Fractal tasks for the Opera/Operetta microscope and drug response profiling
Project description
operetta-compose ![](https://pypi-camo.freetls.fastly.net/4e476dd859063f461fd736c88da5a6fb45afcde6/646f63732f696d616765732f6f706572657474612d636f6d706f73655f6c6f676f2e706e67)
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 |
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 |
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/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
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 under contract with eXact lab S.r.l..
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