fractal-uzh-converters 0.7.0

A collection of fractal tasks to convert HCS Plates to OME-Zarr

Fractal UZH Converters

A collection of Fractal tasks to convert High-Content Screening (HCS) plate data from several microscopes into OME-Zarr format.

Tasks

Task	Use case
Convert Operetta Plate to OME-Zarr	Operetta / Opera Phenix (Revvity) HCS plates.
Convert Evident ScanR Plate to OME-Zarr	ScanR (Evident) HCS plates.
Convert Yokogawa CQ3K Plate to OME-Zarr	CQ3K (Yokogawa) HCS plates.
Convert Yokogawa CellVoyager Plate to OME-Zarr	CellVoyager (Yokogawa) HCS plates.
Convert MD ImageXpress HCS.ai Plate to OME-Zarr	ImageXpress HCS.ai (Molecular Devices) HCS plates.
Convert Custom TIFF HCS Plate to OME-Zarr	Custom TIFF HCS plates from any source.
Convert Custom TIFF Images to OME-Zarr	Custom TIFF single images from any source.

Each task is a Fractal compound task: an init step parses the microscope metadata and builds the parallelization list, and a compute step writes the image data well-by-well (or image-by-image).

Installation

pip install fractal-uzh-converters

Part of the OME-Zarr converters ecosystem

This converter is a thin, format-specific layer built on ome-zarr-converters-tools, the shared engine that handles tiling, image registration, and OME-Zarr writing for the whole Fractal converter family. Because they all share that engine, every converter offers the same options, behavior, and development workflow.

Sibling converters built on the same tooling:

• fractal-czi-converters — Zeiss .czi
• fractal-lif-converters — Leica .lif
• fractal-nd2-converters — Nikon .nd2

Documentation

Full documentation — including the supported file layouts, all converter parameters, and the condition-table format — is available at https://fractal-analytics-platform.github.io/fractal-uzh-converters/.