The dynamics of genome regions are associated to the functional or dysfunctional behaviour of the human cell. In order to study these dynamics it is necessary to remove perturbations coming from movement and deformation of the nucleus, i.e. the container holding the genome. In literature models have been proposed to cope with the transformations corresponding to nuclear dynamics of healthy cells. However for pathological cells, the nucleus deforms in an apparently random way, making the use of such models a non trivial task. In this paper we propose a mapping of the cell nucleus which is based on the matching of the nuclear contours. The proposed method does not put constraints on the possible shapes nor on the possible deformations, making this method suited for the analysis of pathological nuclei.