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Comparison of segmentation algorithms for fluorescence microscopy images of cells



Alden A. Dima, John T. Elliott, James J. Filliben, Michael W. Halter, Adele P. Peskin, Javier Bernal, Marcin Kociolek, Mary C. Brady, Hai C. Tang, Anne L. Plant


Segmentation results from nine different segmentation techniques applied to two different cell lines and five different sets of imaging conditions were compared. Significant variability in the results of segmentation was observed that was due solely to differences in imaging conditions or applications of different algorithms. We quantified and compared the results with a similarity index metric that evaluates the degree of underestimating or overestimating a cell object. The results show that commonly used threshold-based segmentation techniques are less accurate than k-means clustering with multiple clusters. Segmentation accuracy varies with imaging conditions that determine the sharpness of cell edges, and with geometric features of a cell. Based on this observation, we propose a method that quantifies cell edge character, to provide an estimate of how accurately an algorithm will perform. The results of this study will assist the development of criteria for evaluating interlaboratory comparability.
Cytometry Part A


segmentation, algorithm comparison, cell biology, fluorescence microscopy


Dima, A. , Elliott, J. , Filliben, J. , Halter, M. , Peskin, A. , Bernal, J. , Kociolek, M. , Brady, M. , Tang, H. and Plant, A. (2011), Comparison of segmentation algorithms for fluorescence microscopy images of cells, Cytometry Part A, [online], (Accessed July 25, 2024)


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Created June 14, 2011, Updated February 19, 2017