Tutorials
=========

Each tutorial runs the full LYNX pipeline on a different multi-modal spatial
application. 

- :doc:`liver` — Xenium spatial transcriptomics + DESI metabolomics; principal
  **curve** trajectory (periportal → pericentral zonation) with cell–cell
  interactions.
- :doc:`breast` — Xenium spatial transcriptomics + H&E histology; principal
  **tree** trajectory (from an immune niche to either DCIS or invasive tumor cores).
- :doc:`thymus` — spatial RNA + protein (CITE-seq); principal **curve**
  trajectory (cortex → medulla axis).

.. toctree::
   :maxdepth: 1

   liver
   breast
   thymus