3D Segmentation of Mammospheres for Localization Studies ⋆ Ju Han 1 , Hang Chang 12 , Qing Yang 2 , Mary Helen Barcellos-Hoff 1 and Bahram Parvin 1 1 Lawrence Berkeley National Laboratory, Berkeley, CA 94720 2 Institute of Automation, Chinese Academy of Sciences, Beijing, China Abstract. Three dimensional cell culture assays have emerged as the basis of an improved model system for evaluating therapeutic agents, molecular probes, and exogenous stimuli. However, there is a gap in ro- bust computational techniques for segmentation of image data that are collected through confocal or deconvolution microscopy. The main is- sue is the volume of data, overlapping subcellular compartments, and variation in scale and size of subcompartments of interest. A geometric technique has been developed to bound the solution of the problem by first localizing centers of mass for each cell and then partitioning clump of cells along minimal intersecting surfaces. An approximate solution to the center of mass is realized through iterative spatial voting, which is tolerant to variation in shape morphologies and overlapping compart- ments and is shown to have an excellent noise immunity. These centers of mass are then used to partition a clump of cells along minimal in- tersecting surfaces that are estimated by Radon transform. Examples on real data and performance of the system over a large population of data are evaluated. Although proposed strategies have been developed and tested on data collected through fluorescence microscopy, they are applicable to other problems in low level vision and medical imaging. 1 Introduction Current models of high throughput and high content screening are based on two dimensional cell culture assays that are grown either on plastic or glass. Although such a model system may be appropriate as an initial step toward discovery or certain aspect of biological studies, the knowledge may not readily extensible to in vivo models. On the other hand, animal studies are expensive and time consuming and as a result cannot scale for high throughput studies that is necessary to build a space-time continuum of responses in the presence of biological heterogeneity. An intermediate step is three-dimensional cell culture ⋆ 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 medical imaging program at the Office of Biological Effects Research U.S. Department of Energy, Grant No. DE-FG03-01ER63240. PubID is LBNL-61402.