Abstract
The task of counting colony forming units (CFUs) manually is repetitive, time consuming and prone to error. Many different approaches have been developed trying to automate this task aiming towards fully automated and reliable software for colony counting. This work presents a new approach to automated counting of CFUs based on histogram modeling using Gaussian mixture models.
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References
J. Marotz, C. Lübbert and W. Eisenbeiß, “Effective object recognition for automated counting of colonies in Petri dishes (automated colony counting),” Computer Methods and Programs in Biomedicine, vol. 66, no. 2-3, pp. 183-198, 2001.
H. Zhifeng, “Automated Counting and Identification of Cell Colonies Based on Distance Transform and Progressive Erosion,” Advances in Intelligent Systems Research, vol. 41, no. 1, p. 139, 2013.
S. Yoon, K. Lawrence and B. F. Park, “Automatic Counting and Classification of Bacterial Colonies Using Hyperspectral Imaging,” Food and Bioprocess Technology, vol. 8, no. 10, p. 2047–2065, 2015.
I. Buzalewicz, K. Wysocka-Król and H. Podbielska, “Image processing guided analysis for estimation of bacteria colonies number by means of optical transforms,” Optics Express, vol. 18, no. 12, pp. 12992-13005, 2010.
S. D. Brugger, C. Baumberger, M. Jost, W. Jenni, U. Brugger and K. Mühlemann, “Automated Counting of Bacterial Colony Forming Units on Agar Plates,” PLoS ONE, vol. 7, no. 3, p. e33695, 2012.
Q. Geissmann, “OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects,” PLoS ONE, vol. 8, no. 2, p. e54072, 2013.
S. Sutton, “Accuracy of Plate Counts,” Journal of Validation Technology, vol. 17, no. 3, pp. 42-46, 2011.
I. S. Maretić and I. Lacković, “Application of Gaussian Mixture Models with Expectation Maximization in Bacterial Colonies Image Segmentation for Automated Counting and Identification,” in XIII Mediterranean Conference on Medical and Biological Engineering and Computing 2013 Volume 41 of the series IFMBE Proceedings, 2013.
G. McLachlan and D. Peel, Finite Mixture Models (Wiley Series in Probability and Statistics), Wiley-Interscience, 2000.
J. Verbeek, N. Vlassis and B. Krose, “Efficient Greedy Learning of Gaussian Mixture Models,” Journal Neural Computation, vol. 15, no. 2, pp. 469-485, 2003.
G. J. McLachlan and T. Krishnan, The EM Algorithm and Extensions (Wiley Series in Probability and Statistics)(2nd Edition), Wiley-Interscience, 2008.
M. Petrou and C. Petrou, Image Processing: The Fundamentals, Wiley, 2010.
R. C. Gonzalez and R. E. Woods, Digital Image Processing (3rd Edition), Prentice Hall, 2007.
MathWorks®, “R2012a MathWorks Documentation,” [Online]. Available: http://www.mathworks.com/help/. [Accessed September 2012].
F. Y. Shih, Image Processing and Mathematical Morphology: Fundamentals and Applications, CRC Press, 2009.
C. S. Pillai, “A Survey of Shape Descriptors for Digital Image Processing,” IRACST - International Journal of Computer Science and Information Technology & Security, vol. 3, no. 1, pp. 44-50, 2013.
S. J. K. Pedersen, “Circular Hough Transform,” Aalborg University, Vision, Graphics, and Interactive Systems, Aalborg, 2007.
J. Kilian, “Simple Image Analysis By Moments,” 2001. [Online]. Available: breckon.eu/toby/teaching/dip/opencv/SimpleImageAnalysisbyMoments.pdf. [Accessed January 2015].
R. M. Merks, “Open CFU,” Centrum Wiskunde & Informatica (CWI) & Netherlands Institute for Systems Biology, The Netherlands, 6 December 2012. [Online]. Available: http://opencfu.sourceforge.net/. [Accessed 23 October 2016].
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Maretić, I.S., Lacković, I. (2017). Automated Colony Counting Based on Histogram Modeling Using Gaussian Mixture Models. In: Badnjevic, A. (eds) CMBEBIH 2017. IFMBE Proceedings, vol 62. Springer, Singapore. https://doi.org/10.1007/978-981-10-4166-2_83
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DOI: https://doi.org/10.1007/978-981-10-4166-2_83
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