Metadata-Version: 2.4
Name: ome-zarr-converters-tools
Version: 0.8.0
Summary: Tooling to build ome-zarr HCS plate converters
Project-URL: homepage, https://github.com/BioVisionCenter/ome-zarr-converters-tools
Project-URL: repository, https://github.com/BioVisionCenter/ome-zarr-converters-tools
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
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Description-Content-Type: text/markdown

# ome-zarr-converters-tools

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A Python library that provides shared utilities for building OME-Zarr image converters. It handles tile management, image registration, filtering, validation, and writing OME-Zarr datasets.

## Features

1. **Abstraction layer** for building OME-Zarr images and HCS plates from microscope metadata and image data
2. **Customizable pipeline** for filtering, validating, registering, and tiling images
3. **Python API** for building custom converters, with optional [Fractal](https://fractal-analytics-platform.github.io/fractal-server/) integration for parallel processing
4. **Flexible input**: parse tiles from DataFrames or construct them programmatically

### Architecture Diagram

![OME-Zarr Converters Tools Architecture](docs/ome-zarr-converter-tools.png)

## Getting Started

Install via pip:

```bash
pip install ome-zarr-converters-tools
```

## Documentation

For detailed documentation, tutorials, and API reference, visit the [official documentation](https://BioVisionCenter.github.io/ome-zarr-converters-tools/).

The documentation includes:

- [HCS Plate Tutorial](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/hcs_tutorial/) -- converting plate-based microscopy data
- [Single Images Tutorial](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/images_tutorial/) -- converting standalone images
- [Advanced Tutorial](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/advanced_tutorial/) -- programmatic tile construction with custom loaders
- [Fractal Tasks Guide](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/converters_as_fractal_tasks/) -- building parallel converters with the Fractal platform
- [Pipeline Configuration](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/pipeline/) -- filters, registration, tiling, and writer modes
- [API Reference](https://BioVisionCenter.github.io/ome-zarr-converters-tools/stable/api/)
