Metadata-Version: 2.2
Name: operetta-compose
Version: 0.2.5
Summary: Fractal tasks for the Opera/Operetta microscope and drug response profiling
Author-email: Fabio Steffen <fabio.steffen@uzh.ch>
License: BSD-3-Clause
Project-URL: Documentation, https://leukemia-kispi.github.io/operetta-compose/
Project-URL: Repository, https://github.com/leukemia-kispi/operetta-compose.git
Project-URL: Issues, https://github.com/leukemia-kispi/operetta-compose/issues
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: fractal-tasks-core
Requires-Dist: ome-zarr
Requires-Dist: imagecodecs
Requires-Dist: tqdm
Requires-Dist: xmltodict
Requires-Dist: pydantic
Requires-Dist: csbdeep
Requires-Dist: stardist
Requires-Dist: tensorflow
Requires-Dist: tensorflow-metal; platform_system == "Darwin"
Requires-Dist: napari-feature-classifier
Provides-Extra: dev
Requires-Dist: devtools; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: requests; extra == "dev"
Requires-Dist: build; extra == "dev"
Requires-Dist: jsonschema; extra == "dev"
Requires-Dist: bumpver; extra == "dev"
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-dependency; extra == "dev"

# operetta-compose <img align="right" height="150" src="https://raw.githubusercontent.com/leukemia-kispi/operetta-compose/master/docs/images/operetta-compose_logo.png">

[![Docs Status](https://github.com/leukemia-kispi/operetta-compose/actions/workflows/build.yml/badge.svg)](https://github.com/leukemia-kispi/operetta-compose/actions/workflows/build_docs.yml)
[![PyPI](https://img.shields.io/pypi/v/operetta-compose)](https://pypi.org/project/operetta-compose/)

[Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/) 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](https://github.com/fractal-napari-plugins-collection/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](https://fractal-analytics-platform.github.io/version_2/)
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`

---

[Fractal](https://fractal-analytics-platform.github.io/fractal-tasks-core/) is developed by the [UZH BioVisionCenter](https://www.biovisioncenter.uzh.ch/de.html) under the lead of [@jluethi](https://github.com/jluethi) and under contract with [eXact lab S.r.l.](https://www.exact-lab.it).
