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Automatic band detection on pulsed-field gel electrophoresis images

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Abstract

Automatic band detection is important for molecular subtyping on gel images. Automatic band detection has been conducted for many years, but only a few incomplete systems have been proposed. Here, we propose a completely automatic band detection system for pulsed-field gel electrophoresis (PFGE) images. The proposed approach mainly comprises lane segmentation and band extraction. In lane segmentation, we characterized the structural features and the spatial distribution of bands in PFGE images to fit pairs of parallel lines. In band extraction, a polynomial fitting method was used to remove the uneven background in a lane; we then used local gradient information to split the stuck bands and extract all bands in every lane. We compared the results with existing semiautomatic methods based on 20 varied PFGE images. The proposed method was shown to be superior to previous methods in most cases; moreover, the proposed approach is a completely automatic processing method.

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References

  1. Ackers ML, Mahon BE, Leahy E, Goode B, Damrow T, Hayes PS, Bibb WF, Rice DH, Barrett TJ, Hutwagner L, Griffin PM, Slutsker L (1998) An outbreak of Escherichia coli O157: H7 infections associated with leaf lettuce consumption. J Infect Dis 177:1588–1593

    Article  Google Scholar 

  2. Graves LM, Swaminathan B, Hunter SB (1999) Subtyping listeria monocytogenes. In: Ryser EM, Marth EH (eds) Listeria, listeriosis and food safety. Marcel Dekker, New York, pp 279–298

    Google Scholar 

  3. Holmberg SD, Wachsmuth IK, Hickman-Brenner FW, Cohen ML (1984) Comparison of plasmid profile analysis, phage typing, and antimicrobial susceptibility testing in characterizing Salmonella typhimurium isolates from outbreaks. J Clin Microbiol 19:100–104

    Google Scholar 

  4. Holmberg SD, Wachsmuth K (1989) Plasmid and chromosomal DNA analyses in the epidemiology of bacterial diseases. In: Swaminathan B, Prakash G (eds) Nucleic acid and monoclonal antibody probes: applications in diagnostic microbiology. Marcel Dekker, New York, pp 105–129

    Google Scholar 

  5. Barrett TJ (1997) Molecular fingerprinting of foodborne pathogenic bacteria: An introduction to methods, uses and problems. In: Tortorello ML, Gendel SM (eds) Food microbiological analysis: new technologies. Marcel Dekker, New York, pp 249–264

    Google Scholar 

  6. Maslanka SE, Kerr JG, Williams G, Barbaree JM, Carson LA, Miller JM, Swaminathan B (1999) Molecular subtyping of Clostridium perfringens by pulsed-field gel electrophoresis to facilitate food-borne-disease outbreak investigations. J Clin Microbiol 37(7):2209–2214

    Google Scholar 

  7. Swaminathan B, Barrett TJ, Hunter SB, Tauxe RV, CDC PulseNet Task Force (2001) PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance. Emerg Infect Dis 7(3):382–389

    Article  Google Scholar 

  8. Threlfall EJ, Hampton MD, Ward LR, Rowe B (1996) Application of pulse-field gel electrophoresis to an international outbreak of Salmonella agona. Emerg Infect Dis 2(2):130–132

    Article  Google Scholar 

  9. Ye X, Suen CY, Cheriet M, Wang E (1999) A recent development in image analysis of electrophoresis gels. In: Noubound F, Parizeau M, Ziou D (eds) Proc vision interface (Vision Interface’99). Nikos Drakos, Computer Based Learning Unit, University of Leeds, Canada, pp 432–438

    Google Scholar 

  10. Akbari A, Albregtsen F (2004) Automatic segmentation of DNA bands in one dimensional gel images produced by hybridizing techniques. In: Hudson DL, Liang ZP (eds) Proceedings of the 26th Annual International Conference of the IEEE EMBS, San Francisco, CA, IEEE Service Center, Piscataway, pp 2852–2855

  11. Agarwal A, Manohar CS, Pujari AK (1995) Identification of lanes and bands in DNA autoradiogram images. In: Proceedings of the 14th IEEE conference on Biomedical Engineering, Shreveport, LA, IEEE Service Center, Piscataway, pp ps1–ps2

  12. Wang D, Keller JM, Carson CA (2001) Pulsed-field gel electrophoresis pattern recognition of bacterial DNA: a systemic approach. Pattern Anal Appl 4:244–255

    Article  MATH  MathSciNet  Google Scholar 

  13. Bajla I, Hollander I, Burg K (2001) Improvement of electrophoretic gel image analysis. Meas Sci Rev 1:5–10

    Google Scholar 

  14. Bajla I, Hollander I, Fluch S, Burg K, Koller M (2005) An alternative method for electrophoretic gel image analysis in the GelMaster software. Comput Methods Programs Biomed 77:209–231

    Article  Google Scholar 

  15. Bajla I, Hollander I, Minichmayr M, Gmeiner G, Reichel CH (2005) GASepo—a software solution for quantitative analysis of digital images in Epo doping control. Comput Methods Programs Biomed 80(3):246–270

    Article  Google Scholar 

  16. Otsu N (1979) A thresholding selection method from gray-level histograms. IEEE Trans Syst Man Cybern A Syst Hum 9:62–66

    Article  Google Scholar 

  17. Cutler P, Heald G, White IR, Ruan J (2003) A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection. Proteomics 3:392–401

    Article  Google Scholar 

  18. Glasbey CA, Wright F (1994) An algorithm for unwarping multitrack electrophoretic gels. Electrophoresis 15:143–148

    Article  Google Scholar 

  19. Stolc S, Bajla I (2006) Improvement of band segmentation in Epo images via column shift transformation with cost functions. Med Biol Eng Comput 44:257–274

    Article  Google Scholar 

  20. Sousa AV, Mendonca AM, Campilho A (2008) Chromatographic pattern classification. IEEE Trans Biomed Eng 55(6):1687–1696

    Article  Google Scholar 

  21. Sousa AV, Mendonca AM, Campilho A (2008) Dissimilarity-based classification of chromatographic profiles. Pattern Anal Appl 11:409–423

    Article  MathSciNet  Google Scholar 

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Authors and Affiliations

  1. Institute of Computer Science and Information Engineering, National Central University, Jhongli, 32001, Taiwan

    Din-Chang Tseng & You-Ching Lee

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  1. Din-Chang Tseng
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  2. You-Ching Lee
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Correspondence to Din-Chang Tseng.

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Tseng, DC., Lee, YC. Automatic band detection on pulsed-field gel electrophoresis images. Pattern Anal Applic 18, 145–155 (2015). https://doi.org/10.1007/s10044-014-0424-4

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  • DOI: https://doi.org/10.1007/s10044-014-0424-4

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