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This article is part of the supplement: Selected articles from the 10th International Workshop on Computational Systems Biology (WCSB) 2013: Bioinformatics

Open Access Research

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)

Sharif Chowdhury1, Meenakshisundaram Kandhavelu1, Olli Yli-Harja12 and Andre S Ribeiro1*

Author Affiliations

1 Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland

2 Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA

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BMC Bioinformatics 2013, 14(Suppl 10):S8  doi:10.1186/1471-2105-14-S10-S8

Published: 12 August 2013



Cell imaging is becoming an indispensable tool for cell and molecular biology research. However, most processes studied are stochastic in nature, and require the observation of many cells and events. Ideally, extraction of information from these images ought to rely on automatic methods. Here, we propose a novel segmentation method, MAMLE, for detecting cells within dense clusters.


MAMLE executes cell segmentation in two stages. The first relies on state of the art filtering technique, edge detection in multi-resolution with morphological operator and threshold decomposition for adaptive thresholding. From this result, a correction procedure is applied that exploits maximum likelihood estimate as an objective function. Also, it acquires morphological features from the initial segmentation for constructing the likelihood parameter, after which the final segmentation is obtained.


We performed an empirical evaluation that includes sample images from different imaging modalities and diverse cell types. The new method attained very high (above 90%) cell segmentation accuracy in all cases. Finally, its accuracy was compared to several existing methods, and in all tests, MAMLE outperformed them in segmentation accuracy.