Bilkent University
Department of Computer Engineering


Perceptual Watersheds for Cell Segmentation in Fluorescence microscopy images


Salim Arslan
MSc Student
Computer Engineering Department
Bilkent University

High content screening aims to analyze complex biological systems and collect quantitative data via automated microscopy imaging to improve the quality of drug discovery in means of speed and accuracy. More rapid and accurate high-throughput screening becomes possible with advances in automated microscopy image analysis, for which cell segmentation commonly constitutes the core step. Since the performance of cell segmentation directly affects the output of the system, it is of great importance to develop effective segmentation algorithms. Although there exist several promising methods for segmenting monolayer isolated and less confluent cells, it still remains an open problem to segment more confluent cells that grow in aggregates on layers.

In order to address this problem, we propose a new marker-controlled watershed algorithm that incorporates human perception into segmentation.

This incorporation is in the form of how a human locates a cell by identifying its correct boundaries and piecing these boundaries together to form the cell. For this purpose, our proposed watershed algorithm defines four different types of primitives to represent different types of boundaries (left, right, top, and bottom) and constructs an attributed relational graph on these primitives to represent their spatial relations.

Then, it reduces the marker identification problem to the problem of finding predefined structural patterns in the constructed graph. Moreover, it makes use of the boundary primitives to guide the flooding process in the watershed algorithm. Working with fluorescence microscopy images, our experiments demonstrate that the proposed algorithm results in locating better markers and obtaining better cell boundaries for both less and more confluent cells, compared to previous cell segmentation algorithms.


DATE: 06 August, 2012, Monday @ 10:00