Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation

Hamid Mohamadlou1, Joseph C Shope4 and Nicholas S Flann123*

Author Affiliations

1 Department of Computer Science, Utah State University, Logan, UT 84322, USA

2 Institute for Systems Biology, Seattle, WA 98109, USA

3 Synthetic Biomanufacturing Institute, Logan, UT 84322, USA

4 Department of Biology, Utah State University, Logan, UT 84322, USA

For all author emails, please log on.

BMC Bioinformatics 2014, 15:32  doi:10.1186/1471-2105-15-32

Published: 30 January 2014



Analysis of cellular processes with microscopic bright field defocused imaging has the advantage of low phototoxicity and minimal sample preparation. However bright field images lack the contrast and nuclei reporting available with florescent approaches and therefore present a challenge to methods that segment and track the live cells. Moreover, such methods must be robust to systemic and random noise, variability in experimental configuration, and the multiple unknowns in the biological system under study.


A new method called maximal-information is introduced that applies a non-parametric information theoretic approach to segment bright field defocused images. The method utilizes a combinatorial optimization strategy to select specific defocused images from each image stack such that set complexity, a Kolmogorov complexity measure, is maximized. Differences among these selected images are then applied to initialize and guide a level set based segmentation algorithm. The performance of the method is compared with a recent approach that uses a fixed defocused image selection strategy over an image data set of embryonic kidney cells (HEK 293T) from multiple experiments. Results demonstrate that the adaptive maximal-information approach significantly improves precision and recall of segmentation over the diversity of data sets.


Integrating combinatorial optimization with non-parametric Kolmogorov complexity has been shown to be effective in extracting information from microscopic bright field defocused images. The approach is application independent and has the potential to be effective in processing a diversity of noisy and redundant high throughput biological data.