Behavioral Analysis
===================

..  figure:: /media/gifs/Locomotion_DLC_and_plot.gif
    :figwidth: 60%
    :align: right

This is the documentation for data analysis of rodent behavioral task data :cite:author:`2020:Aristieta` and unpublished [*]_. The codes are available in this repository_. 



.. _repository: https://github.com/Shiva-A-Lindi/Behavioral-Analysis

As a user you do not need to be fluent in Python. You can follow this guide and by respecting the requirementes and file data hirerachy you should be fine!



..  figure:: /media/gifs/Rat_lever_demo_h.gif
    :figwidth: 55%
    :align: right

.. toctree::
   :maxdepth: 5
   :caption: Contents:

   Projects/Locomotion/index
   Projects/Lever Reaching/index
   Projects/Laser Detection/index
   Projects/DeepLabCut/index
   
This package consists data analysis tools for two different behavioral tasks. A Locomotion task where animals are continously running on a treadmill while being subjected to optogenetic stimulation. 
Another task is lever reaching task where the animal has to follow the auditory cues presented in the experiment chamber and reach and press a lever to receive reward. There are numerous protocols for this task where the animal would be either lesioned, chemogentically or optogenetically manipulated.
   
.. bibliography::
    :style: unsrt

.. [*] Unpublished data provided by Nicolas Mallet at the Physiology and pathophysiology of executive functions team at the Institut des Maladies Neurodégénératives (IMN_), CNRS, Bordeaux)
.. _IMN: https://www.imn-bordeaux.org/en/teams/physiology-and-pathophysiology-of-executive-functions/



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

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