Laser Scanning Microscopy for Microbial Flocs and Particles

Environmental Colloids and Particles: Behaviour, Separation and Characterisation

Volumn , Issue , 2007, Pages 469-505

  Lawrence, John R ^a   Neu, Thomas R ^b  

^a ENVIRONMENT CANADA   (Canada)

^b HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

Author keywords

Confocal laser scanning microscopy (CLSM); Digital image analysis (DIA) methodology and limitations; Fluorescence recovery after photobleaching (FRAP); Image processing and 3D visualisation; Imaging techniques; Laser scanning microscopy for microbial flocs and particles; Second harmonic imaging microscopy (SHIM) and coherent anti Stokes Raman scattering (CARS) microscopy; Sequential and simultaneous image acquisition; Transmission electron microscopy (TEM)

Indexed keywords

COHERENT SCATTERING; HIGH RESOLUTION TRANSMISSION ELECTRON MICROSCOPY; IMAGING TECHNIQUES; LASER APPLICATIONS; PHOTOBLEACHING; RAMAN SPECTROSCOPY; SCANNING; SCANNING ELECTRON MICROSCOPY; TRANSMISSION ELECTRON MICROSCOPY;

3D VISUALISATION; COHERENT ANTI-STOKES RAMAN SCATTERING MICROSCOPY; CONFOCAL LASER SCANNING MICROSCOPY; DIGITAL IMAGE ANALYSIS; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; MICROBIAL FLOC;

RAMAN SCATTERING;

EID: 80455170683     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470024539.ch10     Document Type: Chapter

References (102)

