A 3D Segmentation Algorithm for Ellipsoidal Shapes - Application to Nuclei Extraction

We propose some improvements of the Multiple Birth and Cut algorithm (MBC) in order to extract nuclei in 2D and 3D images. This algorithm based on marked point processes was proposed recently in (Gamal Eldin et al., 2012). We introduce a new contrast invariant energy that is robust to degradations encountered in fluorescence microscopy (e.g. local radiometry attenuations). Another contribution of this paper is a fast algorithm to determine whether two ellipses (2D) or ellipsoids (3D) intersect. Finally, we propose a new heuristic that strongly improves the convergence rates. The algorithm alternates between two birth steps. The first one consists in generating objects uniformly at random and the second one consists in perturbing the current configuration locally. Performance of this modified birth step is evaluated and examples on various image types show the wide applicability of the method in the field of bio-imaging.