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Estimating the motion of given kinds of objects within cells, such as proteins, requires the development of the framework for modelling the dynamics of the objects and how these appear on the microscope. A suitably general mathematical framework is then required to translate the modelling choices into a proper estimation algorithm. In this presentation, we will focus on the modelling part as it can be explained and detailed in a intuitive way, mostly without equations. The limitations of ad hoc approaches from the target tracking literature will be discussed and how these are overcome by considering the physical description of the populations.