Computational Modeling of Fluorescence Loss in Photobleaching

Fluorescence loss in photobleaching (FLIP) is a modern microscopy method for visualization of transport processes in living cells. Although FLIP is widespread, an automated reliable analysis of image data is still lacking. This paper presents a framework for modeling and simulation of FLIP sequences as reaction–diffusion systems on segmented cell images. The cell geometry is extracted from microscopy images using the Chan–Vese active contours algorithm (IEEE Trans Image Process 10(2):266–277, 2001). The PDE model is subsequently solved by the automated Finite Element software package FEniCS (Logg et al. in Automated solution of differential equations by the finite element method. Springer, Heidelberg, 2012). The flexibility of FEniCS allows for spatially resolved reaction diffusion coefficients in two (or more) spatial dimensions.