.. figure:: /docs/images/scipion_logo.gif
   :alt: scipion logo

Welcome to Scipion's documentation!
===================================
Scipion is an image processing framework for obtaining 3D models of
macromolecular complexes using Electron Microscopy (3DEM). It integrates
several software packages and presents a unified interface for both
biologists and developers. Scipion allows you to execute workflows
combining different software tools, while taking care of formats and
conversions. Additionally, all steps are tracked and can be reproduced
later on.

.. toctree::
   :maxdepth: 1
   :caption: Set up

   docs/scipion-modes/how-to-install
   docs/scipion-modes/scipion-configuration
   docs/scipion-modes/host-configuration
   docs/user/troubleshooting

.. _user-docs:

.. toctree::
   :maxdepth: 1
   :glob:
   :caption: User documentation

   docs/user/user-documentation

.. _facilities-docs:

.. toctree::
   :maxdepth: 1
   :glob:
   :caption: Facilities

   docs/facilities/facilities
   docs/facilities/facilities-workflows
   docs/facilities/customize-report

.. _dev-docs:

.. toctree::
   :maxdepth: 1
   :glob:
   :caption: Developer documentation

   docs/developer/developers

.. _api-docs:

.. toctree::
   :maxdepth: 1
   :titlesonly:
   :caption: API Documentation

   docs/api/scipion-API
   docs/api/plugins-API
   docs/api/xmipp-API


.. _contact:

.. toctree::
   :maxdepth: 1
   :caption: Get in touch

   docs/misc/contact-us

.. _license:

.. toctree::
   :maxdepth: 1
   :caption: Licences

   docs/user/license


How to Contribute
=================

There are many ways to help make Scipion better:

* `Open a New Issue <https://github.com/scipion-em/scipion-pyworkflow/issues/new>`_ to report bugs or suggest new features.We would like to hear from you.

* :ref:`Extend Scipion <extending-scipion>` with new protocols or packages (requires some Python programming skills).

* Add or improve content in the documentation.
  To do so, you will need a `GitHub <http://github.com>`__ account and send us a mail to add you
  to the project as collaborator. After that, you will be able to create new wiki pages or edit
  existing ones.


Scipion in the Cloud
====================
* ScipionCloud images are available on commercial and academic :ref:`clouds <scipion-on-the-cloud>`


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

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