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czitools.export_tools #

OME-Zarr / OME-NGFF export tools for czitools (Stage 5).

Convert CZI files to OME-Zarr, including HCS (high-content-screening) plate layouts. The default ngff-zarr backend writes OME-NGFF 0.6 images; its HCS and RFC-9 OZX writers use 0.5. The ome-zarr-py compatibility backend writes its current 0.5 format. A MagicGUI application is also provided.

These features require optional dependencies. Install them with::

pip install "czitools[omezarr]"        # conversion + validation
pip install "czitools[omezarr-gui]"    # additionally the MagicGUI app

Public API (import lazily; a clear :class:ImportError is raised when the optional dependencies are missing)::

from czitools.export_tools import (
    convert_czi2hcs_ngff,
    convert_czi2hcs_omezarr,
    write_omezarr,
    write_omezarr_ngff,
    convert_hcs_omezarr2ozx,
    validate_ome_zarr,
    resolve_hcs_layout,
    compression_type,
    omezarr_package,
    setup_logging,
    run_gui,
)

Modules:

  • conversion –

    Core CZI -> OME-Zarr conversion functions.

  • display –

    Image display helpers for the OME-Zarr export tools.

  • gui –

    MagicGUI Application for CZI to OME-ZARR Conversion

  • plate –

    HCS plate helpers for the OME-Zarr export tools.

  • resolver –

    Canonical HCS layout resolver for OME-Zarr export (Stage 5.5).

  • validation –

    Validate local OME-Zarr image and HCS stores.