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.. _reference:

Welcome to brain_diffusion
===========================================

.. automodule:: brain_diffusion

brain_diffusion is a python library designed to analyze and visualize trajectory
data from the ImageJ plugin `MOSAIC <http://mosaic.mpi-cbg.de/?q=downloads/imageJ>`_.

Usage
-----

.. code-block:: python

  import brain_diffusion.msd as msd

  DIR = '../data/'
  file = 'sample_data'

  # Prepare trajectory file
  total, frames, x, y, xs, ys = msd.MSD_iteration(DIR, file)

  # Calculate mean squared displacements and their geometric averages
  geoM2xy, gSEM, SM1x, SM1y, SM2xy = msd.vectorized_MMSD_calcs(frames, total, xs, ys)


Motivation
----------

Mean squared displacement (MSD) calculations are a standard calculation performed by
scientists and researchers who use multi-particle tracking techniques.
Brain_diffusion is a centralized analysis and visualization package to calculate
MSDs and diffusion coefficients from trajectory data as calculated using the MOSIAC
ImageJ plugin developed by in the MOSAIC Group at the Max Planck Institute of
Molecular Cell Biology and Genetics in Dresden.  This calculation package is the
primary tool for MSD calculations of nanoparticles in the brain in the `Nance
research group <https://www.nancelab.com/>`_ at the University of Washington.

.. toctree::
   :maxdepth: 2
   :caption: User Documentation

   getting started
   documentation
   api/index
   examples <https://github.com/ccurtis7/brain_diffusion/tree/master/brain_diffusion/notebooks>
   code <https://github.com/ccurtis7/brain_diffusion>
   bugs <https://github.com/ccurtis7/brain_diffusion/issues>