Dist: pytest-cov; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 
-# NGIO - Next Generation file format IO
+# Ngio - Next Generation file format IO
 
 [![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
@@ -71,36 +71,69 @@ Description-Content-Type: text/markdown
 [![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
 
-NGIO is a Python library to streamline OME-Zarr image analysis workflows.
-
-**Main Goals:**
-
-- Abstract object base API for handling OME-Zarr files
-- Powerful iterators for processing data using common access patterns
-- Tight integration with [Fractal's Table Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/tables/)
-- Validation of OME-Zarr files
-
-To get started, check out the [Getting Started](https://fractal-analytics-platform.github.io/ngio/getting-started/) guide. Or checkout our [Documentation](https://fractal-analytics-platform.github.io/ngio/)
-
-## 🚧 Ngio is Under active Development 🚧
-
-### Roadmap
-
-| Feature | Status | ETA | Description |
-|---------|--------|-----|-------------|
-| Metadata Handling | ✅ | | Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready) |
-| OME-Zarr Validation | ✅ | | Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data |
-| Base Image Handling | ✅ | | Load data from OME-Zarr files, retrieve basic metadata, and write data |
-| ROI Handling | ✅ | | Common ROI models |
-| Label Handling | ✅ | Mid-September | Based on Image Handling |
-| Table Validation | ✅ | Mid-September | Validate Table fractal V1 + Compliance between Metadata and Data |
-| Table Handling | ✅ | Mid-September | Read, Write ROI, Features, and Masked Tables |
-| Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
-| Base Documentation | ✅ | End-September | API Documentation and Examples |
-| Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | Ongoing | December | Ngio can stream OME-Zarr from fractal |
-| Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
-| Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
-| Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |
-| Full Documentation | Not started | 2025 | Complete Documentation |
-| Release 1.0 (Commitment to API) | Not started | 2025 | API is stable; breaking changes will be avoided |
+ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
+
+## What is Ngio?
+
+Ngio is built for the [OME-Zarr](https://ngff.openmicroscopy.org/) file format, a modern, cloud-optimized format for biological imaging data. OME-Zarr stores large, multi-dimensional microscopy images and metadata in an efficient and scalable way.
+
+Ngio's mission is to streamline working with OME-Zarr files by providing a simple, object-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates. It also offers comprehensive support for labels, tables and regions of interest (ROIs), making it easy to extract and analyze specific regions in your data.
+
+## Key Features
+
+### 📊 Simple Object-Based API
+
+- Easily open, explore, and manipulate OME-Zarr images and HCS plates
+- Create and derive new images and labels with minimal boilerplate code
+
+### 🔍 Rich Tables and Regions of Interest (ROI) Support
+
+- Extract and analyze specific regions of interest
+- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+
+### 🔄 Scalable Data Processing (Coming Soon)
+
+- Powerful iterators for processing data at scale
+- Efficient memory management for large datasets
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+
+## Supported OME-Zarr versions
+
+Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.
+
+## Development Status
+
+!!! warning
+    Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
+
+### Available Features
+
+- ✅ OME-Zarr metadata handling and validation
+- ✅ Image and label access across pyramid levels
+- ✅ ROI and table support
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### Upcoming Features
+
+- Advanced image processing iterators
+- Parallel processing capabilities
+- Support for OME-Zarr v0.5 and Zarr v3
+
+## Contributors
+
+Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html), University of Zurich, by [@lorenzocerrone](https://github.com/lorenzocerrone) and [@jluethi](https://github.com/jluethi).
+
+## License
+
+Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.

