Assessment of three-dimensional biofilm models through direct comparison with confocal microscopy imaging

Water Science and Technology

Volumn 49, Issue 11-12, 2004, Pages 177-185

  Xavier, J B ^a   Picioreanu, C ^a   van Loosdrecht, M C M ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

3D modeling; Biofilm; Confocal microscopy; Image analysis; Model validation; Morphology quantification

Indexed keywords

CONFORMAL MAPPING; DENITRIFICATION; MATHEMATICAL MODELS; MICROSCOPIC EXAMINATION; SUBSTRATES;

BIOFILM STRUCTURE; SUBSTRATE PROFILES;

BIOFILMS;

BIOFILM; MATHEMATICAL MODELING;

ACCURACY; ARTICLE; BIOFILM; COMPARATIVE STUDY; CONFOCAL LASER MICROSCOPY; CONTROLLED STUDY; DATA ANALYSIS; DENITRIFICATION; EXPERIMENTATION; IMAGE ANALYSIS; LABORATORY TEST; MATHEMATICAL MODEL; METHODOLOGY; MICROMORPHOLOGY; MONITORING; PHYSICAL PARAMETERS; PREDICTION; QUANTITATIVE ANALYSIS; SPECIES; STRUCTURE ANALYSIS; THICKNESS; VOLUMETRY;

EID: 4344639715     PISSN: 02731223     EISSN: None     Source Type: Journal    
DOI: 10.2166/wst.2004.0834     Document Type: Article

References (24)

1. Atkinson, B. and Davies, I.J. (1974). The overall rate of substrate uptake (reaction) by microbial films. Part I - A biological rate equation. Trans. Instn Chem. Engrs, 52, 248-259.
2. Dockery, J. and Klapper, I. (2001). Finger formation in biofilm layers. SIAM J. Appl. Math., 62, 853-869.
3. Eberl, H.J., Parker, D.F. and van Loosdrecht, M.C.M. (2001). A new deterministic spatiotemporal continuum model for biofilm development. J. Theor. Med., 3, 161-175.
4. Forsythe, G.E., Malcom, M.A. and Moler, C.B. (1977). Computer Methods for Mathematical Computations. Prentice Hall, Englewood Cliffs.
5. Hermanowicz, S.W. (1999). Two-dimensional simulations of biofilm development: effect of external environmental conditions. Wat. Sci. Tech., 39(7), 107-114.
6. Hermanowicz, S.W. (2001). A simple 2D biofilm model yields a variety of morphological features. Mathematical Biosciences, 169, 1-14.
7. Heydorn, A., Ersboll, B.K., Hentzer, M., Parsek, M.R., Givskov, M. and Molin, S. (2000). Experimental reproducibility in flow-chamber biofilms. Microbiology, 146, 2409-2415.
8. Kreft, J.U., Booth, G. and Wimpenny, J.W.T. (1998). BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology, 144, 3275-3287.
9. Kreft, J.U., Picioreanu, C., Wimpenny, J.W.T. and van Loosdrecht, M.C.M. (2001). Individual-based modelling of biofilms. Microbiology-Sgm, 147, 2897-2912.
10. Kuehn, M., Hausner, M., Bungartz, H., Wagner, M., Wilderer, P. and Wertz, S. (1998). Automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms. Appl. Environ. Microbiol., 64, 4115-4127.
11. Lawrence, J.R., Wolfaardt, G.M. and Neu, T.R. (1998). The Study of Biofilms Using Confocal Laser Scanning Microscopy. Page 431 in M.H.F. Wilkinson and F. Schut (eds). Digital Image Analysis of Microbes: Imaging, Morphometry, Fluorometry and Motility Techniques and Applications. John Wiley & Sons, Chichester.
12. Murga, R., Stewart, P.S. and Daly, D. (1995). Quantitative analysis of biofilm thickness variability. Biotech. Bioeng., 45, 503-510.
13. Picioreanu, C., Loosdrecht, M.C.M. and Heijnen, J. (1998). Mathematical modelling of biofilm structure with a hybrid differential-discrete cellular automaton approach. Biotech. Bioeng., 58, 101-116.
14. Picioreanu, C., van Loosdrecht, M.C.M. and Heijnen, J.J. (1999). Discrete-differential modelling of biofilm structure. Wat. Sci. Tech., 39(7), 115-122.
15. Picioreanu, C., van Loosdrecht, M.C.M. and Heijnen, J.J. (2000). Effect of diffusive and convective substrate transport on biofilm structure formation: A two-dimensional modeling study. Biotechnology and Bioengineering, 69, 504-515.
16. Pizarro, G., Griggeath, D. and Noguera, D.R. (2001). Quantitative cellular automaton model for biofilms. Journal of Environmental Engineering, 127, 782-789.
17. Press, W.H., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1993). Numerical Recipes in C: the Art of Scientific Computing, 2nd edition. Cambridge University Press, Cambridge.
18. Rittman, B.E. and McCarthy, P.L. (1980). Model of steady-state biofilm kinetics. Biotechnol. Bioeng., 59, 261-272.
19. van Loosdrecht, M.C.M., Heijnen, J.J., Eberl, H.J., Kreft, J.U. and Picioreanu, C. (2002). Mathematical modelling of biofilm structures. Antonie van Leeuwenhoek, 81, 245-256.
20. Wanner, O. and Gujer, W. (1986). A multispecies biofilm model. Biotech. Bioeng., 28, 314-328.
21. Wanner, O. and Reichert, P. (1996). Mixed modeling of mixed-culture biofilms. Biotechnol. Bioeng., 49, 172-184.
22. Wimpenny, J.W.T. and Colasanti, R. (1997). A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models. FEMS Microbiol. Ecol., 22, 1-16.
23. Xavier, J.B., Schnell, A., Wuertz, S., Palmer, R., White, D.C. and Almeida, J.S. (2001). Objective threshold selection procedure (OTS) for segmentation of scanning confocal laser microscopy images. J. Microbiol. Meth., 47, 169-180.
24. Xavier, J.B., White, D.C. and Almeida, J.S. (2003). Automated Biofilm Morphology Quantification from Confocal Laser Scanning Microscopy Imaging. Wat. Sci. Tech., 47(5), 31-37.