Fractal tasks for the Opera/Operetta microscope and drug response profiling

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Project description

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

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 dist folder of the package with python -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..

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fdsteffen

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This version

0.2.11

Apr 3, 2025

0.2.10

Mar 28, 2025

0.2.9

Mar 17, 2025

0.2.8

Mar 10, 2025

0.2.7

Mar 4, 2025

0.2.6

Jan 30, 2025

0.2.5

Jan 29, 2025

0.2.4

Dec 7, 2024

0.2.3

Nov 13, 2024

0.2.2

Oct 27, 2024

0.2.1

Sep 23, 2024

0.2.0

Jul 27, 2024

0.1.4

Jul 20, 2024

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