title: Smart markers for watershed-based cell segmentation.
abstract: 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 potential to greatly improve segmentation results. In this work, 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 1,954 cells. The experimental results demonstrate that this approach, which uses the proposed definition of smart markers, 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.
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, Turkey.
authors.forename: Can Fahrettin
authors.initials: CF
authors.lastname: Koyuncu
authors.forename: Salim
authors.initials: S
authors.lastname: Arslan
authors.forename: Irem
authors.initials: I
authors.lastname: Durmaz
authors.forename: Rengul
authors.initials: R
authors.lastname: Cetin-Atalay
authors.forename: Cigdem
authors.initials: C
authors.lastname: Gunduz-Demir
mesh_terms: D000465:Algorithms; D002460:Cell Line; D006801:Humans; D007089:Image Enhancement; D008853:Microscopy; D061848:Optical Imaging / Q000379:methods*; D015203:Reproducibility of Results