(c) 2016
Author: Alan Aberdeen
Email: alanaberdeen (at) gmail (dot) com

Python implementation of the tracking methodology as presented in:
Padfield, Dirk, Jens Rittscher, and Badrinath Roysam. "Coupled minimum-cost flow cell tracking for high-throughput quantitative analysis." Medical image analysis 15.4 (2011): 650-668.

This project uses the GLPK (GNU Linear Programming Kit). Installation instructions can be found on the webpage. It was realtively easy to install. The Pyomo python package interfaces with the solver, the directory containing the glpsol executable must be in the list of paths defined by the PATH environment variable.

Sometimes, wehn working with a Python virtualenv the Pyomo package can't locate the solver despite it's location being included in the PATH variable. I think this is a known issue, but coping the glpsol exectable to the venv directory fixes this - a little bit of a rubbish workaround but a workaround none the less.

Currently returning tracking output as list of lists structure.

 |Tracks                                     |
 |   --> cell ID                             |
 |       --> frame,                          |
 |           centroid,                       |
 |           area,                           |
 |           parent cell ID                  |

This set of tools was built (and tested on) a few particular sets of data. The functions are not error free and have not been extensively tested. Application to new datasets may require some new developments.