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Fractal CZI Converters

Fractal CZI Converters is a collection of Fractal tasks that convert Zeiss CZI microscopy files into OME-Zarr format.

Supported Tasks

Task Output Description
Convert CZI Plate to OME-Zarr OME-Zarr HCS Plate Converts a multi-well plate acquisition stored in one or more CZI files
Convert CZI Image to OME-Zarr OME-Zarr Image Converts the scenes of a CZI file into a single standalone OME-Zarr image

Each converter reads the native Zeiss metadata embedded in the CZI file and produces a well-structured OME-Zarr dataset that can be viewed in tools like napari or processed with downstream Fractal tasks.

Installation

pip install fractal-czi-converters

How It Works

Each converter is implemented as a Fractal Compound Task that consists of two steps:

  1. Init task — Parses the CZI metadata, creates the OME-Zarr structure, and generates a parallelization list.
  2. Compute task — Reads the raw image tiles and writes them into the OME-Zarr dataset. This task runs in parallel across wells or images.

You configure the init task with one or more acquisitions (paths to your CZI files) and the converter handles the rest.

Condition Tables

You can attach experimental metadata (drug treatments, concentrations, replicates, etc.) to wells using a condition table CSV file. See the Condition Tables guide for details.

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: