Awesome
operetta-compose <img align="right" height="150" src="https://raw.githubusercontent.com/leukemia-kispi/operetta-compose/master/docs/images/operetta-compose_logo.png">
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
- Install the package in dev mode with
python -m pip install -e ".[dev]" - Develop the function according to the Fractal API
- Update the image list and the Fractal manifest with
python src/operetta_compose/dev/create_manifest.py - Build a wheel file in the
distfolder of the package withpython -m build - Collect the tasks on a Fractal server
Updating docs
- Update the documentation under
/docs - Update the function API with
quartodoc build - Preview the documentation with
quarto preview
Fractal is developed by the UZH BioVisionCenter under the lead of @jluethi and under contract with eXact lab S.r.l..