ngio 0.4.7__tar.gz → 0.5.0__tar.gz

{ngio-0.4.7 → ngio-0.5.0}/.github/workflows/build_docs.yml

@@ -3,7 +3,6 @@ name: Build Docs
 on:
   push:
     branches:
-      - hotfix/*
       - main
     tags:
       - "v*"
@@ -41,7 +40,7 @@ jobs:
 
       - name: Restore shared data cache
         id: cache-data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: data/
           key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
@@ -59,8 +58,8 @@ jobs:
             mike set-default --push stable
             echo "Deployed stable version $VERSION (stable)"
 
-          elif [[ $GITHUB_REF == refs/heads/dev ]]; then
+          elif [[ $GITHUB_REF == refs/heads/main ]]; then
             mike deploy --push dev
             mike set-default --push dev
-            echo "Deployed development version (dev)"
+            echo "Deployed development version (dev) from main"
           fi

{ngio-0.4.7 → ngio-0.5.0}/.github/workflows/ci.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-      - hotfix/*
+      - dev
     tags:
       - "v*"
   pull_request:
@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -54,7 +54,7 @@ jobs:
 
       - name: Restore shared data cache
         id: cache-data
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: data/
           key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
@@ -79,6 +79,7 @@ jobs:
           update_existing: true
 
       - name: Coverage
+        if: success() && matrix.platform == 'ubuntu-latest'
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

{ngio-0.4.7 → ngio-0.5.0}/.gitignore

@@ -131,4 +131,8 @@ tests/_v01
 # Ignore locks
 *.lock
 
-benchmark/*
+benchmark/*
+
+# Agents files (for now let's not track them)
+AGENTS.md
+CLAUDE.md