ngio-0.3.2/README.md

@@ -0,0 +1,74 @@
+# Ngio - Next Generation file format IO
+
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio)
+[![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org)
+[![CI](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/fractal-analytics-platform/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/fractal-analytics-platform/ngio)
+
+ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
+
+## What is Ngio?
+
+Ngio is built for the [OME-Zarr](https://ngff.openmicroscopy.org/) file format, a modern, cloud-optimized format for biological imaging data. OME-Zarr stores large, multi-dimensional microscopy images and metadata in an efficient and scalable way.
+
+Ngio's mission is to streamline working with OME-Zarr files by providing a simple, object-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates. It also offers comprehensive support for labels, tables and regions of interest (ROIs), making it easy to extract and analyze specific regions in your data.
+
+## Key Features
+
+### 📊 Simple Object-Based API
+
+- Easily open, explore, and manipulate OME-Zarr images and HCS plates
+- Create and derive new images and labels with minimal boilerplate code
+
+### 🔍 Rich Tables and Regions of Interest (ROI) Support
+
+- Extract and analyze specific regions of interest
+- Tight integration with [Tabular Data](https://fractal-analytics-platform.github.io/ngio/stable/table_specs/overview/)
+
+### 🔄 Scalable Data Processing (Coming Soon)
+
+- Powerful iterators for processing data at scale
+- Efficient memory management for large datasets
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://fractal-analytics-platform.github.io/ngio/stable/getting_started/0_quickstart/).
+
+## Supported OME-Zarr versions
+
+Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.
+
+## Development Status
+
+!!! warning
+    Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
+
+### Available Features
+
+- ✅ OME-Zarr metadata handling and validation
+- ✅ Image and label access across pyramid levels
+- ✅ ROI and table support
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### Upcoming Features
+
+- Advanced image processing iterators
+- Parallel processing capabilities
+- Support for OME-Zarr v0.5 and Zarr v3
+
+## Contributors
+
+Ngio is developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html), University of Zurich, by [@lorenzocerrone](https://github.com/lorenzocerrone) and [@jluethi](https://github.com/jluethi).
+
+## License
+
+Ngio is released under the BSD-3-Clause License. See [LICENSE](https://github.com/fractal-analytics-platform/ngio/blob/main/LICENSE) for details.

{ngio-0.3.0a1 → ngio-0.3.2}/docs/index.md

@@ -1,4 +1,3 @@
-
 ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
 
 ## What is Ngio?
@@ -30,12 +29,14 @@ Refer to the [Getting Started](getting_started/0_quickstart.md) guide to integra
 For more advanced usage and API documentation, see our [API Reference](api/ngio.md).
 
 ## Supported OME-Zarr versions
+
 Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.
 
 ## Development Status
 
 !!! warning
     Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected.
+    We follow [Semantic Versioning](https://semver.org/). Which means for 0.x releases potentially breaking changes can be introduced in minor releases.
 
 ### Available Features
 

{ngio-0.3.0a1 → ngio-0.3.2}/docs/table_specs/backend.md

@@ -14,7 +14,8 @@ AnnData is a widely used format in single-cell genomics, and can natively store
 The following normalization steps are applied to each table before saving it to the AnnData backend:
 
 - We separate the table in two parts: The floating point columns are casted to `float32` and stored as `X` in the AnnData object, while the categorical, boolean, and integer columns are stored as `obs`.
-- The index column is cast to a string, and the name and original type is stored in the zarr attributes.
+- The index column is cast to a string, and is stored in the `obs` index.
+- The index column name must match the `index_key` specified in the metadata.
 
 AnnData backend metadata:
 

{ngio-0.3.0a1 → ngio-0.3.2}/docs/table_specs/table_types/roi_table.md

@@ -33,7 +33,7 @@ Moreover the ROI table must include the following columns:
 
 Additionally, each ROI can include the following optional columns:
 
-- `x_micrometer_original` and `y_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
+- `x_micrometer_original`, `y_micrometer_original` and `z_micrometer_original` which are the original coordinates of the ROI in micrometers. These are typically used when the data is saved in different coordinates during conversion, e.g. to avoid overwriting data from overlapping ROIs.
 - `translation_x`, `translation_y` and `translation_z`, which are used during registration of multiplexing acquisitions.
 
 The user can also add additional columns to the ROI table, but these columns will not be exposed in the ROI table API.

{ngio-0.3.0a1 → ngio-0.3.2}/mkdocs.yml

@@ -104,6 +104,7 @@ nav:
     - "Overview": table_specs/overview.md
     - "Table Backends": table_specs/backend.md
     - "Table Types":
+      - "Generic Table": table_specs/table_types/generic_table.md 
       - "ROI Table": table_specs/table_types/roi_table.md
       - "Masking ROI Table": table_specs/table_types/masking_roi_table.md
       - "Feature Table": table_specs/table_types/feature_table.md

{ngio-0.3.0a1 → ngio-0.3.2}/src/ngio/common/_array_pipe.py

@@ -1,10 +1,11 @@
 from collections.abc import Collection, Iterable
 from typing import Literal
 