1. Minsky, M. (1988). Memoir on inventing the confocal microscope, Scanning, 10, 128-138.
2. Göppert-Mayer, M. (1931). Über Elementarakte mit zwei Quantensprüngen, Ann. Phys., 9, 273-295.
3. Denk, W., Strickler, J. H. and Webb, W. W. (1990). Two-photon laser scanning fluorescence microscopy, Science, 248, 73-76.
4. Lawrence, J. R., Korber, D. R., Hoyle, B. D., Costerton, J. W. and Caldwell, D. E., (1991). Optical sectioning of microbial biofilms, J. Bacteriol., 173, 6558-6567.
5. Vroom, J. M., Grauw,. C. J., Gerritsen, H. C., Bradshaw, A. M., Marsh, P. D., Watson, G. K., Birmingham, J. J. and Allison, C. (1999). Depth penetration and detection of pH gradients in biofilms by two-photon excitation microscopy, Appl. Environ. Microbiol., 65, 3502-3511.
6. Neu, T. R., Kuhlicke, U. and Lawrence, J. R. (2002). Assessment of fluorochromes for two-photon laser scanning microscopy of biofilms, Appl. Environ. Microbiol., 68, 901-909.
7. Neu, T. R., Walczysko, P. and Lawrence, J. R. (2004). Two-photon imaging for studying the microbial ecology of biofilm systems, Microbes Environ., 19, 1-6.
8. Lawrence, J. R., Wolfaardt, G. M. and Korber, D. R. (1994). Monitoring diffusion in biofilm matrices using scanning confocal laser microscopy, Appl. Environ. Microbiol., 60, 1166-1173.
9. Wuertz, S., Mueller, E., Spaeth, R., Pfleiderer, P. and Flemming, H.-C. (2000). Detection of heavy metals in bacterial biofilms and microbial flocs with the fluorescent complexing agent Newport Green, J. Ind. Microbiol. Biotechnol., 24, 116-123.
10. Amann, R. I., Ludwig, W. and Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol. Rev., 59, 143-169.
11. Neu, T. R., Swerhone, G. D. W. and Lawrence, J. R. (2001). Assessment of lectin-binding analysis for in situ detection of glycoconjugates in biofilm systems, Microbiology, 147, 299-313.
12. Neu, T. R. and Lawrence, J. R. (2002). Laser scanning microscopy in combination with fluorescence techniques for biofilm study. In The Encyclopedia of Environmental Microbiology, ed. Bitton, G. John Wiley & Sons, Inc., New York, pp. 1772-1788.
13. Poulsen, L. K., Ballard, G. and Stahl, D. A. (1993). Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms, Appl. Environ. Microbiol., 59, 1354-1360.
14. Lawrence, J. R., Korber, D. R., Wolfaardt, G. M., Caldwell, D. E. and Neu, T. R. (2002). Analytical imaging and microscopy techniques. In Manual of Environmental Microbiology, 2nd edn, eds Hurst, C. J., Crawford, R. L., Knudsen, G. R., McInerney, M. and Stetzenbach, L. D. American Society for Microbiology Press, Washington, DC, pp. 39-61.
15. Lawrence, J. R. and Neu, T. R. (1999). Confocal laser scanning microscopy for analysis of microbial biofilms, Methods Enzymol., 310, 131-144.
16. Lawrence, J. R., Neu, T. R. and Swerhone, G. D. W. (1998). Application of multiple parameter imaging for the quantification of algal, bacterial and exopolymer components of microbial biofilms, J. Microb. Methods, 32, 253-261.
17. Fatin-Rouge, N. and J. Buffle. (2007). Study of environmental systems by means of fluorescence correlation spectroscopy. In Environmental Colloids: Behaviour, Structure and Characterization, eds Wilkinson K. J. and Lead J. R. IUPAC Series on Analytical and Physical Chemistry of Environmental Systems, Vol. 10. John Wiley and Sons, Ltd, Chichester, Chapter 11.
18. Leppard, G. G. (1993). Organic flocs in surface waters: their native state and aggregation behavior in relation to contaminant dispersion. In Particulate Matter and Aquatic Contaminants, ed. Rao S. S. Lewis, Boca Raton, FL, pp. 169-195.
19. Leppard, G. G. (1992). Evaluation of electron microscope techniques for the description of aquatic colloids. In Environmental Particles, eds Buffle, J. and van Leeuwen, H. P. IUPAC Series on Analytical and Physical Chemistry of Environmental Systems, Vol. 1. Lewis, Boca Raton, FL, pp. 231-289.
20. Leppard, G. G., Burnison, B. K. and Buffle, J. (1990). Transmission electron microscopy of the natural organic matter of surface waters, Anal. Chim. Acta, 232, 107-121.
21. Droppo, I. G., Flannigan, D. T., Leppard, G. G., Jaskot, C. and Liss, S. N. (1996). Floc stabilization for multiple microscopic techniques, Appl. Environ. Microbiol., 62, 3508-3515.
