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Blinking Molecule Tracking

We discuss a method for tracking individual molecules which globally optimizes the likelihood of the connections between molecule positions fast and with high reliability even for high spot densities and blinking molecules. Our method works with cost functions which can be freely chosen to combine costs for distances between spots in space and time and which can account for the reliability of positioning a molecule. To this end, we describe a top-down polyhedral approach to the problem of tracking many individual molecules. This immediately yields an effective implementation using standard linear programming solvers. Our method can be applied to 2D and 3D tracking.