ngio-0.5.0/CHANGELOG.md

@@ -0,0 +1,190 @@
+# Changelog
+
+## [v0.5.0]
+
+### Features
+- Add support for OME-NGFF v0.5
+- Move to zarr-python v3
+- API to delete labels and tables from OME-Zarr containers and HCS plates.
+- Allow to explicitly set axes order when building masking roi tables.
+- New metadata modification APIs for `Image`, `Label`, and `OmeZarrContainer`:
+  - `set_channel_labels` - Update channel labels
+  - `set_channel_colors` - Update channel colors
+  - `set_channel_windows` - Update channel display windows (start/end values)
+  - `set_channel_windows_with_percentiles` - Update display windows based on data percentiles
+  - `set_axes_names` - Rename axes in the metadata
+  - `set_axes_unit` - Set space and time units for axes
+  - `set_name` - Set the image/label name in metadata
+- Add translation support in all image/label creation and derivation APIs.
+
+### API Breaking Changes
+
+- New `Roi` models, now supporting arbitrary axes.
+- The `compressor` argument has been renamed to `compressors` in all relevant functions and methods to reflect the support for multiple compressors in zarr v3.
+- The `version` argument has been renamed to `ngff_version` in all relevant functions and methods to specify the OME-NGFF version.
+- Remove the `parallel_safe` argument from all zarr related functions and methods. The locking mechanism is now handled internally and only depends on the
+`cache`.
+- Remove the unused `parent` argument from `ZarrGroupHandler`.
+- Internal changes to `ZarrGroupHandler` to support cleanup unused apis.
+- Remove `ngio_logger` in favor of standard warnings module.
+
+### Migration Guide (v0.4 → v0.5)
+
+#### Roi API Changes
+
+The `Roi` class now uses a flexible slice-based model supporting arbitrary axes:
+
+```python
+# Old (v0.4)
+roi = Roi(x=34.1, y=10, x_length=321.6, y_length=330)
+
+# New (v0.5)
+roi = Roi.from_values(slices={"x": (34.1, 321.6), "y": (10, 330)}, name=None)
+
+# Accessing coordinates
+# Old: roi.x, roi.y, roi.x_length, roi.y_length
+# New: roi.get("x").start, roi.get("y").start, roi.get("x").length, roi.get("y").length
+```
+
+#### Argument Renames
+
+```python
+# compressor → compressors
+# Old (v0.4)
+create_empty_ome_zarr(..., compressor=Blosc())
+
+# New (v0.5)
+create_empty_ome_zarr(..., compressors=Blosc())
+
+# version → ngff_version
+# Old (v0.4)
+create_empty_ome_zarr(..., version="0.4")
+
+# New (v0.5)
+create_empty_ome_zarr(..., ngff_version="0.4")
+```
+
+#### Removed Arguments
+
+- `parallel_safe`: No longer needed, locking is handled internally
+- `ngio_logger`: Use Python's standard `warnings` module instead
+
+### Deprecations
+- Standardized all deprecation warnings to indicate removal in `ngio=0.6`.
+- Deprecated `set_channel_percentiles` method, use `set_channel_windows_with_percentiles` instead.
+
+### Bug Fixes
+- Fix bug in `consolidate` function when using coarsening mode with non power-of-two shapes.
+- Fix HCS plate column name formatting to use standardized zero-padding (e.g., column `3` is now stored as `"03"`).
+- Fix `_stringify_column` not passing `num_digits` parameter to `_format_int_column`.
+
+### Documentation
+- Fix incorrect and incomplete docstrings across the codebase:
+  - `compute_masking_roi`: Added Args/Returns, fixed description (supports 2D, 3D, 4D).
+  - `lazy_compute_slices`: Added Args/Returns sections.
+  - `LabelsContainer.list`: Fixed description (was "Create the /labels group").
+  - `build_masking_roi_table`: Added Args/Returns sections.
+  - `TablesContainer`: Fixed class and method descriptions (were referencing labels instead of tables).
+  - `NgioPlateMeta.add_well`: Fixed description (was "Add an image to the well").
+  - `NgioPlateMeta.derive`: Fixed type annotation in docstring (`NgffVersion` → `NgffVersions`).
+  - Added missing docstrings to several HCS helper functions.
+
+## [v0.4.7]
+
+### Bug Fixes
+- Fix bug adding time axis to masking roi tables.
+
+### Bug Fixes
+- Fix channel selection from `wavelength_id`
+- Fix table opening mode to stop wrtiting groups when opening in append mode.
+
+## [v0.4.5]
+
+### Bug Fixes
+- Pin Dask to version <2025.11 to avoid errors when writing zarr pyramids with dask (see https://github.com/dask/dask/issues/12159#issuecomment-3548421833)
+
+## [v0.4.4]
+
+### Bug Fixes
+
+- Fix bug in channel visualization when using hex colors with leading '#'.
+- Remove strict range check in channel window.
+
+## [v0.4.3]
+
+### Bug Fixes
+
+- Fix bug in deriving labels and image from OME-Zarr with non standard path names.
+- Add missing pillow dependency.
+- Update pixi workspace config.
+
+## [v0.4.2]
+
+### API Changes
+
+- Make roi.to_slicing_dict(pixel_size) always require pixel_size argument for consistency with other roi methods.
+- Make PixelSize object a Pydantic model to allow for serialization.
+
+### Bug Fixes
+
+- Improve robustness when rounding Rois to pixel coordinates. 
+
+## [v0.4.1]
+
+### Bug Fixes
+- Fix bug in zoom transform when input axes contain unknown axes (e.g. virtual axes). Now unknown axes are treated as virtual axes and set to 1 in the target shape.
+
+## [v0.4.0]
+
+### Features
+
+- Add Iterators for image processing pipelines
+- Add support for time in rois and roi-tables
+- Building masking roi tables expanded to time series data
+- Add zoom transformation
+- Add support for rescaling on-the-fly masks for masked images
+- Big refactor of the io pipeline to support iterators and lazy loading
+- Add support for customize dimension separators and compression codecs
+- Simplify AxesHandler and Dataset Classes
+
+### API Changes
+
+- The image-like `get_*` api have been slightly changed. Now if a single int is passed as slice_kwargs, it is interpreted as a single index. So the dimension is automatically squeezed.
+- Remove the `get_*_delayed` methods, now data cam only be loaded as numpy or dask array.Use the `get_as_dask` method instead, which returns a dask array that can be used with dask delayed.
+- A new model for channel selection is available. Now channels can be selected by name, index or with `ChannelSelectionModel` object.
+- Change `table_name` keyword argument to `name` for consistency in all table concatenation functions, e.g. `concatenate_image_tables`,  `concatenate_image_tables_as`, etc.
+- Change to `Dimension` class. `get_shape` and `get_canonical_shape` have been removed, `get` uses new keyword arguments `default` instead of `strict`.
+- Image like objects now have a more clean API to load data. Instead of `get_array` and `set_array`, they now use `get_as_numpy`, and `get_as_dask` for delayed arrays.
+- Also for `get_roi` now specific methods are available. For ROI objects, the `get_roi_as_numpy`, and `get_roi_as_dask` methods.
+- Table ops moved to `ngio.images`
+- int `label` as an explicit attribute in `Roi` objects (previously only in stored in name and relying on convention)
+- Slight changes to `Image` and `Label` objects. Some minor attributes have been renamed for consistency.
+
+### Table specs
+
+- Add `t_second` and `len_t_second` to ROI tables and masking ROI tables
+
+## [v0.3.5]
+
+- Remove path normalization for images in wells. While the spec requires paths to be alphanumeric, this patch removes the normalization to allow for arbitrary image paths.
+
+## [v0.3.4]
+
+- allow to write as `anndata_v1` for backward compatibility with older ngio versions.
+
+## [v0.3.3]
+
+### Chores
+
+- improve dataset download process and streamline the CI workflows
+
+## [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/BioVisionCenter/fractal-converters-tools/issues/13) (converters tools)
+- fix [#88](https://github.com/BioVisionCenter/ngio/issues/88)

