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Welcome to Fractal Tasks Core's documentation!

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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.

This project is under active development 🔨. If you need help or found a bug, open an issue here.

Fractal overview 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.

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 Processing:

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

Segmentation:

  • Threshold Segmentation: Segments objects using Otsu or simple threshold methods, with optional ROI masking table creation.

Measurement:

  • Measure Features: Extracts morphological and intensity features from label images and stores results as Fractal tables.

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.

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.