.. polarityjam documentation master file, created by
   sphinx-quickstart on Mon Aug  8 12:40:46 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root ``toctree`` directive.

Welcome to polarityjam's documentation!
=======================================
.. role:: raw-html(raw)
    :format: html

.. container:: twocol

   .. container:: leftside

      .. image:: images/polarityjam_logo.png
         :width: 300
         :align: center

   .. container:: rightside

      :raw-html:`<br />`
      :raw-html:`<br />`
      :raw-html:`<br />`


      The `Polarity-JaM <https://www.nature.com/articles/s41467-025-56643-x>`_ suite is a software package that lets you study cell polarity, junctions and morphology.
      :raw-html:`<br />`
      :raw-html:`<br />`
      Explore the :ref:`software suite <software suite>` here!
      :raw-html:`<br />`
      :raw-html:`<br />`
      :raw-html:`<br />`
      :raw-html:`<br />`
      :raw-html:`<br />`
      :raw-html:`<br />`


.. image:: images/collaboration_logo.png
   :width: 800
   :align: center


.. toctree::
   :maxdepth: 2
   :caption: Contents:

   What is PolarityJaM?<whatis>
   Installation
   Usage
   Features
   notebooks/polarityjam-notebook_vis.ipynb
   Web-App
   notebooks/polarityjam-notebook.ipynb
   notebooks/polarityjam-notebook_api.ipynb
   notebooks/polarityjam-notebook_seg.ipynb
   notebooks/polarityjam-notebook_omero.ipynb
   Methods
   FAQs
   Contribute
   Cite

..
   Indices and tables
   ==================

   * :ref:`genindex`
   * :ref:`modindex`
   * :ref:`search`