:sd_hide_title: true

waxMorph
========

.. raw:: html

   <div class="wm-hero">
     <img class="wm-hero-logo wm-logo-light dark-light" src="_static/logo-1024w.png"
          alt="waxMorph — interacting cells resolving into a learned graph network">
     <img class="wm-hero-logo wm-logo-dark dark-light" src="_static/logo-dark.png"
          alt="waxMorph — interacting cells resolving into a learned graph network">
     <p class="wm-tagline">A differentiable cell-based framework for three-dimensional morphogenesis.</p>
     <p class="wm-sub">
       Cells build tissues through local exchanges of force and information.
       waxMorph represents tissue as interacting spheroidal cells and couples a
       prescribed forward simulator with a differentiable learned inverse
       emulator. They share state conventions and provide purpose-built dynamics.
     </p>
     <div class="wm-cta">
       <a class="wm-btn wm-btn-primary" href="installation.html">Install</a>
       <a class="wm-btn wm-btn-ghost" href="tutorials/index.html">Tutorials</a>
       <a class="wm-btn wm-btn-ghost"
          href="https://github.com/Computational-Morphogenomics-Group/waxmorph">GitHub</a>
     </div>
   </div>

   <figure class="wm-showcase">
     <img src="_static/images/fig1.png"
          alt="waxMorph pipeline: forward simulation and inverse learning of shape assembly">
     <figcaption>
       waxMorph represents tissue as interacting polarized spheroids, couples
       forward and inverse models of morphogenesis over that representation, and
       recovers spatially organized latent signals.
     </figcaption>
   </figure>

Explore
-------

.. grid:: 1 2 2 3
   :gutter: 3
   :class-container: wm-cards

   .. grid-item-card:: Installation
      :link: installation
      :link-type: doc
      :class-card: wm-card

      Install the package and pick the ``simulation``, ``learning``, or ``jax``
      extras for your workflow.

   .. grid-item-card:: Tutorials
      :link: tutorials/index
      :link-type: doc
      :class-card: wm-card

      End-to-end notebooks: run a forward simulation and train a learned
      emulator from a mesh pair.

   .. grid-item-card:: Gallery
      :link: gallery
      :link-type: doc
      :class-card: wm-card

      Play reconstructed morphogenesis trajectories in an interactive 3D
      viewer, with a timeline and a free-flying camera.

   .. grid-item-card:: How-to guides
      :link: how_to/index
      :link-type: doc
      :class-card: wm-card

      Task-focused recipes for people who already know waxMorph and want to get
      something specific done.

   .. grid-item-card:: Explanation
      :link: explanation/index
      :link-type: doc
      :class-card: wm-card

      The modelling choices: cell state, locality, differentiable
      physics, forward and inverse modes.

   .. grid-item-card:: API reference
      :link: reference/index
      :link-type: doc
      :class-card: wm-card

      Public modules with PyTorch defaults and explicit JAX/Equinox
      counterparts.

   .. grid-item-card:: Contributing
      :link: contributing
      :link-type: doc
      :class-card: wm-card

      Development setup, testing across both backends, and the conventions
      changes should follow.

.. toctree::
   :hidden:
   :maxdepth: 1

   installation
   tutorials/index
   gallery
   how_to/index
   explanation/index
   reference/index
   contributing
   changelog
   references