fractal-tasks-utils

General utilities for building Fractal tasks.

Modules

• segmentation — utilities for running segmentation models over OME-Zarr images (compute_segmentation, setup_segmentation_iterator, IteratorConfiguration, MaskingConfiguration)
• transforms — standard image transforms (GaussianBlurConfig, MedianFilterConfig, HistogramEqualizationConfig, SizeFilterConfig)
• measurement — utilities for computing measurements (WIP)

Development

Pixi is used for development tasks such as formatting, type-checking, and testing. To run these tasks, use the following commands:

pixi run format    # format code with ruff
pixi run typecheck # type-check with ty
pixi run test      # run tests with pytest