operetta-compose

Fractal tasks to convert and process images from Perkin-Elmer Opera/Operetta high-content microscopes. Workflows for drug response profiling built upon the OME-ZARR file standard.

Task library

Currently the following tasks are available:

Task	Description
harmony_to_ome_zarr	Convert TIFFs which were exported from Harmony (Operetta/Opera, Perkin-Elmer) to OME-ZARR
stardist_segmentation	Segment cells with Stardist
regionprops_measurement	Take measurements using regionprops and write the features to the OME-ZARR
feature_classification	Classify cells using the napari-feature-classifier and write them to the OME-ZARR
condition_registration	Register the experimental conditions in the OME-ZARR

Development and installation in Fractal

1. Install the package in dev mode with python -m pip install -e ".[dev]"
2. Develop the function according to the Fractal API
3. Update the image list and the Fractal manifest with python src/operetta_compose/dev/create_manifest.py
4. Build a wheel file in the dist folder of the package with python -m build
5. Collect the tasks on a Fractal server

Updating docs

1. Update the documentation under /docs
2. Update the function API with quartodoc build
3. Preview the documentation with quarto preview

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Fractal is developed by the UZH BioVisionCenter under the lead of @jluethi and under contract with eXact lab S.r.l..