fractal-czi-converters 0.1.2

Converter from CZI files (Zeiss Microscope) to OME-Zarr format.

Fractal CZI Converters

A collection of Fractal tasks to convert Zeiss .czi files into OME-Zarr format.

Tasks

Task	Use case
Convert CZI Plate to OME-Zarr	Convert one or more .czi files containing a multi-well plate acquisition into an OME-Zarr HCS plate.
Convert CZI Image to OME-Zarr	Convert the scenes of a .czi file into a single standalone OME-Zarr image.

Each task is a Fractal compound task: an init step parses the .czi 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-czi-converters

Part of the Fractal 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-lif-converters — Leica .lif
• fractal-nd2-converters — Nikon .nd2
• fractal-uzh-converters — HCS plates (Operetta, ScanR, CQ3K, CellVoyager, ImageXpress, custom TIFF)

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-czi-converters/.