MesoSPIM Fractal Tasks for Lightsheet Image Processing

This package provides a collection of Fractal-compatible tasks to process mesoSPIM 3D fluorescence microscopy data.

It currently offers tasks for:

• Converting mesoSPIM raw 3D stacks to OME-Zarr (currently for TIFF, H5, RAW images)
• Importing an existing mesoSPIM OME-Zarr dataset and preparing it for processing
• Illumination correction:
  • Flatfield
  • Z-intensity correction
  • Global intensity multi-tile optimization
• Multitile stitching
• View or channel fusion
• ROI cropping from large 3D OME-Zarr datasets

These tasks are intended to run on the Fractal Analytics Platform, where they can be integrated into scalable workflows and executed efficiently on a cluster environment. However, all tasks can also be executed locally and individually on a single machine using standard shell commands, without requiring a full Fractal deployment. Instructions for running tasks manually are provided in the Usage section.