-import dask
-import dask.delayed
+import dask.array as da
 import numpy as np
 import zarr
+from dask.array import Array as DaskArray
+from dask.delayed import Delayed, delayed
 
 from ngio.common._axes_transforms import transform_dask_array, transform_numpy_array
 from ngio.common._common_types import ArrayLike
@@ -55,26 +56,26 @@ def _numpy_get_pipe(
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
 ) -> np.ndarray:
-    array = numpy_get_slice(array, slices)
-    return transform_numpy_array(array, transformations)
+    _array = numpy_get_slice(array, slices)
+    return transform_numpy_array(_array, transformations)
 
 
 def _delayed_numpy_get_pipe(
     array: zarr.Array,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.delayed:
-    array = dask.delayed(numpy_get_slice)(array, slices)
-    return dask.delayed(transform_numpy_array)(array, transformations)
+) -> Delayed:
+    _array = delayed(numpy_get_slice)(array, slices)
+    return delayed(transform_numpy_array)(_array, transformations)
 
 
 def _dask_get_pipe(
     array: zarr.Array,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.array:
-    array = dask_get_slice(array, slices)
-    return transform_dask_array(array, transformations)
+) -> DaskArray:
+    _array = dask_get_slice(array, slices)
+    return transform_dask_array(_array, transformations)
 
 
 def _numpy_set_pipe(
@@ -89,22 +90,22 @@ def _numpy_set_pipe(
 
 def _dask_set_pipe(
     array: zarr.Array,
-    patch: np.ndarray,
+    patch: DaskArray,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
 ) -> None:
-    patch = transform_dask_array(patch, transformations)
-    dask_set_slice(array, patch, slices)
+    _patch = transform_dask_array(patch, transformations)
+    dask_set_slice(array, _patch, slices)
 
 
 def _delayed_numpy_set_pipe(
     array: zarr.Array,
-    patch: np.ndarray,
+    patch: np.ndarray | Delayed,
     slices: SliceTransform,
     transformations: tuple[AxesTransformation, ...],
-) -> dask.delayed:
-    patch = dask.delayed(transform_numpy_array)(patch, transformations)
-    return dask.delayed(numpy_set_slice)(array, patch, slices)
+) -> Delayed:
+    _patch = delayed(transform_numpy_array)(patch, transformations)
+    return delayed(numpy_set_slice)(array, _patch, slices)
 
 
 def get_pipe(
@@ -144,7 +145,7 @@ def set_pipe(
     slices, transformations = _compute_to_disk_transforms(
         dimensions=dimensions, axes_order=axes_order, **slice_kwargs
     )
-    if isinstance(patch, dask.array.Array):
+    if isinstance(patch, DaskArray):
         _dask_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
@@ -152,7 +153,7 @@ def set_pipe(
         _numpy_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
-    elif isinstance(patch, dask.delayed.Delayed):
+    elif isinstance(patch, Delayed):
         _delayed_numpy_set_pipe(
             array=array, patch=patch, slices=slices, transformations=transformations
         )
@@ -193,12 +194,15 @@ def _mask_pipe_common(
         **slice_kwargs,
     )
 
-    if isinstance(array_patch, np.ndarray):
+    if isinstance(array_patch, np.ndarray) and isinstance(label_patch, np.ndarray):
         label_patch = np.broadcast_to(label_patch, array_patch.shape)
-    elif isinstance(array_patch, dask.array.Array):
-        label_patch = dask.array.broadcast_to(label_patch, array_patch.shape)
+    elif isinstance(array_patch, DaskArray) and isinstance(label_patch, DaskArray):
+        label_patch = da.broadcast_to(label_patch, array_patch.shape)
     else:
-        raise NgioValueError(f"Mode {mode} not yet supported for masked array.")
+        raise NgioValueError(
+            "Incompatible types for array and label: "
+            f"{type(array_patch)} and {type(label_patch)}"
+        )
 
     mask = label_patch == label
     return array_patch, mask
@@ -225,7 +229,14 @@ def get_masked_pipe(
         mode=mode,
         **slice_kwargs,
     )
-    array_patch[~mask] = 0
+    if isinstance(array_patch, np.ndarray):
+        array_patch[~mask] = 0
+    elif isinstance(array_patch, DaskArray):
+        array_patch = da.where(mask, array_patch, 0)
+    else:
+        raise NgioValueError(
+            "Mode not yet supported for masked array. Expected a numpy or dask array."
+        )
     return array_patch
 