{ngio-0.4.7 → ngio-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.4.7
+Version: 0.5.0
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -13,25 +13,25 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
-Requires-Python: <3.14,>=3.11
+Requires-Python: <3.15,>=3.11
 Requires-Dist: aiohttp
-Requires-Dist: anndata<0.11.4,>=0.8.0
+Requires-Dist: anndata
 Requires-Dist: dask[array]<2025.11.0
 Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
-Requires-Dist: pandas>=1.2.0
+Requires-Dist: pandas<3.0.0,>=1.2.0
 Requires-Dist: pillow
 Requires-Dist: polars
 Requires-Dist: pooch
 Requires-Dist: pyarrow
 Requires-Dist: pydantic
 Requires-Dist: requests
-Requires-Dist: zarr<3
+Requires-Dist: zarr>3
 Provides-Extra: dev
-Requires-Dist: devtools; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: napari; extra == 'dev'
@@ -43,6 +43,7 @@ Requires-Dist: pyqt5; extra == 'dev'
 Requires-Dist: rich; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
 Requires-Dist: scikit-image; extra == 'dev'
+Requires-Dist: zarrs; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: griffe-typingdoc; extra == 'docs'
 Requires-Dist: markdown-exec[ansi]; extra == 'docs'
@@ -57,11 +58,17 @@ Requires-Dist: mkdocs-jupyter; extra == 'docs'
 Requires-Dist: mkdocs-material; extra == 'docs'
 Requires-Dist: mkdocstrings[python]; extra == 'docs'
 Requires-Dist: rich; extra == 'docs'
+Requires-Dist: ruff; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
 Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test
+Requires-Dist: boto; extra == 'test'
+Requires-Dist: devtools; extra == 'test'
+Requires-Dist: moto[server]; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-httpserver; extra == 'test'
+Requires-Dist: s3fs; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 

ngio-0.5.0/docs/api/ngio/ngio.md

@@ -0,0 +1,17 @@
+# ngio API documentation
+
+::: ngio
+    options:
+      members:
+        - AxesSetup
+        - ChannelSelectionModel
+        - DefaultNgffVersion
+        - Dimensions
+        - ImageInWellPath
+        - NgffVersions
+        - NgioSupportedStore
+        - PixelSize
+        - Roi
+        - RoiSlice
+        - StoreOrGroup
+        - create_synthetic_ome_zarr

