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WormLib documentation
=====================

WormLib is a modular open-source image analysis library for quantifying microscopy images of Caenorhabditis elegans embryos. It provides an end-to-end pipeline from image loading, embryo segmentation, cell identity prediction, single-molecule FISH (smFISH) spot detection, and spatial mRNA analysis.

.. toctree::
   :maxdepth: 3
   :caption: BASICS:

   installation
   inputs
   settings
   outputs
   models
   examples