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Fractal UZH Converters

Fractal UZH Converters is a collection of Fractal tasks that convert High-Content Screening (HCS) plate data from various microscopes into OME-Zarr format.

Supported Microscopes

Microscope Manufacturer Task Name
Opera Phenix / Operetta PerkinElmer Convert Operetta Plate to OME-Zarr
ScanR Olympus Convert Olympus ScanR Plate to OME-Zarr
CQ3K Yokogawa Convert Yokogawa CQ3K Plate to OME-Zarr
CellVoyager Yokogawa Convert Yokogawa CellVoyager Plate to OME-Zarr
ImageXpress HCS.ai Molecular Devices Convert MD ImageXpress HCS.ai Plate to OME-Zarr

Each converter reads the microscope's native metadata and image files, then produces a well-structured OME-Zarr HCS plate that can be viewed in tools like napari or processed with downstream Fractal tasks.

Installation

pip install fractal-uzh-converters

How It Works

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

  1. Init task — Parses the microscope metadata, creates the OME-Zarr plate 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.

You configure the init task with one or more acquisitions (paths to your raw data directories) 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.