fractal-tasks-core 2.0.0a1

Reference task package for the Fractal analytics platform

Fractal Tasks Core

Fractal tasks core is the reference task package for the Fractal framework. It provides a collection of ready-to-use tasks for processing bioimaging data, including OME-Zarr conversion, image registration, and illumination correction.

Fractal is a framework developed at the BioVisionCenter to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.

Roadmap fo Fractal Tasks Core V2.0

• Remove all the tooling around manifest creation and validation (DONE)
• Remove napari workflows task (DONE)
• Remove cellpose segmentation task (DONE)
• Adopt Pixi for environment management and task execution (DONE)
• Refactor dev tooling (DONE)
• Refactor Illumination correction task to use ngio (DONE)
• Cleanup docs (DONE)
• Refactor registration tasks to use ngio (DONE)
• Refactor import OME-Zarr task to use ngio (DONE)
• Improve test_v2 suite to cover all legacy edge cases
• Remove the cellvoyager conversion tasks (to be moved into fractal-uzh-converters)
• Refactor test suite to rely more on ngio "correctness" in writing
• Remove all non-task related code (e.g. NGFF validation, ROI table handling, etc.)
• Add a new simple segmentation task (like thresholding-based segmentation)
• Add a new simple measurement task (like regionprops-based measurement)

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.

This package includes the following tasks:

• Image Conversion:

  • Convert Cellvoyager to OME-Zarr: Converts CV7000/CV8000 images to OME-Zarr format.
  • Convert Cellvoyager Multiplexing to OME-Zarr: Converts multiplexed images from CV7000/CV8000 to OME-Zarr.

• 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 at the University of Zurich, who contracts eXact lab s.r.l. 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.