22. Mavrocordatos, D., Perret, D. and Leppard, G. G. (2007). Strategies and advances in the characterisation of environmental colloids by electron microscopy. In Environmental Colloids: Behaviour, Structure and Characterization, eds Wilkinson, K. J. and Lead, J. R., IUPAC Series on Analytical and Physical Chemistry of Environmental Systems, Vol. 10. John Wiley & Sons, Ltd, Chichester, Chapter 8.
23. Neu, T. R. (2000). In situ cell and glycoconjugate distribution of river snow as studied by confocal laser scanning microscopy, Aquat. Microb. Ecol., 21, 85-95.
24. Decho, A. W. and Kawaguchi, T. (1999). Confocal imaging of in situ natural microbial communities and their extracellular polymeric secretions using Nanoplast resin, BioTechniques, 27, 1246-1252.
25. Kawaguchi, T. and Decho, A. (2002). In situ microspatial imaging using two-photon and confocal laser scanning microscopy of bacteria and extracellular polymeric secretions (EPS) within marine stromatolites, Mar. Biotechnol., 4, 127-131.
26. Perret, D., Leppard, G. G., Muller, M., Belzile, N., De Vitre, R. and Buffle, J. (1991) Electron microscopy of aquatic colloids: non-perturbating preparation of specimens in the field, Water Res., 25, 1333-1343.
27. Rocheleau, S, Greer C. W., Lawrence, J. R., Cantin C., Laramee, L. and Guiot S. R. (1999). Differentiation of Methanosaeta concilii and Methanosarcina barkeri in anaerobic mesophilic granular sludge by fluorescent in situ hybridization and confocal scanning laser microscopy, Appl. Environ. Microbiol., 65, 2222-2229.
28. Yu, F. P., Callis, G. M., Stewart, P. S., Griebe, T. and McFeters, G. A. (1994). Cryosectioning of biofilms for microscopic examination, Biofouling, 8, 85-91.
29. Massol-Deya, A., Whallon, J., Hickey, R. F. and Tiedje, J. (1995). Channel structures in aerobic biofilms of fixed film reactors treating contaminated groundwater, Appl. Environ. Microbiol., 61, 767-777.
30. Christensen, B. B., Sternberg, C., Andersen, J. B., Eberl, L., Møller, S., Givskov, M. and Molin, S. (1999). Molecular tools for study of biofilm physiology, Methods Enzymol., 310, 20-42.
31. Neu, T. R., Woelfl, S. and Lawrence, J. R. (2004). Three-dimensional differentiation of photo-autotrophic biofilm constituents by multi-channel laser scanning microscopy (singlephoton and two-photon excitation), J. Microbiol. Methods, 56, 161-172.
32. Sytsma, J., Vroom, J. M., Grauw, C. J. and Gerritsen, H.-C. (1998). Time-gated fluorescence lifetime imaging and microvolume spectroscopy using two-photon excitation, J. Microsc., 191, 39-51.
33. Bryers, J. D. (2001). Two-photon excitation microscopy for analyses of biofilm processes, Methods Enzymol., 337, 259-269.
34. Caldwell, D. E., Korber, D. R. and Lawrence, J. R. (1992). Confocal laser microscopy and digital image analysis in microbial ecology, Adv. Microb. Ecol., 12, 1-67.
35. Denk, W., Piston, D. W. and Webb, W. W. (1995). Two-photon molecular excitation in laser-scanning microscopy. In Handbook of Biological Confocal Microscopy, ed. Pawley, J. B. Plenum Press, New York, pp. 445-458.
36. Lawrence, J. R., Swerhone, G. D. W., Leppard, G. G., Araki, T., Zhang, X., West, M. M. and Hitchcock, A. P. (2003). Scanning transmission x-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofilms, Appl. Environ. Microbiol., 69, 5543-5554.
37. Ulrich, S., Karrasch, B., Hoppe, H. G., Jeskulke, K. and Mehrens, M. (1996). Toxic effects on bacterial metabolism of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride, Appl. Environ. Microbiol., 62, 4587-4593.
38. Gerlich, D. and Ellenberg, J. (2003). 4D imaging to assay complex dynamics in live specimens. Nat. Cell Biol., Suppl., 5, S14-S19.
39. Lawrence, J. R, Kwong, Y. T. J. and Swerhone, G. D. W. (1997). Colonization and weathering of natural sulfide mineral assemblages by Thiobacillus ferrooxidans, Can. J. Microbiol., 43, 68-78.
40. Lawrence, J. R., Chenier, M. R., Roy, R., Beaumier, D., Fortin, N., Swerhone, G. D. W., Neu, T. R. and Greer C. W. (2004). Microscale and molecular assessment of the impacts of nickel, nutrients and oxygen level on structure and function of river biofilm communities, Appl. Environ. Microbiol., 70, 4326-4339.
