ngio 0.1.0b3__tar.gz → 0.4.6__tar.gz

ngio-0.4.6/.github/pull_request_template.md

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

ngio-0.4.6/.github/workflows/build_docs.yml

@@ -0,0 +1,66 @@
+name: Build Docs
+
+on:
+  push:
+    branches:
+      - dev
+      - main
+    tags:
+      - "v*"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  deploy:
+    name: Deploy Docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[dev]
+          python -m pip install .[docs]
+
+      - name: Configure Git user
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+        
+      - name: Restore shared data cache
+        id: cache-data
+        uses: actions/cache@v4
+        with:
+          path: data/
+          key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
+          restore-keys: |
+            "${{ runner.os }}-data-"
+            
+      - name: Deploy docs
+        run: |
+          VERSION=$(echo $GITHUB_REF | sed 's/refs\/tags\///' | sed 's/refs\/heads\///')
+          echo "Deploying version $VERSION"
+          # Check if the version is a stable release
+          # Meaning that starts with "v" and contains only numbers and dots
+          if [[ $GITHUB_REF == refs/tags/* ]] && [[ $VERSION =~ ^v[0-9.]+$ ]]; then
+            mike deploy --push --update-aliases $VERSION stable
+            mike set-default --push stable
+            echo "Deployed stable version $VERSION (stable)"
+
+          elif [[ $GITHUB_REF == refs/heads/dev ]]; then
+            mike deploy --push dev
+            mike set-default --push dev
+            echo "Deployed development version (dev)"
+          fi

{ngio-0.1.0b3 → ngio-0.4.6}/.github/workflows/ci.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - dev
     tags:
       - "v*"
   pull_request:
@@ -23,7 +24,7 @@ jobs:
     # included in the sdist (unless explicitly excluded)
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - run: pipx run check-manifest
 
   test:
@@ -32,17 +33,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-        # Skip Windows for now It's seems there are some issues with the
-        # ZarrV3 on Windows
+        python-version: ["3.11", "3.12", "3.13"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        # platform: [ubuntu-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           cache-dependency-path: "pyproject.toml"
@@ -53,6 +51,15 @@ jobs:
           python -m pip install -U pip
           # if running a cron job, we add the --pre flag to test against pre-releases
           python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+      
+      - name: Restore shared data cache
+        id: cache-data
+        uses: actions/cache@v4
+        with:
+          path: data/
+          key: "${{ runner.os }}-data-${{ hashFiles('tests/conftest.py') }}"
+          restore-keys: |
+            "${{ runner.os }}-data-"
 
       - name: 🧪 Run Tests
         run: pytest
@@ -72,36 +79,11 @@ jobs:
           update_existing: true
 
       - name: Coverage
-        if: ${{ matrix.python-version == '3.10' }} && ${{ matrix.platform == 'ubuntu-latest' }}
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: /home/runner/work/ngio/ngio/coverage.xml
 
-  zarrv3:
-    name: Test zarr-python v3 compatibility
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
-          cache-dependency-path: "pyproject.toml"
-          cache: "pip"
-
-      - name: Install Dependencies
-        run: |
-          python -m pip install -U pip
-          # if running a cron job, we add the --pre flag to test against pre-releases
-          python -m pip install .[dev3] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
-
-      - name: 🧪 Run Tests
-        run: pytest
-        continue-on-error: true
-
   deploy:
     name: Deploy
     needs: test
@@ -116,12 +98,12 @@ jobs:
       contents: write
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: 🐍 Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 

{ngio-0.1.0b3 → ngio-0.4.6}/.gitignore

@@ -116,8 +116,19 @@ ENV/
 pixi.lock
 *.egg-info
 
+# Ignore all .zarr directories
 *.zarr
+# but allow .zarr in tests/data
+!tests/data/**/**/test_*.zarr
 
 # ignore data directory
-data/
-*.zip
+./data/
+*.zip
+
+src/ngio/_v01
+tests/_v01
+
+# Ignore locks
+*.lock
+
+benchmark/*