 
@@ -240,7 +251,7 @@ def set_masked_pipe(
     axes_order: Collection[str] | None = None,
     **slice_kwargs: slice | int | Iterable[int],
 ):
-    if isinstance(patch, dask.array.Array):
+    if isinstance(patch, DaskArray):
         mode = "dask"
     elif isinstance(patch, np.ndarray):
         mode = "numpy"
@@ -259,7 +270,19 @@ def set_masked_pipe(
         mode=mode,
         **slice_kwargs,
     )
-    patch = np.where(mask, patch, array_patch)
+    if isinstance(patch, np.ndarray):
+        assert isinstance(array_patch, np.ndarray)
+        _patch = np.where(mask, patch, array_patch)
+    elif isinstance(patch, DaskArray):
+        _patch = da.where(mask, patch, array_patch)
+    else:
+        raise NgioValueError(
+            "Mode not yet supported for masked array. Expected a numpy or dask array."
+        )
     set_pipe(
-        array, patch, dimensions=dimensions_array, axes_order=axes_order, **slice_kwargs
+        array,
+        _patch,
+        dimensions=dimensions_array,
+        axes_order=axes_order,
+        **slice_kwargs,
     )

{ngio-0.3.0a1 → ngio-0.3.2}/src/ngio/common/_roi.py

@@ -57,6 +57,7 @@ class Roi(BaseModel):
             x_length=_to_raster(self.x_length, pixel_size.x, dim_x),
             y_length=_to_raster(self.y_length, pixel_size.y, dim_y),
             z_length=_to_raster(self.z_length, pixel_size.z, dim_z),
+            **self.model_extra,
         )
 
     def zoom(self, zoom_factor: float = 1) -> "Roi":
@@ -94,6 +95,7 @@ class RoiPixels(BaseModel):
             y_length=_to_world(self.y_length, pixel_size.y),
             z_length=_to_world(self.z_length, pixel_size.z),
             unit=pixel_size.space_unit,
+            **self.model_extra,
         )
 
     def to_slices(self) -> dict[str, slice]:

{ngio-0.3.0a1 → ngio-0.3.2}/src/ngio/common/_table_ops.py

@@ -9,7 +9,7 @@ from typing import Literal
 import pandas as pd
 import polars as pl
 
-from ngio.images.ome_zarr_container import OmeZarrContainer
+from ngio.images._ome_zarr_container import OmeZarrContainer
 from ngio.tables import Table, TableType
 
 

{ngio-0.3.0a1 → ngio-0.3.2}/src/ngio/hcs/__init__.py

@@ -1,6 +1,6 @@
 """OME-Zarr HCS objects models."""
 
-from ngio.hcs.plate import (
+from ngio.hcs._plate import (
     OmeZarrPlate,
     OmeZarrWell,
     create_empty_plate,

ngio-0.3.0a1/src/ngio/hcs/plate.py → ngio-0.3.2/src/ngio/hcs/_plate.py

@@ -27,6 +27,7 @@ from ngio.ome_zarr_meta import (
 )
 from ngio.tables import (
     ConditionTable,
+    DefaultTableBackend,
     FeatureTable,
     GenericRoiTable,
     MaskingRoiTable,
@@ -39,7 +40,6 @@ from ngio.tables import (
 )
 from ngio.utils import (
     AccessModeLiteral,
-    NgioValidationError,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
@@ -805,22 +805,38 @@ class OmeZarrPlate:
             parallel_safe=parallel_safe,
         )
 
-    @property
-    def tables_container(self) -> TablesContainer:
+    def _get_tables_container(self) -> TablesContainer | None:
         """Return the tables container."""
         if self._tables_container is None:
-            self._tables_container = _default_table_container(self._group_handler)
-            if self._tables_container is None:
-                raise NgioValidationError("No tables found in the image.")
+            _tables_container = _default_table_container(self._group_handler)
+            if _tables_container is None:
+                return None
+            self._tables_container = _tables_container
         return self._tables_container
 
-    def list_tables(self, filter_types: str | None = None) -> list[str]:
+    @property
+    def tables_container(self) -> TablesContainer:
+        """Return the tables container."""
+        _table_container = self._get_tables_container()
+        if _table_container is None:
+            raise NgioValueError(
+                "No tables container found. Please add a tables container to the plate."
+            )
+        return _table_container
+
+    def list_tables(self, filter_types: TypedTable | str | None = None) -> list[str]:
         """List all tables in the image."""
         return self.tables_container.list(filter_types=filter_types)
 
     def list_roi_tables(self) -> list[str]:
         """List all ROI tables in the image."""
-        return self.tables_container.list_roi_tables()
+        masking_roi = self.tables_container.list(
+            filter_types="masking_roi_table",
+        )
+        roi = self.tables_container.list(
+            filter_types="roi_table",
+        )
+        return masking_roi + roi
 
     def get_roi_table(self, name: str) -> RoiTable:
         """Get a ROI table from the image.
@@ -929,7 +945,7 @@ class OmeZarrPlate:
         self,
         name: str,
         table: Table,
-        backend: TableBackend = "anndata",
+        backend: TableBackend = DefaultTableBackend,
         overwrite: bool = False,
     ) -> None:
         """Add a table to the image."""

