Metadata-Version: 2.4
Name: fractal-tasks-core
Version: 2.0.1
Summary: Reference task package for the Fractal analytics platform
Project-URL: Homepage, https://github.com/fractal-analytics-platform/fractal-tasks-core
Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-tasks-core
Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-tasks-core
Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-tasks-core/blob/main/CHANGELOG.md
Author-email: Lorenzo Cerrone <lorenzo.cerrone@uzh.ch>, Joel Lüthi <joel.luethi@uzh.ch>, Tommaso Comparin <tommaso.comparin@exact-lab.it>
License: BSD-3-Clause
License-File: LICENSE
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Description-Content-Type: text/markdown

# Fractal Tasks Core

<p align="center">
  <img src="https://raw.githubusercontent.com/fractal-analytics-platform/fractal-logos/refs/heads/main/projects/fractal_tasks_core.png" alt="Fractal tasks core logo" width="400">
</p>

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Fractal tasks core is the reference task package for the [Fractal](https://fractal-analytics-platform.github.io/) framework. It provides a collection of ready-to-use tasks for processing bioimaging data, including OME-Zarr conversion, image registration, and illumination correction.

![Fractal_overview_small](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)

[Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.

## Documentation

See https://fractal-analytics-platform.github.io/fractal-tasks-core

## Available Tasks

For a complete list of all available Fractal tasks (including tasks from other packages), visit the [Fractal task list](https://fractal-analytics-platform.github.io/fractal_tasks/).

This package includes the following tasks:

- **Image Processing**:
  - *Project Image (HCS Plate)*: Generates intensity projections (e.g., maximum intensity projection) for images in an HCS plate.
  - *Illumination Correction*: Applies flatfield correction and background subtraction using pre-calculated illumination profiles.

- **Registration**:
  - *Calculate Registration (image-based)*: Computes translations for aligning images in multiplexed image analysis.
  - *Find Registration Consensus*: Generates consensus transformations for aligning multiple acquisitions, updating ROI tables as necessary.
  - *Apply Registration to Image*: Applies registration to images based on existing or newly created ROI tables.

- **Other Utilities**:
  - *Import OME-Zarr*: Validates and processes existing OME-Zarr files, adding ROI tables and metadata for further processing in Fractal.

## Installation

```
pip install fractal-tasks-core
```

If you collect this package on Fractal server to run the tasks, make sure to use the package name `fractal-tasks-core` in the corresponding field.

## Contributors and license

The Fractal project is developed by the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich, who contracts [eXact lab s.r.l.](https://www.exact-lab.it/en/) for software engineering and development support.

Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
