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Changelog

[v0.1.1]

Chores

  • Align repository tooling with ome-zarr-converters-tools: adopt its .pre-commit-config.yaml (validate-pyproject v0.25, crate-ci/typos, astral-sh/ruff-pre-commit v0.15.17, nbstripout) with a per-repo _typos.toml, add a chores pixi task, bump GitHub Actions pins (checkout v7, codecov-action v7, action-gh-release v3, setup-python v6), and add a terse CLAUDE.md.

[v0.1.0]

Changed

  • Breaking: renamed the Convert CZI to OME-Zarr task to Convert CZI Image to OME-Zarr; renamed the czi_single package to czi_image, CziSingleAcqAcquisitionModel to CziImageAcquisitionModel, and convert_czi_single_acq_init_task to convert_czi_image_init_task.

Features

  • Add Convert CZI Image to OME-Zarr task to convert the scenes of a Zeiss CZI file into a single OME-Zarr image.
  • Add Convert CZI Plate to OME-Zarr task to convert multi-well plate CZI acquisitions into an OME-Zarr HCS plate, with support for merging multiple CZI files into one plate via shared plate name and distinct acquisition IDs.
  • Support mosaic scenes (CZI M dimension) via the mosaic_mode option (tiles / assembled).
  • Support condition tables to attach experimental metadata to plate wells.
  • Add Python API functions (convert_czi_image, convert_czi_plate) for programmatic use outside Fractal.

Chores

  • Build on ome-zarr-converters-tools>=0.10.0,<0.11.0, fractal-task-tools>=0.5.0,<0.6.0, and ngio>=0.5.8,<0.6.0.
  • Read CZI files with czifile.
  • Add GitHub Actions CI (build, test, coverage, PyPI release) and MkDocs documentation.
  • Remove the local SingleImage setup handler — built into ome-zarr-converters-tools>=0.10.0.

Docs

  • Add "How to Run the Converters" page and per-converter Python API sections.