**MINT**
========

**M**\odified **I**\ntraneuronal **N**\anoparticle **T**\racking (**MINT**) is a Python script used to extract intraneuronal transport parameters from the trajectories of optically active nanoparticles.

It relies on `\trackpy <https://github.com/soft-matter/trackpy>`_ to extract trajectories from videos, from which transport parameters are then calculated and statistically tested.

Its purpose is to automate analysis to the point where a folder of raw video files can be turned into graphs and p-values.

It can reasonably be applied to videos of fluorophore-labelled organelles, or any object that can be tracked with trackpy.

.. image:: https://badgen.net/badge/icon/github?icon=github&label
   :target: https://github.com/biophotlumin/mint



.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5713847.svg
   :target: https://doi.org/10.5281/zenodo.5713847



.. image:: 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YuOTRMMTUwLjAwIDEzLjYwTDE1Mi4zMCAxMy42MEwxNDkuMDggMTguOTlMMTQ5LjA4IDIyTDE0Ni43MSAyMkwxNDYuNzEgMTguOTVaIiBmaWxsPSIjRkZGRkZGIiB4PSI4NS45MiIvPjwvc3ZnPg==
   :target: https://www.lumin.universite-paris-saclay.fr/en

|

.. toctree:: 
   :caption: Table of Contents
   :maxdepth: 1

   Install & run <install>
   User guide <user_guide>
   Modules (autogenerated documentation) <modules>
   Sources <sources>



Quickstart
----------

.. code:: console

    $ git clone https://github.com/biophotlumin/mint.git
    $ cd mint
    $ pip install .

Check the `installation instructions <install.html>`_ for more details.


You can run MINT with :

.. code:: console

    $ mint -f <input_folder> -p <path/to/file> -l -e -s


``-f, --folder``
    Path to raw data folder.

``-p, --params``
    Path to config file (YAML or JSON).

``-l, --locate``
    Run tracking.

``-e, --extract``
    Extract transport parameters from trajectories.

``-s, --stats``
    Run statistical analysis.