Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples

Applied and Environmental Microbiology

Volumn 73, Issue 9, 2007, Pages 2956-2962

  Zhou, Zhi ^a   Pons, Marie Noëlle ^b   Raskin, Lutgarde ^a,c   Zilles, Julie L ^a  

^a United States of America   (United States)

^b UNIVERSITÉ DE LORRAINE   (France)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; FLUORESCENCE; FUZZY CLUSTERING; IMAGE ANALYSIS; QUALITY CONTROL; SOILS;

AUTOMATED IMAGE ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION (FISH); MANUAL QUALITY CONTROL; MICROBIAL CELL AGGREGATES;

ENVIRONMENTAL ENGINEERING;

4',6 DIAMIDINO 2 PHENYLINDOLE; RNA 16S;

CLUSTER ANALYSIS; FLUORESCENCE; HYBRIDIZATION; IMAGE ANALYSIS; MANURE; QUALITY CONTROL; RNA;

ARTICLE; AUTOANALYSIS; CLUSTER ANALYSIS; COMPUTER PROGRAM; FLUORESCENCE IN SITU HYBRIDIZATION; FUZZY SYSTEM; IMAGE ANALYSIS; QUANTITATIVE ANALYSIS; SIGNAL PROCESSING; SOIL; SWINE; VALIDATION PROCESS;

ANIMALS; ENVIRONMENTAL MICROBIOLOGY; IMAGE PROCESSING, COMPUTER-ASSISTED; IN SITU HYBRIDIZATION, FLUORESCENCE; INDOLES; MANURE; SOIL MICROBIOLOGY; SWINE;

ARCHAEA; BACTERIA (MICROORGANISMS); SUIDAE;

EID: 34248208501     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02954-06     Document Type: Article

References (30)

1. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
2. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
3. Angenent, L. T., S. Sung, and L. Raskin. 2002. Methanogenic population dynamics during startup of a full-scale anaerobic sequencing batch reactor treating swine waste. Water Res. 36:4648-4654.
4. Bauman, J. G., J. Wiegant, P. Borst, and P. van Duijn. 1980. A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochrome labelled RNA. Exp. Cell Res. 128:485-490.
5. Blackburn, N., A. Hagstrom, J. Wikner, R. Cuadros-Hansson, and P. K. Bjornsen. 1998. Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis. Appl. Environ. Microbiol. 64:3246-3255.
6. Budny, B., M. Kanik, and A. Latos-Bieleniska. 2002. Fluorescence in situ hybridization (FISH) - application in research and diagnostics. Folia Histochem. Cytobiol. 40:107-108.
7. Burrough, P. A., P. F. M. van Gaans, and R. A. MacMillan. 2000. High-resolution landform classification using fuzzy k-means. Fuzzy Sets Syst. 113: 37-52.
8. Christensen, H., M. Hansen, and J. Sorensen. 1999. Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl. Environ. Microbiol. 65:1753-1761.
9. Cotta, M. A., T. R. Whitehead, and R. L. Zeltwanger. 2003. Isolation, characterization and comparison of bacteria from swine faeces and manure storage pits. Environ. Microbiol. 5:737-745.
10. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
11. de los Reyes, F. L., W. Ritter, and L, Raskin. 1997. Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl. Environ. Microbiol. 63:1107-1117.
12. Dembele, D., and P. Kastner. 2003. Fuzzy C-means method for clustering microarray data. Bioinformatics 19:973-980.
13. Fraley, C., and A. E. Raftery. 2002. Model-based clustering, discriminant analysis, and density estimation. Technical report no. 380, Department of Statistics. J. Am. Stat. Assoc. 97:611-631.
14. Garini, Y., A. Gil, I. Bar-Am, D. Cabib, and N. Katzir. 1999. Signal to noise analysis of multiple color fluorescence imaging microscopy. Cytometry 35: 214-226.
15. Gasch, A. P., and M. B. Eisen. 2002. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome. Biol. 3:RESEARCH0059.
16. Gorsevski, P. V., P. E. Gessler, and P. Jankowski. 2003. Integrating a fuzzy k-means classification and a Bayesian approach for spatial prediction of landslide hazard. J. Geograph. Syst. 5:223-251.
17. Griffin, M. E., K. D. McMahon, R. I. Mackie, and L. Raskin. 1998. Methanogenic population dynamics during start-up of anaerobic digesters treating municipal solid waste and biosolids. Biotechnol. Bioeng. 57:342-355.
18. Jindal, A. 2002. Antimicrobial resistance in swine waste treatment processes. M.S. thesis. University of Illinois, Urbana.
19. Kapur, J. N., P. K. Sahoo, and A. K. C. Wong. 1985. A new method for gray-level picture thresholding using the entropy of the histogram. Comput. Vis. Graphics Image Process. 29:273-285.
20. Kobabe, S., D. Wagner, and E.-M. Pfeiffer. 2004. Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiol. Ecol. 50:13-23.
21. Langendijk, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61: 3069-3075.
22. Lerner, B. 2004. Bayesian fluorescence in situ hybridisation signal classification. Artif. Intellig. Med. 30:301-316.
23. Li, S., R. N. Spear, and J. H. Andrews. 1997. Quantitative fluorescence in situ hybridization of Aureobasidium pullulans on microscope slides and leaf surfaces. Appl. Environ. Microbiol. 63:3261-3267.
24. McMahon, K. D., P. G. Stroot, R. I. Mackie, and L. Raskin. 2001. Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions. II. Microbial population dynamics. Water Res. 35:1817-1827.
25. Pernthaler, J., A. Pernthaler, and R. Amann. 2003. Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 69:2631-2637.
26. Shopov, A., S. C. Williams, and P. G. Verity. 2000. Improvements in image analysis and fluorescence microscopy to discriminate and enumerate bacteria and viruses in aquatic samples. Aquat. Microb. Ecol. 22:103-110.
27. Singleton, S., J. G. Cahill, G. K. Watson, C. Allison, D. Cummins, T. Thurnheer, B. Guggenheim, and R. Gmur. 2001. A fully automated microscope bacterial enumeration system for studies of oral microbial ecology. J. Immunoass. Immunochem. 22:253-274.
28. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, England.
29. Vincent, L., and P. Soille. 1991. Watersheds in digital spaces: an efficient algorithm based on immersion simulations. IEEE Trans. Pattern Analysis Machine Intelligence 13:583-598.
30. Wang, J., T. H. Bo, I. Jonassen, O. Myklebost, and E. Hovig. 2003. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics 4:60.