41. Packroff, G., Lawrence, J. R. and Neu, T. R. (2002). In situ confocal laser scanning microscopy of protozoans in pure cultures and complex communities, Acta Protozool., 41, 245-253.
42. Shotton, D. M. (1989). Confocal scanning optical microscopy and its applications for biological specimens, J. Cell Sci., 94, 175-206.
43. Breeuwer, P., Drocourt, J.-L., Rombouts, F. M. and Abee T. (1996). A novel method for continuous determination of the intracellular pH in bacteria with the internally conjugated fluorescent probe 5-(and 6-)-carboxyfluorescein succinimidyl ester, Appl. Environ. Microbiol., 62, 178-183.
44. Molenaar, D., Abee, T. and Konings, W. N. (1991). Continuous measurement of the cytoplasmic pH in Lactococcus lactis with a fluorescent pH indicator, Biochim. Biophys. Acta, 1115, 75-83.
45. Siegumfeldt, H., Bjornrechinger, K. and Jakobsen, M. (2000). Dynamic changes of intracellular pH in individual lactic acid bacterium cells in response to a rapid drop in extracellular pH, Appl. Environ. Microbiol., 66, 2330-2335.
46. Axelrod, D., Koppel, D. E., Schlessigner, J., Elson, E. and Webb, W. W. (1976). Mobility measurements by analysis of fluorescence photobleaching recovery kinetics, Biophys. J., 16, 1055-1069.
47. Lippincott-Schwartz, J., Altan-Bonnet, N. and Patterson, G. H. (2003). Photobleaching and photoactivation: following protein dynamics in living cells, Nat. Cell Biol., Suppl., 5, S7-S14.
48. Wolfaardt, G. M., Lawrence, J. R, Robarts, R. D. and Caldwell, D. E. (1995). Bioaccumulation of the herbicide diclofop in extracellular polymers and its utilization by a biofilm community during starvation, Appl. Environ. Microbiol., 61, 152-158.
49. Booth, M. J. and Wilson, T. (2004). Low-cost, frequency-domain, fluorescence lifetime confocal microscopy, J. Microsc., 214, 36-42.
50. Clegg, R. M., Holub, O. and Gohlke, C. (2003). Fluorescence lifetime-resolved imaging: measuring lifetimes in an image, Methods Enzymol., 360, 509-542.
51. Gadella, T. W. J. Jr. (1999). Fluorescence lifetime imaging microscopy (FLIM): instrumentation and applications. In Fluorescent and Luminescent Probes for Biological Activity, ed. Mason, W. T. B. Academic Press, San Diego, CA, pp. 467-479.
52. Sanders, R., Draaijer, A., Gerritsen, H. C., Houpt, P. M. and Levine, Y. K. (1995). Quantitative pH imaging in cells using confocal fluorescence lifetime imaging microscopy, Anal. Biochem., 227, 302-308.
53. Lin, H.-J., Herman, P., Kang, J. S. and Lakowicz, J. R. (2001). Fluorescence lifetime characterization of novel low-pH probes, Anal. Biochem., 294, 118-125.
54. Guiot, E., Georges, P., Brun, A., Fontaine, M. P., Bellon-Fontaine, M.-N. and Briandet, R. (2002). Heterogeneity of diffusion inside microbial biofilms determined by fluorescence correlation spectroscopy under two photon excitation, Photochem. Photobiol., 75, 570-578.
55. Szmacinski, H. and Lakowicz, J. R. (1993). Optical measurements of pH using fluorescent lifetimes and phase-modulation fluorometry, Anal. Chem., 65, 1668-1674.
56. Jares-Erijman, E. A. and Jovin, T. M. (2003). FRET imaging, Nat. Biotechnol., 21, 1387-1395.
57. Clegg, R. M. (1996). Fluorescence resonance energy transfer (FRET). In Fluorescence Imaging Spectroscopy and Microscopy, eds Wang, X. F. and Herman, B. J. John Wiley & Sons, Inc., New York, pp. 179-252.
58. Centonze, V. E., Sun, M., Masuda, A., Gerritsen, H. C. and Herman, B. (2003). Fluorescence resonance energy transfer imaging microscopy, Methods Enzymol., 360, 542-560.
59. Derdowski, A. A., Ding, L. and Spearman, P. (2004). A novel fluorescence resonance energy transfer assay demonstrates that the human immunodeficiency virus type 1 Pr55Gag I domain mediates Gag-Gag interactions, J. Virol., 78, 1230-1242.
60. Kloepfer, J. A., Mielke, R. E., Wong, M. S., Nealson, K. H., Stucky, G. and Nadeau, J. L. (2003). Quantum dots as strain-and metabolism-specific microbiological labels, Appl. Environ. Microbiol., 69, 4205-4213.
61. Neu, T. R. and Lawrence, J. R. (1997). Development and structure of microbial biofilms in river water studied by confocal laser scanning microscopy, FEMS Microb. Ecol., 24, 11-25.
