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README

Copyright 2016 Jochen Kursawe. See the LICENSE file at the top-level directory 
of this distribution and at https://github.com/kursawe/MCSTracker/blob/master/LICENSE.

Welcome to the repository for our cell tracking project! If you want to learn more about this project please have a look at our paper `Robust cell tracking in epithelial tissues through identification of maximum common subgraphs' in the Journal of the Royal Society Interface (http://rsif.royalsocietypublishing.org/content/13/124/20160725)

Currently, the repository contains four folders:

./src This folder contains python modules and packages that we have build for the project. There are class definitions for meshes, elements, and nodes, and functions to draw meshes with different properties. Tracking algorithms are in the src/tracking package.

./test This folder contains tests for the modules and packages in /src. We try to employ test driven development, and hence there should be a unit test for most units in the src folder. Evaluation of tracking algorithms is also done in tests: Since we know the matching that the algorithm should find, we apply the alogorithm and check the output in standard python unit tests.

./docs This folder contains a structure to autogenerate html documentation from our code. This is still experimental, but you should be able to generate a small website for this project by going into this folder and typing
    make api
    make html 

./paper This folder contains all source files for the figures in our paper 

Installation:
------------

The code is written using python 2.7. In order to access the modules and packages in this project from your python interpreter you will need to add the ./src folder to your PYTHONPATH environment variable. In most linux distrubtions you can do so by adding the line

    export PYTHONPATH="$PYTHONPATH:/path/to/project/src"

to your ~/.bashrc file.

All dependencies are listed below. In brackets are download instructions that work on Ubuntu 16.04.

* nosetests (sudo apt-get install python-nose),
* numpy and scipy (http://www.scipy.org/install.html), 
* networkx (sudo pip install networkx),
* mahotas (sudo pip install mahotas)
* pyhull (sudo pip install pyhull), 
* sphinx (sudo apt-get install python-sphinx python-numpydoc) 
* openCV (sudo apt-get install libopencv-dev python-opencv)

Please ask Jochen (kursawe AT maths DOT ox DOT ac DOT uk) if you run into any problems, or have any further questions.
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