ngio 0.1.6__tar.gz → 0.2.0__tar.gz

ngio-0.2.0/.github/scripts/download_data.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+# filepath: download_zarr_datasets.sh
+
+# Default download directory
+DOWNLOAD_DIR="data"
+
+# Create download directory if it doesn't exist
+mkdir -p "$DOWNLOAD_DIR"
+
+# Function to check MD5 hash
+check_md5() {
+    local file="$1"
+    local expected="$2"
+    
+    if [[ "$(uname)" == "Darwin" ]]; then
+        # macOS
+        actual=$(md5 -q "$file")
+    else
+        # Linux/Ubuntu
+        actual=$(md5sum "$file" | awk '{print $1}')
+    fi
+
+    echo "Expected: $expected"
+    echo "Actual: $actual"
+    
+    if [[ "$actual" == "$expected" ]]; then
+        return 0  # Success
+    else
+        return 1  # Failure
+    fi
+}
+
+# Function to download a file
+download_file() {
+    local url="$1"
+    local output="$2"
+    
+    echo "Downloading $url to $output..."
+    
+    if command -v curl &> /dev/null; then
+        curl -L -o "$output" "$url"
+    elif command -v wget &> /dev/null; then
+        wget -O "$output" "$url"
+    else
+        echo "Error: Neither curl nor wget is available. Please install one of them."
+        exit 1
+    fi
+}
+
+# Function to process a dataset
+process_dataset() {
+    local filename="$1"
+    local url="$2"
+    local expected_hash="$3"
+    
+    local file_path="$DOWNLOAD_DIR/$filename"
+    
+    echo "Processing $filename..."
+    
+    # Check if file exists and has the correct hash
+    if [[ -f "$file_path" ]] && check_md5 "$file_path" "$expected_hash"; then
+        echo "File exists and has the correct hash."
+    else
+        # File doesn't exist or has incorrect hash
+        if [[ -f "$file_path" ]]; then
+            echo "File exists but has incorrect hash. Redownloading..."
+        else
+            echo "File doesn't exist. Downloading..."
+        fi
+        
+        download_file "$url" "$file_path"
+        
+        # Verify the downloaded file
+        if check_md5 "$file_path" "$expected_hash"; then
+            echo "Download successful and hash verified."
+        else
+            echo "Error: Downloaded file has incorrect hash."
+            return 1
+        fi
+    fi
+    
+    echo "File is ready at $file_path"
+    return 0
+}
+
+# Process the CardioMyocyte dataset
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "https://zenodo.org/records/13305156/files/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr.zip" \
+                "efc21fe8d4ea3abab76226d8c166452c"
+
+process_dataset "20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "https://zenodo.org/records/13305316/files/20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr.zip" \
+                "3ed3ea898e0ed42d397da2e1dbe40750"
+# To add more datasets, add more calls to process_dataset like this:
+# process_dataset "filename.zip" "download_url" "expected_md5_hash"
+
+echo "All datasets processed."

ngio-0.2.0/.github/workflows/build_docs.yml

@@ -0,0 +1,61 @@
+name: Build Docs
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+
+jobs:
+  download-test-ome-zarr:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check and Download Artifacts
+        run: |
+          bash .github/scripts/download_data.sh
+
+  deploy:
+    name: Deploy Docs
+    needs: download-test-ome-zarr
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: 🐍 Set up Python
+        uses: actions/setup-python@v5
+        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: 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"
+          else
+            mike deploy --push dev
+            mike set-default --push dev
+            echo "Deployed development version"
+          fi

{ngio-0.1.6 → ngio-0.2.0}/.github/workflows/ci.yml

@@ -26,21 +26,49 @@ jobs:
       - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
+  
+  download-test-ome-zarr:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check and Download Artifacts
+        run: |
+          bash .github/scripts/download_data.sh
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: data
+          path: data
+
+
   test:
     name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    needs: download-test-ome-zarr
     runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
-        # 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]
+        exclude:
+          - python-version: "3.11"
+            platform: windows-latest
+          - python-version: "3.12"
+            platform: windows-latest
 
     steps:
       - uses: actions/checkout@v4
 
+      - uses: actions/download-artifact@v4
+        with:
+          name: data
+          path: data
+
+      - name: Check Artifacts
+        run: |
+          ls -l data
+
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
@@ -78,30 +106,6 @@ jobs:
           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