{ngio-0.1.0b3 → ngio-0.4.6}/.pre-commit-config.yaml

@@ -9,19 +9,19 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.18
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/crate-ci/typos
-    rev: typos-dict-v0.11.20
+    rev: v1.36.2
     hooks:
       - id: typos
         #args: [--force-exclude]  # omitting --write-changes
         args: [--force-exclude, --write-changes]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.12.12
     hooks:
       - id: ruff
         args: [--fix]  # may also add '--unsafe-fixes'
@@ -37,7 +37,7 @@ repos:
   #      #   - numpy
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
 

ngio-0.4.6/CHANGELOG.md

@@ -0,0 +1,98 @@
+# Changelog
+
+## [v0.4.6]
+
+### Bug Fixes
+- Fix channel selection from `wavelenght_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-0.4.6/PKG-INFO

@@ -0,0 +1,142 @@
+Metadata-Version: 2.4
+Name: ngio
+Version: 0.4.6
+Summary: Next Generation file format IO
+Project-URL: homepage, https://github.com/BioVisionCenter/ngio
+Project-URL: repository, https://github.com/BioVisionCenter/ngio
+Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>
+License: BSD-3-Clause
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Typing :: Typed
+Requires-Python: <3.14,>=3.11
+Requires-Dist: aiohttp
+Requires-Dist: anndata<0.11.4,>=0.8.0
+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: pillow
+Requires-Dist: polars
+Requires-Dist: pooch
+Requires-Dist: pyarrow
+Requires-Dist: pydantic
+Requires-Dist: requests
+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'
+Requires-Dist: notebook; extra == 'dev'
+Requires-Dist: pdbpp; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: pympler; extra == 'dev'
+Requires-Dist: pyqt5; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-image; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: griffe-typingdoc; extra == 'docs'
+Requires-Dist: markdown-exec[ansi]; extra == 'docs'
+Requires-Dist: matplotlib; extra == 'docs'
+Requires-Dist: mike; extra == 'docs'
+Requires-Dist: mkdocs; extra == 'docs'
+Requires-Dist: mkdocs-autorefs; extra == 'docs'
+Requires-Dist: mkdocs-git-committers-plugin-2; extra == 'docs'
+Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
+Requires-Dist: mkdocs-include-markdown-plugin; extra == 'docs'
+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: scikit-image; extra == 'docs'
+Requires-Dist: tabulate; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: scikit-image; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Ngio - Next Generation file format IO
+
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/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/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/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
+
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
+- Extract and analyze specific regions of interest
+- Store measurements and other metadata in the OME-Zarr container
+- Extensible & modular allowing users to define custom table schemas and on disk serialization
+
+### 🔄 Scalable Data Processing
+
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://BioVisionCenter.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
+
+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
+- ✅ Image processing iterators
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### 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 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/BioVisionCenter/ngio/blob/main/LICENSE) for details.

ngio-0.4.6/README.md

@@ -0,0 +1,75 @@
+# Ngio - Next Generation file format IO
+
+[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/BioVisionCenter/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/BioVisionCenter/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/BioVisionCenter/ngio/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/BioVisionCenter/ngio/graph/badge.svg?token=FkmF26FZki)](https://codecov.io/gh/BioVisionCenter/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
+
+- Tight integration with [tabular data](https://biovisioncenter.github.io/ngio/stable/table_specs/overview/)
+- Extract and analyze specific regions of interest
+- Store measurements and other metadata in the OME-Zarr container
+- Extensible & modular allowing users to define custom table schemas and on disk serialization
+
+### 🔄 Scalable Data Processing
+
+- Powerful iterators for building scalable and generalizable image processing pipelines
+- Extensible mapping mechanism for custom parallelization strategies
+
+## Installation
+
+You can install ngio via pip:
+
+```bash
+pip install ngio
+```
+
+To get started check out the [Quickstart Guide](https://BioVisionCenter.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
+
+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
+- ✅ Image processing iterators
+- ✅ Streaming from remote sources
+- ✅ Documentation and examples
+
+### 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 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/BioVisionCenter/ngio/blob/main/LICENSE) for details.

