Semiparametric point process modelling of blinking artifacts in PALM

Photoactivated localization microscopy (PALM) is a powerful imaging technique for characterization of protein organization in biological cells. Due to the stochastic blinking of fluorescent probes, and camera discretization effects, each protein gives rise to a cluster of artificial observations. These blinking artifacts are an obstacle for qualitative analysis of PALM data, and tools for their correction are in high demand. We develop the Independent Blinking Cluster point process (IBCpp) family of models, and present results on the mark correlation function. We then construct the PALM-IBCpp - a semiparametric IBCpp tailored for PALM data. We describe a procedure for estimation of parameters, which can be used without parametric assumptions on the spatial organization of proteins. The parameters include the kinetic rates that control blinking, and as such can be used to correct subsequent data analysis. The method is demonstrated on real data, and in a simulation study, where blinking artifacts were precisely quantified in a range of realistic settings.