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The lacking of automatic screen systems that can deal with large volume of time-lapse optical microscopy imaging is a bottleneck of modern bio-imaging research. In this paper, we propose an effective automated analytic system that can be used to acquire, track and analyze cell-cycle behaviors of a large population of cells. We use traditional watershed algorithm for cell nuclei segmentation and then a novel hybrid merging method is proposed for fragments merging. After a distance and size based tracking procedure, the performance of fragments merging is improved again by the sequence context information. At last, the cell nuclei can be classified into different phases accurately in a continuous hidden Markov model (HMM). Experimental results show the proposed system is very effective for cell sequence segmentation, tracking and cell phase identification.