Segmentation of Three Dimensional Cell Culture Models from a Single Focal Plane

Abstract

Three dimensional cell culture models offer new opportunities for development of computational techniques for segmentation and localization. These assays have a unique signature of a clump of cells that correspond to a functioning colony. Often the nuclear compartment is labeled and then imaged with fluorescent microscopy to provide context for protein localization. These colonies are first delineated from background using the level set method. Within each colony, nuclear regions are then bounded by their center of mass through radial voting, and a local neighborhood for each nucleus is established through Voronoi tessellation. Finally, the level set method is applied again within each Voronoi region to delineate the nuclear compartment. The paper concludes with the application of the proposed method to a dataset of experimental data demonstrating a stable solution when iterative radial voting and level set methods are used synergistically.

The Research was supported by National Aeronautics and Space Administration Grant no. T6275W, NASA Specialized Center for Research in Radiation Health Effects, the low dose radiation research program and the medical imaging program, Office of Biological Effects Research, U.S. Department of Energy, Grant No. DE-FG03-01ER63240. PubID is LBNL-61401.