.. figure:: https://i.imgur.com/hcOUEif.png
   :alt: 

|PyPI status| |PyPI version| |Build Status| |PyPI pyversions|
|Maintainability| |Code style: black|

|image6| |image7| |image8|

Results videos adapted from `Open Worm Movement
Database <http://movement.openworm.org/>`__ license `CC
4.0 <https://creativecommons.org/licenses/by/4.0/legalcode>`__

Overview
--------

The WormPose package estimates the challenging poses of C. elegans in
videos including coils and overlaps.

We train a convolutional neural network with synthetic worm images so
that there is no need for human annotated labels.

Get started quickly
-------------------

`Try the tutorial
notebook <https://github.com/iteal/wormpose/blob/main/examples/tutorial_sample_data.ipynb>`__

This notebook goes over the whole WormPose pipeline with some sample
data and an already trained model. You can run it in Google Colab.

Read the documentation
----------------------

Check the `Documentation
website <https://iteal.github.io/wormpose/index.html>`__ for detailed
instructions.

Read the paper
--------------

| `WormPose: Image synthesis and convolutional networks for pose
  estimation in C.
  elegans <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008914>`__
| Hebert L, Ahamed T, Costa AC, O’Shaughnessy L, Stephens GJ (2021)
  WormPose: Image synthesis and convolutional networks for pose
  estimation in C. elegans. PLOS Computational Biology 17(4): e1008914.
  https://doi.org/10.1371/journal.pcbi.1008914

Manuscript data
---------------

Manuscript data is available here: https://wormpose.unit.oist.jp.

.. |PyPI status| image:: https://img.shields.io/pypi/status/wormpose.svg
   :target: https://pypi.python.org/pypi/wormpose/
.. |PyPI version| image:: https://badge.fury.io/py/wormpose.svg
   :target: https://pypi.python.org/pypi/wormpose/
.. |Build Status| image:: https://travis-ci.com/iteal/wormpose.svg?branch=main
   :target: https://travis-ci.com/iteal/wormpose
.. |PyPI pyversions| image:: https://img.shields.io/pypi/pyversions/wormpose.svg
   :target: https://pypi.python.org/pypi/wormpose/
.. |Maintainability| image:: https://img.shields.io/codeclimate/maintainability/iteal/wormpose
   :target: https://codeclimate.com/github/iteal/wormpose/maintainability
.. |Code style: black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black
.. |image6| image:: https://i.imgur.com/l76dxbM.gif
.. |image7| image:: https://i.imgur.com/4b8zz68.gif
.. |image8| image:: https://i.imgur.com/e4oox2p.gif

Contents
--------

.. toctree::
    :maxdepth: 2

    Installation <install>
    WormPose pipeline <pipeline>
    Use with Tierpsy <tierpsy>
    Load custom data <custom_loader>
    Documentation <documentation>


.. _Indices_and_Tables:

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

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