A two-step procedure for automatic and accurate segmentation of volumetric CLSM biofilm images

Journal of Microbiological Methods

Volumn 70, Issue 3, 2007, Pages 424-433

  Yerly, Jerome ^a   Hu, Yaoping ^a   Jones, Steven M ^a   Martinuzzi, Robert J ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

3D Otsu; Anisotropic diffusion; Biofilm; Segmentation; Volumetric CLSM images

Indexed keywords

ANALYTIC METHOD; ANISOTROPY; ARTICLE; BACTERIAL STRAIN; BIOFILM; CONFOCAL LASER MICROSCOPY; DIFFUSION; IMAGE ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT;

ANISOTROPY; BIOFILMS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, CONFOCAL; PROTEUS MIRABILIS; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS);

EID: 34548120576     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2007.05.022     Document Type: Article

References (34)

1. Baveye P. Comment on "Evaluation of biofilm image thresholding methods". Water Res. 36 (2002) 805-806
2. Beyenal H., Donovan C., Lewandowski Z., and Harkin G. Three-dimensional biofilm structure quantification. J. Microbiol. Methods 59 (2004) 395-413
3. Beyenal H., Lewandowski Z., and Harkin G. Quantifying biofilm structure: facts and fiction. Biofouling 20 (2004) 1-23
4. Black M., Sapiro G., Marimont D., and Heeger D. Robust anisotropic diffusion. IEEE Trans. Image Process. 7 (1998) 421-432
5. Catté F., Lions P.L., Morel J.M., and Coll T. Image selective smoothing and edge detection by nonlinear diffusion. SIAM J. Numer. Anal. 29 (1992) 182-193
6. Chang C.I., Chen K., Wang J., and Althouse M.L.G. A relative entropy-based approach to image thresholding. Pattern Recogn. 27 (1994) 1275-1289
7. Daims H., Lucker S., and Wagner M. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 8 (2006) 200-213
8. Davies D.G., Parsek M.R., Pearson J.P., Iglewski B.H., Costerton J.W., and Greenberg E.P. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science 12 (1998) 299-312
9. Fisher R. The use of multiple measures in taxonomic problems. Ann. Eugen. 7 (1936) 179-188
10. Glasbey C.A., and Horgan G.W. Image Analysis for the Biological Sciences (1995), Wiley, Chichester, UK
11. Harrison J.J., Ceri H., Yerly J., Stremick C.A., Hu Y., Martinuzzi R., and Turner R.J. The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device. Biol. Proced. Online 8 (2006) 194-215
12. Heydorn A., Nielsen A.T., Hentzer M., Sternberg C., Givskov M., Ersboll B.K., and Molin S. Quantification of biofilm structures by the novel computer program COMSTAT. Microbiology 146 (2000) 2395-2407
13. Huh Y., and Hwang J.J. The new extended JPEG coder with variable quantizer using block wavelet transform. IEEE Trans. Consum. Electron. 43 (1997) 401-409
14. Jansen A.M., Lockatell C.V., Johnson D.E., and Mobley H.L. Visualization of Proteus mirabilis morphotypes in the urinary tract: the elongated swarmer cell is rarely observed in ascending urinary tract infection. Infect. Immun. 71 (2003) 3607-3613
15. Kittler J., Illingworth J., and Foglein J. Threshold selection based on a simple image statistic. CVGIP 20 (1985) 125-147
16. Magid A., Rotman S.R., and Weiss A.M. Comment on "Picture thresholding using an iterative selection method". IEEE Trans. Syst. Man Cybern. 20 (1990) 1238-1239
17. Mah T.F., and O'Toole G.A. Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol. 9 (2001) 34-39
18. Miller M.B., and Bassler B.L. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55 (2001) 165-199
19. Mueller L., de Brouwer J., Almeida J., Stal L., and Xavier J. Analysis of a marine phototrophic biofilm by confocal laser scanning microscopy using the new image quantification software PHLIP. BMC Ecol. 6 (2006) 15 pages
20. Neu T.R., and Lawrence J.R. Development and structure of microbial stream biofilms as studied by confocal laser scanning microscopy. FEMS Microbiol. Ecol. 24 (1997) 11-25
21. Otsu N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. SMC-9 (1979) 62-66
22. Pal N.R., and Pal S.K. Entropy thresholding. Signal Process. 16 (1989) 97-108
23. Palmer R.J., and Sternberg C. Modern microscopy in biofilm research: confocal microscopy and other approaches. Curr. Opin. Biotechnol. 10 (1999) 263-268
24. Paranjape R.B. Fundamental enhancement technique. In: Bankman I.N. (Ed). Handbook of Medical Imaging Processing and Analysis (2000), Academic Press, San Diego 3-18
25. Pawley J.B. Sources of noise in three-dimensional microscopical data sets. In: Stevens J.K., Mills L.R., and Trogadis J.E. (Eds). Three-Dimensional Confocal Microscopy: Volume Investigation of Biological Specimens (1994), Academic Press, New York 47-93
26. Pawley J.B. Handbook of Biological Confocal Microscopy. 2nd edition (1996), Plenum Press, New York
27. Perona P., and Malik J. Scale-space and edge detection using anisotropic diffusion. IEEE Trans. Pattern Anal. Mach. Intell. 12 (1990) 629-639
28. Ridler T.W., and Calvard S. Picture thresholding using an iterative selection method. IEEE Trans. Syst. Man Cybern. SMC-8 (1978) 630-632
29. Sahoo P., Wilkins C., and Yeager J. Threshold selection using Renyi's entropy. Pattern Recogn. 30 (1997) 71-84
30. Segall C.A., and Acton S.T. Morphological anisotropic diffusion. Proc. IEEE Int. Conf. Image Process., Santa Barbara, CA, Oct. 26-29 vol. 3 (1997) 348-351
31. Stoodley P., Dodds I., Boyle J.D., and Lappin-Scott H.M. Influence of hydrodynamics and nutrients on biofilm structure. J. Appl. Microbiol. 85 (1999) 19S-28S
32. Xavier J.B., Schnell A., Wuertz S., Palmer R., White D.C., and Almeida J.S. Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images. J. Microbiol. Methods 47 (2001) 169-180
33. Yang X., Beyenal H., Harkin G., and Lewandowski Z. Quantifying biofilm structure using image analysis. J. Microbiol. Methods 39 (2000) 109-119
34. Yang X., Beyenal H., Harkin G., and Lewandowski Z. Evaluation of biofilm image thresholding methods. Water Res. 35 (2001) 1149-1158