62. Wolfaardt, G. M., Lawrence, J. R., Robarts, R. D. and Caldwell, D. E. (1998). In situ characterization of biofilm exopolymers involved in the accumulation of chlorinated organics, Microbiol. Ecol., 35, 213-223.
63. Paul, J. H. and Jeffrey, W. H. (1985). Evidence for separate adhesion mechanisms for hydrophilic and hydrophobic surfaces in Vibrio proteolytica, Appl. Environ. Microbiol., 50, 431-37.
64. Neu, T. R. and Marshall, K. C. (1991). Microbial 'footprints' -a new approach to adhesive polymers, Biofouling, 3, 101-112.
65. Neu, T. R. and Lawrence, J. R. (1999). In situ characterization of extracellular polymeric substances (EPS) in biofilm systems. In Microbial Extracellular Substances., eds Wingender, J., Neu, T. R. and Flemming, H.-C. Springer, Berlin, pp. 21-48.
66. Böckelmann, U., Manz, W., Neu, T. R. and Szewzyk, U. (2002). A new combined technique of fluorescent in situ hybridization and lectin-binding-analysis (FISH-LBA) for the investigation of lotic microbial aggregates, J. Microbiol. Methods, 49, 75-87.
67. De Beer, D., Stoodley, P. and Lewandowski, Z. (1997). Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy, Biotechnol. Bioeng., 53, 151-8.
68. Nielsen, J. L., Mikkelsen, L. H. and Nielsen, P. H. (2000). In situ detection of cell surface hydrophobicity of probe-defined bacteria in activated sludge, Water Sci. Technol., 43, 97-103.
69. Lawrence, J. R., Kopf, G., Headley, J. V. and Neu, T. R. (2001). Sorption and metabolism of selected herbicides in river biofilm communities, Can. J. Microbiol., 47, 634-641.
70. Steward, G. F. and Azam, F. (1999). Bromodeoxyuridine as an alternative to H-thymidine for measuring bacterial productivity in aquatic samples, Aquat. Microb. Ecol., 19, 57-66.
71. Rodrigues, G. G., Phipps, D., Ishiguro, K. and Ridgway, H. F. (1992). Use of a fluorescent redox probe for direct visualization of actively respiring bacteria, Appl. Environ. Microbiol., 58, 1801-1808.
72. Choi, J.-W., Sherr, B. F. and Sherr, E. B. (1999). Dead or alive? A large fraction of ETSinactive marine bacterioplankton cells, as assessed by reduction of CTC, can become ETSactive with incubation and substrate addition, Aquat. Microb. Ecol., 18, 105-115.
73. Lopez-Amoros, R., Comas, J. and Vives-Rego, J. (1995). Flow cytometric assessment of Escherichia coli and Salmonella typhimurium starvation-survival in seawater using rhodamine 123, propidium iodide and oxonol, Appl. Environ. Microbiol., 61, 2521-2526.
74. Muller, M, Loffhagen, N., Bley, T. and Babel, W. (1996). Membrane-potential-related fluorescence intensity indicates bacterial injury, Microbiol. Res., 151, 127-31.
75. Van Ommen Kloeke, F. and Geesey, G. G. (1999). Localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs, Microb. Ecol., 38, 201-214.
76. Davies, D. G., Chakrabarty, A. and Geesey G. G. (1993). Exopolysaccharide production in biofilms: substratum activation of alginate gene expression by Pseudomonas aeruginosa, Appl. Environ. Microbiol., 59, 1181-1186.
77. Davies, D. G. and Geesey G. G. (1995). Regulation of the alginate biosynthesis gene algC in Pseudomonas aeruginosa during biofilm development in continuous culture, Appl. Environ. Microbiol., 61, 860-87.
78. Errampali, D., Leung, K., Cassidy, M. B., Kostrzynska, M., Blears, M., Lee, H. and Trevors, J. T. (1999). Applications of the green fluorescent protein as a molecular marker in environmental microorganisms, J. Microbiol. Meth., 35, 187-199.
79. Møller, S., Sternberg, C., Andersen, J.-B., Christensen, B. B., Ramos, J. L., Givskov, M. and Molin, S. (1998). In situ gene expression in mixed-culture biofilms: evidence of metabolic interactions between community members, Appl. Environ. Microbiol., 64, 721-732.
80. Christensen, B. B., Haagensen, J. A. J., Heydorn, A. and Molin, S. (2002). Metabolic commensalism and competition in a two-species microbial consortium, Appl. Environ. Microbiol., 68, 2495-2502.
81. Hausner, M. and Wuertz, S. (1999). High rates of conjugation in bacterial biofilms as determined by quantitative in situ analysis, Appl. Environ. Microbiol., 65, 3710-3713.
82. Hodson, R. E., Dustman, W. A, Garg, R. P. and Moran M. A. (1995). In situ PCR for visualization of microscale distribution of specific genes and gene products in prokaryotic communities, Appl. Environ. Microbiol., 61, 4074-4082.
