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.. include:: ../README.md
   :parser: myst_parser.sphinx_

.. toctree::
   :hidden:
   :maxdepth: 1
   :caption: Contents

   Overview <self>

.. toctree::
   :hidden:
   :caption: Workflow notebooks

   Simulations <simulation>
   Analysis <analysis>
   Visualization <visualization>

.. autosummary::
   :toctree: _summary
   :caption: API reference
   :template: custom_summary.rst
   :recursive:

   subcell_pipeline.simulation
   subcell_pipeline.analysis
   subcell_pipeline.visualization

.. toctree::
   :hidden:
   :caption: Project links

   GitHub <https://github.com/simularium/subcell-pipeline>