{ngio-0.1.6 → ngio-0.2.0}/.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-0.1.6 → ngio-0.2.0}/.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
         args: [--force-exclude, --write-changes]
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.4.8
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [--fix]  # may also add '--unsafe-fixes'

{ngio-0.1.6 → ngio-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.1.6
+Version: 0.2.0
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -10,55 +10,40 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
+Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata>=0.8.0
 Requires-Dist: dask[array]
+Requires-Dist: dask[distributed]
+Requires-Dist: filelock
 Requires-Dist: numpy
+Requires-Dist: ome-zarr-models
 Requires-Dist: pandas>=1.2.0
+Requires-Dist: pooch
 Requires-Dist: pydantic
 Requires-Dist: requests
-Provides-Extra: core
-Requires-Dist: dask-image; extra == 'core'
-Requires-Dist: dask[distributed]; extra == 'core'
-Requires-Dist: zarr<3; extra == 'core'
-Provides-Extra: dev2
-Requires-Dist: dask-image; extra == 'dev2'
-Requires-Dist: dask[distributed]; extra == 'dev2'
-Requires-Dist: ipython; extra == 'dev2'
-Requires-Dist: matplotlib; extra == 'dev2'
-Requires-Dist: mypy; extra == 'dev2'
-Requires-Dist: napari; extra == 'dev2'
-Requires-Dist: notebook; extra == 'dev2'
-Requires-Dist: pdbpp; extra == 'dev2'
-Requires-Dist: plotly; extra == 'dev2'
-Requires-Dist: pre-commit; extra == 'dev2'
-Requires-Dist: pyqt5; extra == 'dev2'
-Requires-Dist: pytest; extra == 'dev2'
-Requires-Dist: pytest-cov; extra == 'dev2'
-Requires-Dist: rich; extra == 'dev2'
-Requires-Dist: ruff; extra == 'dev2'
-Requires-Dist: scikit-image; extra == 'dev2'
-Requires-Dist: zarr<3; extra == 'dev2'
-Provides-Extra: dev3
-Requires-Dist: dask-image; extra == 'dev3'
-Requires-Dist: dask[distributed]; extra == 'dev3'
-Requires-Dist: ipython; extra == 'dev3'
-Requires-Dist: mypy; extra == 'dev3'
-Requires-Dist: notebook; extra == 'dev3'
-Requires-Dist: pdbpp; extra == 'dev3'
-Requires-Dist: pre-commit; extra == 'dev3'
-Requires-Dist: pytest; extra == 'dev3'
-Requires-Dist: pytest-cov; extra == 'dev3'
-Requires-Dist: rich; extra == 'dev3'
-Requires-Dist: ruff; extra == 'dev3'
-Requires-Dist: zarr==v3.0.0-alpha.4; extra == 'dev3'
+Requires-Dist: xarray
+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: pyqt5; extra == 'dev'
+Requires-Dist: rich; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: scikit-image; extra == 'dev'
 Provides-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'
@@ -66,11 +51,13 @@ Requires-Dist: mkdocs-git-revision-date-localized-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: zarr<3; extra == 'test'
+Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 
 # NGIO - Next Generation file format IO
@@ -78,7 +65,7 @@ Description-Content-Type: text/markdown
 [![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/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![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.
@@ -86,9 +73,9 @@ NGIO is a Python library to streamline OME-Zarr image analysis workflows.
 **Main Goals:**
 
 - Abstract object base API for handling OME-Zarr files
-- Powefull iterators for processing data using common access patterns
+- 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/)
-- Validate OME-Zarr files
+- 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/)
 
@@ -108,7 +95,7 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | 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 |
+| 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 |

{ngio-0.1.6 → ngio-0.2.0}/README.md

@@ -3,7 +3,7 @@
 [![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/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml)
+[![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.
@@ -11,9 +11,9 @@ NGIO is a Python library to streamline OME-Zarr image analysis workflows.
 **Main Goals:**
 
 - Abstract object base API for handling OME-Zarr files
-- Powefull iterators for processing data using common access patterns
+- 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/)
-- Validate OME-Zarr files
+- 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/)
 
@@ -33,7 +33,7 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | 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 |
+| 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 |

{ngio-0.1.6 → ngio-0.2.0}/_typos.toml

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

ngio-0.2.0/docs/api/common.md

@@ -0,0 +1,6 @@
+# ngio.common API documentation
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/api/hcs.md

