  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.