ngio-0.5.0/docs/changelog.md

@@ -0,0 +1,3 @@
+{%
+    include-markdown "../CHANGELOG.md"
+%}

{ngio-0.4.7 → ngio-0.5.0}/docs/getting_started/0_quickstart.md

@@ -96,4 +96,4 @@ Also, checkout our jupyer notebook tutorials for more examples:
 - [Image Processing](../tutorials/image_processing.ipynb): Learn how to perform simple image processing operations.
 - [Image Segmentation](../tutorials/image_segmentation.ipynb): Learn how to create new labels from images.
 - [Feature Extraction](../tutorials/feature_extraction.ipynb): Learn how to extract features from images.
-- [HCS Processing](../tutorials/hcs_processing.ipynb): Learn how to process high-content screening data using ngio.
+- [HCS Exploration](../tutorials/hcs_exploration.ipynb): Learn how to explore high-content screening data using ngio.

{ngio-0.4.7 → ngio-0.5.0}/docs/getting_started/1_ome_zarr_containers.md

@@ -58,8 +58,8 @@ Examples of the OME-Zarr metadata access:
 === "Available Paths"
     Show the paths to all available resolution levels:
     ```pycon exec="true" source="console" session="get_started"
-    >>> ome_zarr_container.levels_paths # Show the paths to all available images
-    >>> print(ome_zarr_container.levels_paths) # markdown-exec: hide
+    >>> ome_zarr_container.level_paths # Show the paths to all available images
+    >>> print(ome_zarr_container.level_paths) # markdown-exec: hide
     ```
 
 === "Dimensionality"
@@ -76,7 +76,7 @@ Examples of the OME-Zarr metadata access:
 
 === "Full Metadata Object"
     ```pycon exec="true" source="console" session="get_started"
-    >>> metadata = ome_zarr_container.image_meta
+    >>> metadata = ome_zarr_container.meta
     >>> print(metadata) # markdown-exec: hide
     ```
     The metadata object contains all the information about the image, for example, the channel labels:
@@ -85,6 +85,65 @@ Examples of the OME-Zarr metadata access:
     >>> print(metadata.channels_meta.channel_labels) # markdown-exec: hide
     ```
 
+## Modifying metadata
+
+ngio provides methods to modify the image metadata, such as channel labels, colors, display windows, axes names, and units.
+
+### Channel metadata
+
+You can update channel labels, colors, and display windows:
+
+=== "Channel Labels"
+    Update the labels (names) of the channels:
+    ```python
+    >>> ome_zarr_container.set_channel_labels(["DAPI", "GFP", "RFP"])
+    ```
+
+=== "Channel Colors"
+    Update the display colors of the channels (hex format):
+    ```python
+    >>> ome_zarr_container.set_channel_colors(["0000FF", "00FF00", "FF0000"])
+    ```
+
+=== "Channel Windows"
+    Update the display windows (start/end values) for each channel:
+    ```python
+    >>> ome_zarr_container.set_channel_windows([(0, 255), (0, 1000), (0, 500)])
+    ```
+
+=== "Channel Windows from Percentiles"
+    Automatically compute display windows based on data percentiles:
+    ```python
+    >>> ome_zarr_container.set_channel_windows_with_percentiles(percentiles=(0.1, 99.9))
+    ```
+
+### Axes metadata
+
+You can update the axes names and units:
+
+=== "Axes Names"
+    Rename the axes in the metadata:
+    ```python
+    >>> ome_zarr_container.set_axes_names(["t", "c", "z", "y", "x"])
+    ```
+
+=== "Axes Units"
+    Set the space and time units:
+    ```python
+    >>> ome_zarr_container.set_axes_units(space_unit="micrometer", time_unit="second")
+    ```
+
+### Image name
+
+You can set the name of the image in the metadata:
+
+```python
+>>> ome_zarr_container.set_name("My Processed Image")
+```
+
+!!! note
+    The `set_name` method only updates the metadata. It does not change the group name or file paths.
+
 ## Accessing images / labels / tables
 
