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README.md

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# ngio Workshop
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Hands-on workshop materials for [ngio](https://github.com/fractal-analytics-platform/ngio), a Python library for reading and writing OME-Zarr / NGFF bioimages. Notebooks are built with [marimo](https://marimo.io) for an interactive, reproducible experience.
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Hands-on workshop materials to get started with [ngio](https://biovisioncenter.github.io/ngio). ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.
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Each notebook is self-contained: it declares its own dependencies inline and marimo uses [uv](https://docs.astral.sh/uv/) to create an isolated environment automatically.
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On first run uv will create an isolated environment for the notebook and install its dependencies. This takes a minute; subsequent runs are instant.
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## Workshop modules
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| Module | Topic |
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|--------|-------|
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| [1 — Introduction to ngio](notebooks/1_ngio_basics.py) | OME-Zarr containers, images, labels, and tables |
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## Documentation
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Live notebooks (read-only): https://&lt;your-org&gt;.github.io/ngio-workshop/
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You can find view a static version of the notebooks in the [documentation](https://biovisioncenter.github.io/ngio-workshop/).
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To build docs locally:
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Or you can build the documentation locally with:
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```bash
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uv run docs/build.py
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```
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## Workshop modules
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| Module | Topic |
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|--------|-------|
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| [1 — Introduction to ngio](notebooks/1_ngio_basics.py) | OME-Zarr containers, images, labels, and tables |

docs/index.html

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<div class="badge">Workshop</div>
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<h1>ngio Workshop</h1>
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<p class="subtitle">
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Hands-on notebooks for <a href="https://github.com/fractal-analytics-platform/ngio">ngio</a>,
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a Python library for reading and writing OME-Zarr bioimages.
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Hands-on notebooks for learning the basics of <a href="https://github.com/fractal-analytics-platform/ngio">ngio</a>.
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</p>
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</div>
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</header>
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<main>
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<section class="install">
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<div class="section-label">Installation</div>
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<div class="section-label">Running the Notebooks</div>
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<div class="install-block">
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<p>Install <strong>ngio</strong> with pip:</p>
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<pre><code>pip install ngio</code></pre>
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<p>Or with uv:</p>
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<pre><code>uv add ngio</code></pre>
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<p>The notebooks are self-contained and manage their own dependencies. You only need <a href="https://docs.astral.sh/uv/">uv</a> installed.</p>
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<p>Clone the repository:</p>
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<pre><code>git clone https://github.com/fractal-analytics-platform/ngio-workshop.git
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cd ngio-workshop</code></pre>
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<p>Run a notebook interactively:</p>
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<pre><code>uvx marimo run --sandbox notebooks/1_ngio_basics.py</code></pre>
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<p>Or open it for editing:</p>
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<pre><code>uvx marimo edit --sandbox notebooks/1_ngio_basics.py</code></pre>
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</div>
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</section>
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<section class="notebooks">
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<div class="section-label">Notebooks</div>
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<div class="nb-list">
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<!-- notebooks:start -->
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<a class="nb-card" href="1_ngio_basics.html">
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<span class="nb-num">1</span>
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<span class="nb-title">Introduction to ngio</span>
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<span class="nb-arrow">&#8594;</span>
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</a>
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<!-- notebooks:end -->
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</div>
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</section>

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