.. Track Analyzer - Quantification and visualization of tracking data
    Authors: Arthur Michaut                                                
    Copyright 2016-2019 Harvard Medical School and Brigham and             
                             Women's Hospital                              
    Copyright 2019-2021 Institut Pasteur and CNRS–UMR3738                  
    See the COPYRIGHT file for details                                     
                                                                           
    This file is part of Track Analyzer package.                           
                                                                           
    Track Analyzer is free software: you can redistribute it and/or modify 
    it under the terms of the GNU General Public License as published by   
    the Free Software Foundation, either version 3 of the License, or      
    (at your option) any later version.                                    
                                                                           
    Track Analyzer is distributed in the hope that it will be useful,      
    but WITHOUT ANY WARRANTY; without even the implied warranty of         
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the           
    GNU General Public License for more details .                          
                                                                           
    You should have received a copy of the GNU General Public License      
    along with Track Analyzer (COPYING).                                   
    If not, see <https://www.gnu.org/licenses/>.                           


Welcome to Track Analyzer's documentation!
==========================================

**Track Analyzer** is Python-based data visualization pipeline for tracking data.
It *does not* perform any tracking, but visualizes and quantifies any kind of tracked data.
It analyzes trajectories by computing standard quantities such as velocity,
acceleration, diffusion coefficient, local density, etc. 
Trajectories can also be plotted on the original image in 2D or 3D using custom color coding.

**Track Analyzer** provides a filtering section that can extract subsets of data based on spatiotemporal criteria.
The filtered subsets can then be analyzed either independently or compared. This filtering section also provides a tool
for selecting specific trajectories based on spatiotemporal criteria which can be useful to perform fate mapping and back-tracking.

**Track Analyzer** is distributed as two versions: an installation-free web-base tool run on `Galaxy <https://galaxyproject.org/>`_, and full version run on a user-friendly Jupyter notebook. On both versions, **Track Analyzer** can be run without any programming knowledge using its graphical interface. The full version interface is launched by running a `Jupyter notebook <https://jupyter.org/>`_ containing widgets allowing the user to load data and set parameters without writing any code. 



==========
User Guide
==========
.. toctree::
   :maxdepth: 2

   user_guide/index


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

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