 To access images, labels, and tables, you can use the `get_image`, `get_label`, and `get_table` methods of the `OME-Zarr Container` object.
@@ -109,7 +168,7 @@ new_image = ome_zarr_container.derive_image(
     "data/new_ome.zarr", 
     overwrite=True, 
     shape=(16, 128, 128), 
-    xy_pixelsize=0.65, 
+    pixelsize=0.65, 
     z_spacing=1.0
 )
 ```
@@ -129,7 +188,7 @@ x = np.random.randint(0, 255, (16, 128, 128), dtype=np.uint8)
 new_ome_zarr_image = create_ome_zarr_from_array(
     store="random_ome.zarr", 
     array=x, 
-    xy_pixelsize=0.65, 
+    pixelsize=0.65, 
     z_spacing=1.0
 )
 ```
@@ -142,7 +201,7 @@ from ngio import create_empty_ome_zarr
 new_ome_zarr_image = create_empty_ome_zarr(
     store="empty_ome.zarr", 
     shape=(16, 128, 128), 
-    xy_pixelsize=0.65, 
+    pixelsize=0.65, 
     z_spacing=1.0
 )
 ```

{ngio-0.4.7 → ngio-0.5.0}/docs/getting_started/2_images.md

@@ -137,7 +137,7 @@ To read or write a specific region of the image defined in world coordinates, yo
 
