.. _example_gallery:

Example gallery
===============
These examples are small code snippets meant to illustrate certain pymaid
functions. As per usual: have a look at the :ref:`API reference <api>` to
find out details about a given function.


.. topic:: Check this out

   Pymaid is built on top of `navis <https://navis.readthedocs.io>`_ and
   navis functions can be used with ``CatmaidNeurons`` and ``CatmaidNeuronLists``.
   Please check out the navis `tutorials <https://navis.readthedocs.io/en/latest/source/gallery.html>`_.

.. raw:: html

   <div class="container-fluid">
      <div class="row">
         <div class="col-md-3">
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">CatmaidNeuron/Lists</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 1

   Overview <neurons>
   Indexing NeuronLists <indexing_neuronlists>
   Parsing skeleton IDs <parsing_skids>

.. raw:: html


               </div>
            </div>
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">Visualization</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 2

   Plotting <plotting>
   EM image data <tiles.ipynb>

.. raw:: html

               </div>
            </div>
         </div>
         <div class="col-md-3">
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">Morphology</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 2

   Morphological analyses <morph_analysis.ipynb>

.. raw:: html


               </div>
            </div>
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">Connectivity</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 1

   Basics <connectivity_basics>
   Compartmentalizing <connectivity_analysis>

.. raw:: html

               </div>
            </div>
         </div>
         <div class="col-md-3">
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">CATMAID</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 2

   Fetching data <fetching_data>
   Pushing data <pushing_data>

.. raw:: html


               </div>
            </div>
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">Interfaces</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 1

   Cytoscape <python2cytoscape>


.. raw:: html

               </div>
            </div>
         </div>
         <div class="col-md-3">
            <div class="panel panel-default">
               <div class="panel-heading">
                  <h3 class="panel-title">Misc</h3>
               </div>
               <div class="panel-body">

.. toctree::
   :maxdepth: 1

   URLs & random sampling <generate_urls>
   User contributions <user_contributions>
   Data caching <data_caching>
   Troubleshooting <troubleshooting>

.. raw:: html

               </div>
            </div>
         </div>
      </div>
   </div>