{ngio-0.3.0a1 → ngio-0.3.2}/src/ngio/images/__init__.py

@@ -1,8 +1,8 @@
 """OME-Zarr object models."""
 
-from ngio.images.image import Image, ImagesContainer
-from ngio.images.label import Label, LabelsContainer
-from ngio.images.ome_zarr_container import (
+from ngio.images._image import Image, ImagesContainer
+from ngio.images._label import Label, LabelsContainer
+from ngio.images._ome_zarr_container import (
     OmeZarrContainer,
     create_empty_ome_zarr,
     create_ome_zarr_from_array,

ngio-0.3.0a1/src/ngio/images/image.py → ngio-0.3.2/src/ngio/images/_image.py

@@ -3,11 +3,11 @@
 from collections.abc import Collection
 from typing import Literal
 
-from dask import array as da
+import dask.array as da
 
 from ngio.common import Dimensions
-from ngio.images.abstract_image import AbstractImage, consolidate_image
-from ngio.images.create import create_empty_image_container
+from ngio.images._abstract_image import AbstractImage, consolidate_image
+from ngio.images._create import create_empty_image_container
 from ngio.ome_zarr_meta import (
     ImageMetaHandler,
     NgioImageMeta,
@@ -152,31 +152,33 @@ class ImagesContainer:
 
     def set_channel_meta(
         self,
-        labels: Collection[str] | int | None = None,
-        wavelength_id: Collection[str] | None = None,
-        start: Collection[float] | None = None,
-        end: Collection[float] | None = None,
+        labels: Collection[str | None] | int | None = None,
+        wavelength_id: Collection[str | None] | None = None,
+        start: Collection[float | None] | None = None,
+        end: Collection[float | None] | None = None,
         percentiles: tuple[float, float] | None = None,
-        colors: Collection[str] | None = None,
-        active: Collection[bool] | None = None,
+        colors: Collection[str | None] | None = None,
+        active: Collection[bool | None] | None = None,
         **omero_kwargs: dict,
     ) -> None:
         """Create a ChannelsMeta object with the default unit.
 
         Args:
-            labels(Collection[str] | int): The list of channels names in the image.
-                If an integer is provided, the channels will be named "channel_i".
-            wavelength_id(Collection[str] | None): The wavelength ID of the channel.
+            labels(Collection[str | None] | int): The list of channels names
+                in the image. If an integer is provided, the channels will
+                be named "channel_i".
+            wavelength_id(Collection[str | None]): The wavelength ID of the channel.
                 If None, the wavelength ID will be the same as the channel name.
-            start(Collection[float] | None): The start value for each channel.
+            start(Collection[float | None]): The start value for each channel.
                 If None, the start value will be computed from the image.
-            end(Collection[float] | None): The end value for each channel.
+            end(Collection[float | None]): The end value for each channel.
                 If None, the end value will be computed from the image.
-            percentiles(tuple[float, float] | None): The start and end percentiles
-                for each channel. If None, the percentiles will not be computed.
-            colors(Collection[str, NgioColors] | None): The list of colors for the
+            percentiles(tuple[float, float] | None): The start and end
+                percentiles for each channel. If None, the percentiles will
+                not be computed.
+            colors(Collection[str | None]): The list of colors for the
                 channels. If None, the colors will be random.
-            active (Collection[bool] | None):active(bool): Whether the channel should
+            active (Collection[bool | None]): Whether the channel should
                 be shown by default.
             omero_kwargs(dict): Extra fields to store in the omero attributes.
         """
@@ -376,9 +378,12 @@ def compute_image_percentile(
     starts, ends = [], []
     for c in range(image.num_channels):
         if image.num_channels == 1:
-            data = image.get_array(mode="dask").ravel()
+            data = image.get_array(mode="dask")
         else:
-            data = image.get_array(c=c, mode="dask").ravel()
+            data = image.get_array(c=c, mode="dask")
+
+        assert isinstance(data, da.Array), "Data must be a Dask array."
+        data = da.ravel(data)
         # remove all the zeros
         mask = data > 1e-16
         data = data[mask]
@@ -391,7 +396,7 @@ def compute_image_percentile(
         # compute the percentiles
         _s_perc, _e_perc = da.percentile(
             data, [start_percentile, end_percentile], method="nearest"
-        ).compute()
+        ).compute()  # type: ignore
 
         starts.append(float(_s_perc))
         ends.append(float(_e_perc))