@@ -0,0 +1,6 @@
+# ngio.hcs API documentation
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/api/images.md

@@ -0,0 +1,6 @@
+# ngio.images API documentation
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/api/ngio.md

@@ -0,0 +1,6 @@
+# ngio API documentation
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/api/tables.md

@@ -0,0 +1,6 @@
+# ngio.tables API documentation
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/api/utils.md

@@ -0,0 +1,6 @@
+# ngio.utils
+
+!!! warning
+    Coming soon, ngio API documentation is not yet available.
+    If you have any questions please reach out to us on GitHub or via email.
+    We are happy to help you with any questions or issues you may have.

ngio-0.2.0/docs/code_of_conduct.md

@@ -0,0 +1,2 @@
+!!! warning
+    The library is still in the early stages of development, the code of conduct is not yet established.

ngio-0.2.0/docs/contributing.md

@@ -0,0 +1,4 @@
+!!! warning
+    The library is still in the early stages of development, no contribution guidelines are established yet.
+    But contributions are welcome! Please open an issue or a pull request to discuss your ideas.
+    We are looking for contributors to help us improve the library and documentation.

ngio-0.2.0/docs/getting_started/0_quickstart.md

@@ -0,0 +1,99 @@
+# Quickstart
+
+`ngio` is a Python package that provides a simple and intuitive API for reading and writing data to and from various data sources. This guide will walk you through the basics of using `ngio` to read and write data.
+
+## Installation
+
+`ngio` can be installed from PyPI, conda-forge, or from source.
+
+- Python `>=3.11`
+
+=== "pip"
+
+    The recommended way to install `ngio` is from PyPI using pip:
+
+    ```bash
+    pip install ngio
+    ```
+
+=== "mamba/conda"
+
+    Alternatively, you can install `ngio` using mamba:
+
+    ```bash
+    mamba install -c conda-forge ngio
+    ```
+
+    or conda:
+
+    ```bash
+    conda install -c conda-forge ngio
+    ```
+
+=== "Source"
+
+    1. Clone the repository:
+    ```bash
+    git clone https://github.com/fractal-analytics-platform/ngio.git
+    cd ngio
+    ```
+
+    2. Install the package:
+    ```bash
+    pip install .
+    ```
+
+### Troubleshooting
+
+Please report installation problems by opening an issue on our [GitHub repository](https://github.com/fractal-analytics-platform/ngio).
+
+## Setup some test data
+
+Let's start by downloading a sample OME-Zarr dataset to work with.
+
+```python exec="true" source="material-block" session="quickstart"
+from pathlib import Path
+from ngio.utils import download_ome_zarr_dataset
+
+# Download a sample dataset
+download_dir = Path("./data")
+download_dir = Path(".").absolute().parent.parent / "data" # markdown-exec: hide
+hcs_path = download_ome_zarr_dataset("CardiomyocyteSmallMip", download_dir=download_dir)
+image_path = hcs_path / "B" / "03" / "0"
+```
+
+## Open an OME-Zarr image
+
+Let's start by opening an OME-Zarr file and inspecting its contents.
+
+```pycon exec="true" source="console" session="quickstart"
+>>> from ngio import open_ome_zarr_container
+>>> ome_zarr_container = open_ome_zarr_container(image_path)
+>>> ome_zarr_container
+>>> print(ome_zarr_container) # markdown-exec: hide
+```
+
+### What is the OmeZarr container?
+
+The `ome_zarr_container` is the core of ngio and the entry point to working with OME-Zarr images. It provides high-level access to the image metadata, images, labels, and tables.
+
+### What is the OmeZarr container not?
+
+The `OmeZarr Container` object does not allow the user to interact with the image data directly. For that, we need to use the `Image`, `Label`, and `Table` objects.
+
+## Next steps
+
+To learn how to work with the `OmeZarr Container` object, but also with the image, label, and table data, check out the following guides:
+
+- [Ome-Zarr Container](1_ome_zarr_containers.md): An overview on how to user the Ome-Zarr Container object and how to create new images and labels.
+- [Images/Labels](2_images.md): To know more on how to work with image data.
+- [Tables](3_tables.md): To know more on how to work with table data, and how you can combine tables with image data.
+- [Masked Images/Labels](4_masked_images.md): To know more on how to work with masked image data.
+- [HCS Plates](5_hcs.md): To know more on how to work with HCS Plate data.
+
+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.