{ngio-0.1.0b3 → ngio-0.4.6}/_typos.toml

@@ -1,3 +1,4 @@
 [default.extend-words]
 # Don't correct the surname "Teh"
-OME = "OME"
+OME = "OME"
+FO = "FO"

ngio-0.4.6/docs/api/hcs.md

@@ -0,0 +1,17 @@
+# HCS API Documentation
+
+## Open a Plate
+
+::: ngio.open_ome_zarr_plate
+
+## ngio.OmeZarrPlate Class Reference
+
+::: ngio.OmeZarrPlate
+
+## Open a Well
+
+::: ngio.open_ome_zarr_well
+
+## ngio.OmeZarrWell Class Reference
+
+::: ngio.OmeZarrWell

ngio-0.4.6/docs/api/images.md

@@ -0,0 +1,17 @@
+# Images Like: API Documentation
+
+## Open an Image
+
+::: ngio.open_image
+
+## ngio.Image Class Reference
+
+::: ngio.Image
+
+## Open a Label
+
+::: ngio.open_label
+
+## ngio.Label Class Reference
+
+::: ngio.Label

ngio-0.4.6/docs/api/iterators.md

@@ -0,0 +1,17 @@
+# Iterators API Reference
+
+## ImageProcessingIterator
+
+::: ngio.experimental.iterators.ImageProcessingIterator
+
+## SegmentationIterator
+
+::: ngio.experimental.iterators.SegmentationIterator
+
+## MaskedSegmentationIterator
+
+::: ngio.experimental.iterators.MaskedSegmentationIterator
+
+## FeatureExtractorIterator
+     
+::: ngio.experimental.iterators.FeatureExtractorIterator

ngio-0.4.6/docs/api/ngio/common.md

@@ -0,0 +1,3 @@
+# ngio.common API documentation
+
+::: ngio.common

ngio-0.4.6/docs/api/ngio/hcs.md

@@ -0,0 +1,3 @@
+# ngio.hcs API documentation
+
+::: ngio.hcs

ngio-0.4.6/docs/api/ngio/images.md

@@ -0,0 +1,3 @@
+# ngio.images API documentation
+
+::: ngio.images

ngio-0.4.6/docs/api/ngio/io_pipes.md

@@ -0,0 +1,3 @@
+# ngio.io_pipes API documentation
+
+::: ngio.io_pipes

ngio-0.4.6/docs/api/ngio/iterators.md

@@ -0,0 +1,3 @@
+# ngio.iterators API documentation
+
+::: ngio.experimental.iterators

ngio-0.4.6/docs/api/ngio/ngio.md

@@ -0,0 +1,3 @@
+# ngio API documentation
+
+::: ngio

ngio-0.4.6/docs/api/ngio/tables.md

@@ -0,0 +1,3 @@
+# ngio.tables API documentation
+
+::: ngio.tables

ngio-0.4.6/docs/api/ngio/transforms.md

@@ -0,0 +1,3 @@
+# ngio.transforms API documentation
+
+::: ngio.transforms

ngio-0.4.6/docs/api/ngio/utils.md

@@ -0,0 +1,3 @@
+# ngio.utils
+
+::: ngio.utils

ngio-0.4.6/docs/api/ome_zarr_container.md

@@ -0,0 +1,14 @@
+# OmeZarrContainer: API Documentation
+
+## Open an OME-Zarr Container
+
+::: ngio.open_ome_zarr_container
+
+## Create an OME-Zarr Container
+
+::: ngio.create_empty_ome_zarr
+::: ngio.create_ome_zarr_from_array
+
+## OmeZarrContainer Class
+
+::: ngio.OmeZarrContainer

ngio-0.4.6/docs/api/tables.md

@@ -0,0 +1 @@
+# Ngio Tables API Documentation