A computational approach for detecting micro-domains and confinement domains in cells: a simulation study

Abstract

In this paper, we aim to detect trapping areas (equivalently microdomains or confinement areas) within cells, corresponding to regions where molecules are trapped and thereby undergo subdiffusion. We propose an original computational approach that takes as input a set of molecule trajectories estimated by appropriate tracking methods. The core of the algorithm is based on a combination of clustering algorithms with trajectory classification procedures able to distinguish subdiffusion, superdiffusion and Brownian motion. The idea is to automatically identify trapping areas where we observe a high concentration of subdiffusive particles. We evaluate our proof of concept on artificial sequences obtained with a biophysics-based simulator (Fluosim), and we illustrate its potential on real TIRF microscopy data.