 ```pycon exec="true" source="console" session="get_started"
 >>> from ngio import Roi
->>> roi = Roi(x=34.1, y=10, x_length=321.6, y_length=330) # Define a ROI in world coordinates
+>>> roi = Roi.from_values(slices={"x": (34.1, 321.6), "y": (10, 330)}, name=None) # Define a ROI in world coordinates
 >>> image.get_roi_as_numpy(roi) # Get the image data in the ROI as a numpy array
 >>> print(image.get_roi_as_numpy(roi).shape) # markdown-exec: hide
 ```

{ngio-0.4.7 → ngio-0.5.0}/docs/getting_started/3_tables.md

@@ -35,17 +35,19 @@ Ngio supports three types of tables: `roi_table`, `feature_table`, and `masking_
     cmap_array[0] = 0
     cmap = ListedColormap(cmap_array)
     image_3 = ome_zarr_container.get_image(path="3")
-    image_data = image_3.get_array(c=0)
+    image_data = image_3.get_as_numpy(c=0)
     image_data = np.squeeze(image_data)
     roi = roi_table.get("FOV_1")
-    roi = roi.to_roi_pixels(pixel_size=image_3.pixel_size)
+    roi = roi.to_pixel(pixel_size=image_3.pixel_size)
+    x_slice = roi.get("x")
+    y_slice = roi.get("y")
     #label_3 = ome_zarr_container.get_label("nuclei", pixel_size=image_3.pixel_size)
-    #label_data = label_3.get_array()
+    #label_data = label_3.get_as_numpy()
     #label_data = np.squeeze(label_data)
     fig, ax = plt.subplots(figsize=(8, 4))
     ax.set_title("FOV_1 ROI")
     ax.imshow(image_data, cmap='gray')
-    ax.add_patch(Rectangle((roi.x, roi.y), roi.x_length, roi.y_length, edgecolor='red', facecolor='none', lw=2))
+    ax.add_patch(Rectangle((x_slice.start, y_slice.start), x_slice.length, y_slice.length, edgecolor='red', facecolor='none', lw=2))
     #ax.imshow(label_data, cmap=cmap, alpha=0.6)
     # make sure the roi is centered
     ax.axis('off')
@@ -58,7 +60,7 @@ Ngio supports three types of tables: `roi_table`, `feature_table`, and `masking_
     ROIs can be used to slice the image data:
     ```pycon exec="true" source="console" session="get_started"
     >>> roi = roi_table.get("FOV_1")
-    >>> roi_data = image.get_roi(roi)
+    >>> roi_data = image.get_roi_as_numpy(roi)
     >>> roi_data.shape
     >>> print(roi_data.shape) # markdown-exec: hide
     ```
@@ -76,10 +78,10 @@ Ngio supports three types of tables: `roi_table`, `feature_table`, and `masking_
     cmap = ListedColormap(cmap_array)
     roi = roi_table.get("FOV_1")
     image_3 = ome_zarr_container.get_image(path="3")
-    image_data = image_3.get_roi(roi, c=0)
+    image_data = image_3.get_roi_as_numpy(roi, c=0)
     image_data = np.squeeze(image_data)
     #label_3 = ome_zarr_container.get_label("nuclei", pixel_size=image_3.pixel_size)
-    #label_data = label_3.get_array()
+    #label_data = label_3.get_as_numpy()
     #label_data = np.squeeze(label_data)
     fig, ax = plt.subplots(figsize=(8, 4))
     ax.set_title("FOV_1 ROI")
@@ -104,7 +106,7 @@ Ngio supports three types of tables: `roi_table`, `feature_table`, and `masking_
     ROIs can be used to slice the image data:
     ```pycon exec="true" source="console" session="get_started"
     >>> roi = masking_table.get_label(100)
-    >>> roi_data = image.get_roi(roi)
+    >>> roi_data = image.get_roi_as_numpy(roi)
     >>> roi_data.shape
     >>> print(roi_data.shape) # markdown-exec: hide
     ```
@@ -122,10 +124,10 @@ Ngio supports three types of tables: `roi_table`, `feature_table`, and `masking_
     cmap = ListedColormap(cmap_array)
     roi = masking_table.get_label(100)
     image_3 = ome_zarr_container.get_image(path="2")
-    image_data = image_3.get_roi(roi, c=0)
+    image_data = image_3.get_roi_as_numpy(roi, c=0)
     image_data = np.squeeze(image_data)
     label_3 = ome_zarr_container.get_label("nuclei", pixel_size=image_3.pixel_size)
-    label_data = label_3.get_roi(roi)
+    label_data = label_3.get_roi_as_numpy(roi)
     label_data = np.squeeze(label_data)
     fig, ax = plt.subplots(figsize=(8, 4))
     ax.set_title("Label 1 ROI")
@@ -156,7 +158,7 @@ Tables (differently from Images and Labels) can be purely in memory objects, and
     ```pycon exec="true" source="console" session="get_started"
     >>> from ngio.tables import RoiTable
     >>> from ngio import Roi
-    >>> roi = Roi(x=0, y=0, x_length=128, y_length=128, name="FOV_1")
+    >>> roi = Roi.from_values(slices={"x": (0, 128), "y": (0, 128)}, name="FOV_1")
     >>> roi_table = RoiTable(rois=[roi])
     >>> print(roi_table) # markdown-exec: hide
     ```

{ngio-0.4.7 → ngio-0.5.0}/docs/getting_started/4_masked_images.md

@@ -30,10 +30,10 @@ Let's create a masked image from the `nuclei` label:
 
 Since the `MaskedImage` is a subclass of `Image`, we can use all the methods available for `Image` objects.
 
-The two most notable exceptions are the `get_roi` and `set_roi` which now instead of requiring a `roi` object, require an integer `label`.
+The two most notable exceptions are the `get_roi_as_numpy` (or `get_roi_as_dask`) and `set_roi` which now instead of requiring a `roi` object, require an integer `label`.
 
