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.
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 |
label_prediction | Make predictions on the selected wells and write them to the OME-ZARR |
condition_registration | Register the experimental conditions in the OME-ZARR |
- 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/operio_fractal/dev/create_manifest.py
- Build a wheel file in the
dist
folder of the package withpython -m build
- Collect the tasks on a Fractal server
- 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..