83. Gray, N. D., Howarth, R., Pickup, R. W., Jones, J. G. and Head, I. M. (2000). Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium, Appl. Environ. Microbiol., 66, 4518-4522.
84. Lee, N., Nielsen, P. H., Andreasen, K. H., Juretschko, S., Nielsen, J. L., Schleifer, K. and Wagner, M. (1999). Combination of fluorescent in situ hybridisation and microautoradiography -a new tool for structure-function analyses in microbial ecology, Appl. Environ. Microbiol., 65, 1289-1297.
85. Nielsen, J. L., Juretschko, S., Wagner, M. and Nielsen, P. H. (2002). Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography, Appl. Environ. Microbiol., 68, 4629-4636.
86. Nielsen, J. L., Christensen, D., Kloppenborg, M. and Nielsen, P. H. (2003). Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization, Environ. Microbiol., 5, 202-211.
87. Ouverney, C. C. and Fuhrman, J. A. (1999). Combined microautoradiography -16sRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ, Appl. Environ. Microbiol., 65, 1746-1752.
88. Agard, D. A. (1984). Optical sectioning microscopy: cellular architecture in three dimensions, Annu. Rev. Biophys. Bioeng., 13, 191-219.
89. Gorby, G. L. (1994) Digital confocal microscopy allows measurements and three-dimensional multiple spectral reconstructions of Neisseria gonorrhoea/epithelial cell interactions in the human fallopian tube organ culture model, J. Histochem. Cytochem., 42, 297-306.
90. Manz, W., Arp, G., Schumann-Kindel, G., Szewzky, U. and Reitner J. (2000). Widefield deconvolution epifluorescence microscopy combined with fluorescence in situ hybridization reveals the spatial arrangement of bacteria in sponge tissue, J. Microbiol. Methods, 40, 125-134.
91. Liu, J., Dazzo, F. B., Glagoleva, O., Yu, B. and. Jain A. K (2001). CMEIAS: a computeraided system for the image analysis of bacterial morphotypes in microbial communities, Microb. Ecol., 41, 173-194.
92. Heydorn, A., Nielsen, A. T., Hentzer, M., Sternberg, C., Givskov, M., Ersböll, B. K. and Molin, S. (2000). Quantification of biofilm structures by the novel computer program COMSTAT, Microbiology, 146, 2395-2407.
93. Beyenal, H., Donovan, C., Lewandowski, Z. and Harkin, G. (2004). Three-dimensional biofilm structure quantification, J. Microbiol. Methods, 59, 395-413.
94. Xavier, J. B., White, D. C. and Almeida, J. S. (2003). Automated biofilm morphology quantification from confocal laser scanning microscopy imaging, Water Sci. Technol., 47, 31-37.
95. Rodenacker, K., Hausner, M. and Gorbushina, A. A. (2003). Quantification and spatial relationship of microorganisms in sub-aquatic and subaerial biofilms. In Fossil and Recent Biofilms, eds Krumbein, W. E., Paterson, D. M. and Zavarzin, G. A. Kluwer, Dordrecht, pp. 387-399.
96. Bergner, S., Pohle, R., Al-Zubi, S., Toennies, K., Eitner, A. and Neu, T. R. (2002). Segmenting microorganisms in multi-modal volumetric datasets using a modified watershed transform. In Lecture Notes in Computer Science, ed. Van Gool, L., Springer, Heidelberg, pp. 429-437.
97. Staudt, C., Horn, H., Hempel, D. C. and Neu, T. R. (2004). Volumetric measurements of bacterial cells and extracellular polymeric substance glycoconjugates in biofilms, Biotechnol. Bioeng., 88, 585-592.
98. Bloem, J., Veninga, M. and Shepherd, J. (1995). Fully automatic determination of soil bacterium numbers, cell volumes and frequency of dividing cells by confocal laser scanning microscopy and image analysis, Appl. Environ. Microbiol., 61, 926-936.
99. Rodenacker, K., Hausner, M., Kühn, M., Wuertz, S. and Purkayastha, S. (2001). Depth intensity correction of biofilm volume data from confocal laser scanning microscopes, In Proceedings of 8th ECS and Image Analysis, Bordeaux, pp. 556-560.
100. Yang, X., Beyenal, H., Harkin, G. and Lewandowski, Z. (2001). Evaluation of biofilm image thresholding methods, Water Res., 35, 1149-1158.
101. Yang, X., Beyenal, H., Harkin, G. and Lewandowski, Z. (2000). Quantifying biofilm structure using image analysis, J. Microbiol. Methods, 39, 109-119.
102. 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 laser confocal microscope images, J. Microbiol. Methods, 47, 169-180.