Paper Title
Modeling and Simulation of Emitter Activations in Superresolution Microscopy

Abstract
In superresolution microscopy (SRM), it is desired to establish a well-reasoned model of data movie so that an advanced localization algorithm can be developed to achieve a high quality of SRM images. A model of data movie can be composed of a model of data frame and a model of emitter activation process. We previously developed a model of a data frame. In this paper, we focus on modeling of emitter activation process. Both continuous and cycled illuminations are considered. While Markov chains are considered for the former, no model is developed for the latter. First, a three-state Markov chain is adopted for the continuous illumination. The state transition probabilities are derived from the first order of kinetics for the emitter activation process. The stationary probabilities of the states on and off are derived when an emitter is photoactivatable. Second, a novel state transition diagram for the cycled illumination is proposed. The state transition probabilities are derived for both the activation frames and deactivation frames. Incorporating the model of emitter activation process and the model of data frames, the models of data movie for both the continuous and cycled illuminations in 2D and 3D imaging are simulated by custom MATLAB codes. The results show that the models can well synthesize a data movie of SRM, thus providing a means to be broadly utilized in simulating SRM systems, evaluating quality of SRM images, and testing performance of localization algorithms. Keywords - Single molecule localization microscopy, data model, emitter activation, Markov chain.