.. SimSpace documentation master file, created by
   sphinx-quickstart on Mon Jul 21 12:33:10 2025.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

SimSpace documentation
======================

.. include:: welcome.md
   :parser: myst_parser.sphinx_


.. toctree::
   :maxdepth: 2
   :caption: Tutorials

   tutorials/reference_free
   tutorials/reference_based_Xenium
   tutorials/reference_based_CODEX
   tutorials/spatial_fitting
   tutorials/3D_simulation

.. toctree::
   :maxdepth: 2
   :caption: API Reference

   modules