 ```pycon exec="true" source="console" session="masked_images"
->>> roi_data = masked_image.get_roi(label=1009, c=0)
+>>> roi_data = masked_image.get_roi_as_numpy(label=1009, c=0)
 >>> roi_data.shape
 >>> print(roi_data.shape) # markdown-exec: hide
 ```
@@ -50,7 +50,7 @@ cmap_array = np.random.rand(1000, 3)
 cmap_array[0] = 0
 cmap = ListedColormap(cmap_array)
 
-image_data = masked_image.get_roi(label=1009, c=0)
+image_data = masked_image.get_roi_as_numpy(label=1009, c=0)
 image_data = np.squeeze(image_data)
 
 fig, ax = plt.subplots(figsize=(8, 4))
@@ -68,13 +68,13 @@ Additionally we can used the `zoom_factor` argument to get more context around t
 For example we can zoom out the ROI by a factor of `2`:
 
 ```pycon exec="true" source="console" session="masked_images"
->>> roi_data = masked_image.get_roi(label=1009, c=0, zoom_factor=2)
+>>> roi_data = masked_image.get_roi_as_numpy(label=1009, c=0, zoom_factor=2)
 >>> roi_data.shape
 >>> print(roi_data.shape) # markdown-exec: hide
 ```
 
 ```python exec="1" html="1" session="masked_images"
-image_data = masked_image.get_roi(label=1009, c=0, zoom_factor=2)
+image_data = masked_image.get_roi_as_numpy(label=1009, c=0, zoom_factor=2)
 image_data = np.squeeze(image_data)
 
 fig, ax = plt.subplots(figsize=(8, 4))
@@ -90,7 +90,7 @@ print(buffer.getvalue())
 
 ## Masked operations
 
-In addition to the `get_roi` method, the `MaskedImage` class also provides a masked operation method that allows you to perform reading and writing only on the masked pixels.
+In addition to the `get_roi_as_numpy` method, the `MaskedImage` class also provides a masked operation method that allows you to perform reading and writing only on the masked pixels.
 
 For these operations we can use the `get_roi_masked` and `set_roi_masked` methods.
 For example, we can use the `get_roi_masked` method to get the masked data for a specific label:
@@ -123,7 +123,7 @@ We can also use the `set_roi_masked` method to set the masked data for a specifi
 ```
 
 ```python exec="1" html="1" session="masked_images"
-masked_data = masked_image.get_roi(label=1009, c=0, zoom_factor=2)
+masked_data = masked_image.get_roi_as_numpy(label=1009, c=0, zoom_factor=2)
 masked_data = np.squeeze(masked_data)
 fig, ax = plt.subplots(figsize=(8, 4))
 ax.set_title("Masked Label 1009 ROI - After setting")

{ngio-0.4.7 → ngio-0.5.0}/docs/index.md

@@ -28,11 +28,11 @@ Ngio's mission is to streamline working with OME-Zarr files by providing a simpl
 ## Getting Started
 
 Refer to the [Getting Started](getting_started/0_quickstart.md) guide to integrate ngio into your workflows. We also provide a collection of [Tutorials](tutorials/image_processing.ipynb) to help you get up and running quickly.
-For more advanced usage and API documentation, see our [API Reference](api/ngio.md).
+For more advanced usage and API documentation, see our [API Reference](api/ome_zarr_container.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.
+Ngio supports OME-Zarr v0.4 and v0.5, with Zarr v2 and v3 storage formats.
 
 ## Development Status
 
@@ -51,7 +51,6 @@ Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher
 
 ### Upcoming Features
 
-- Support for OME-Zarr v0.5 and Zarr v3 (via `zarr-python` v3)
 - Enhanced performance optimizations (parallel iterators, optimized io strategies)
 
 ## Contributors

{ngio-0.4.7 → ngio-0.5.0}/docs/tutorials/create_ome_zarr.ipynb

@@ -42,7 +42,7 @@
     "ome_zarr = create_ome_zarr_from_array(\n",
     "    store=\"./data/human_mitosis.zarr\",\n",
     "    array=skimage.data.human_mitosis(),\n",
-    "    xy_pixelsize=0.1,  # Just a guess\n",
+    "    pixelsize=0.1,  # Just a guess\n",
     ")\n",
     "ome_zarr"
    ]
@@ -93,7 +93,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.13"
+   "version": "3.11.14"
   }
  },
  "nbformat": 4,