Graph Cut Based Segmentation of Predefined Shapes: Applications to Biological Imaging
We propose an algorithm to segment 2D ellipses or 3D ellipsoids . This problem is of fundamental importance in various applications of cell biology. The algorithm consists of minimizing a contrast invariant energy defined on sets of non overlapping ellipsoids. This highly non convex problem is solved by combining a stochastic approach based on marked point processes and a graph-cut algorithm that selects the best admissible configuration. In order to accelerate the computing times, we delineate fast algorithms to assess whether two ellispoids intersect or not and various heuristics to improve the convergence rate.
KeywordsNuclei segmentation 2D and 3D images Graph-cuts Marked point processes Ellipses and ellipsoids Multiple objects detection Multiple birth and cut Bio-imaging
This work was partially funded by the Mission pour l’interdisci- plinarité from CNRS, Région Midi Pyrénées, PEPII CASPA3D, ANR SPHIM3D and ANR MOTIMO. The authors wish to thank F. Malgouyres and J. Fehrenbach for interesting discussions. They also thank V. Lobjois, C. Emery, J. Thomazeau, P. Escande and B. Ducommun for their help in this project. They thank L. Aoun and C. Vieu for providing images and interesting discussions regarding micro pillars detection. They thank all the ITAV staff for their warm welcome in a biology laboratory.
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