CellColoc Documentation
========================

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   :alt: CellColoc overview
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`CellColoc <https://github.com/FabrizioMusacchio/CellColoc>`_ is a Python package
for interactive, segmentation-based colocalization analysis in microscopy
images. It combines reusable core analysis logic with project-specific user
scripts that can be executed step by step in VS Code or notebook-like
environments.

CellColoc supports both neural-network segmentation with Cellpose and
classical threshold-based segmentation on a per-channel basis, including ROI-
wise analysis, occupancy quantification, optional third-channel logic, fast
post hoc refinement, and interactive napari inspection.


.. toctree::
   :maxdepth: 3
   :caption: Contents

   overview
   installation
   usage
   api
   changelog
   contributing