Smart markers for watershed-based cell segmentation
Koyuncu, Can Fahrettin
Demir, Çiğdem Gündüz
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Automated cell imaging systems facilitate fast and reliable analysis of biological events at the cellular level. In these systems, the first step is usually cell segmentation that greatly affects the success of the subsequent system steps. On the other hand, similar to other image segmentation problems, cell segmentation is an ill-posed problem that typically necessitates the use of domain specific knowledge to obtain successful segmentations even by human subjects. The approaches that can incorporate this knowledge into their segmentation algorithms have a potential to greatly improve the segmentation results. In this study, we propose a new approach for the effective segmentation of live cells from phase-contrast microscopy. This approach introduces a new set of “smart markers” for a marker-controlled watershed algorithm, for which the identification of its markers is critical. The proposed approach relies on using domain specific knowledge, in the form of visual characteristics of the cells, to define the markers. We evaluate our approach on a total of 1954 cells. The experimental results demonstrate that the proposed approach is quite effective in identifying better markers compared to its counterparts. This will in turn be effective in improving the segmentation performance of a marker-controlled watershed algorithm.
Live cell segmentation
Phase contrast microscopy images