ome-zarr-converters-tools

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 integration for parallel processing
4. Flexible input: parse tiles from DataFrames or construct them programmatically

Architecture Diagram

Getting Started

Install via pip:

pip install ome-zarr-converters-tools

Documentation

For detailed documentation, tutorials, and API reference, visit the official documentation.

The documentation includes:

• HCS Plate Tutorial -- converting plate-based microscopy data
• Single Images Tutorial -- converting standalone images
• Advanced Tutorial -- programmatic tile construction with custom loaders
• Fractal Tasks Guide -- building parallel converters with the Fractal platform
• Pipeline Configuration -- filters, registration, tiling, and writer modes
• API Reference