semvec/pypi-packages huggingface dataset:
ome-zarr-converters-tools 0.7.0
Tooling to build ome-zarr HCS plate converters
License: BSD-3-Clause
Requires Python: <3.15,>=3.11

# 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/)