.. HCRprocess master

HCRprocess
===================================

HCRprocess (`GitHub <https://github.com/economolab/HCRprocess>`_) is an `HCR-mFISH <https://journals.biologists.com/dev/article/145/12/dev165753/48466/Third-generation-in-situ-hybridization-chain>`_ image processing pipeline written in MATLAB and Python 3 by Jack Vincent. It is composed of components developed by Jack Vincent, Michael Economo, and Will Cunningham.

.. image:: doc_assets/beauty_HCR.png
    :width: 400px
    :align: center
    :alt: HCR example

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.. toctree::
   :maxdepth: 1
   :caption: Quickstart guide:

   install
   input

.. toctree::
   :maxdepth: 2
   :caption: Usage:

   main
   core
   post
   core_manual
   post_manual
   hist