The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.
daime , a novel image analysis program for microbial ecology and biofilm research
Abstract
Summary: Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA‐targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime ( d igital image a nalysis i n m icrobial e cology), a new computer program integrating 2‐D and 3‐D image analysis and visualization functionality, which has previously not been available in a single open‐source software package. For example, daime automatically finds 2‐D and 3‐D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with ‘3D‐FISH’, which preserves the 3‐D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure–function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.
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Cites
Nucleic acid techniques in bacterial systematics
Stackebrandt, E. S., & Goodfellow, M. (1991) · Wiley eBooks · Cited by 9,460
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
Amann, R., Ludwig, W., & SCHLEIFER, K. H. (1995) · Microbiological Reviews · doi:10.1128/mmbr.59.1.143-169.1995 · Cited by 9,093
Image analysis and mathematical morphology
(1982) · Computer Graphics and Image Processing · doi:10.1016/0146-664x(82)90078-8 · Cited by 8,151
Amann, R. I., Binder, B. J., Olson, R. J., Chisholm, S. W., Devereux, R., & Stahl, D. A. (1990) · Applied and Environmental Microbiology · doi:10.1128/aem.56.6.1919-1925.1990 · Cited by 4,021
Image Analysis and Mathematical Morphology.
Diggle, P. J., & Serra, J. (1983) · Biometrics · doi:10.2307/2531038 · Cited by 3,894
Daims, H., Brühl, A., Amann, R., Schleifer, K.-H., & Wagner, M. (1999) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(99)80053-8 · Cited by 2,274
Self-citationPicture Thresholding Using an Iterative Selection Method
(1978) · IEEE Transactions on Systems, Man, and Cybernetics · doi:10.1109/tsmc.1978.4310039 · Cited by 2,262
Quantification of biofilm structures by the novel computer program comstat
Heydorn, A., Nielsen, A. T., Hentzer, M., Sternberg, C., Givskov, M., Ersbøll, B. K., & Molin, S. (2000) · Microbiology · doi:10.1099/00221287-146-10-2395 · Cited by 2,179
Manz, W., Amann, R., Ludwig, W., Wagner, M., & Schleifer, K.-H. (1992) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(11)80121-9 · Cited by 2,043
Self-citationStable-isotope probing as a tool in microbial ecology
Radajewski, S., Ineson, P., Parekh, N. R., & Murrell, J. C. (2000) · Nature · doi:10.1038/35001054 · Cited by 1,252
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Self-citationA Bioinformatician's Guide to Metagenomics
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., & Hugenholtz, P. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00009-08 · Cited by 490
Wagner, M. (2009) · Annual Review of Microbiology · doi:10.1146/annurev.micro.091208.073233 · Cited by 264
Self-citationSpatial organization of a model 15-member human gut microbiota established in gnotobiotic mice
Mark Welch, J. L., Hasegawa, Y., McNulty, N. P., Gordon, J. I., & Borisy, G. G. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1711596114 · Cited by 236
Bacterial fight-and-flight responses enhance virulence in a polymicrobial infection
Stacy, A., Everett, J., Jorth, P., Trivedi, U., Rumbaugh, K. P., & Whiteley, M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400586111 · Cited by 192
Metadata
- Authors
- Daims, H., Lücker, S., & Wagner, M.
- Venue
- Environmental Microbiology
- Publisher
- Wiley
- Published
- 2005-08-10
- Volume
- 8
- Issue
- 2
- Pages
- 200-213
- ISSN
- 1462-2912 (ISSN-L)
- 1462-2920
- OpenAlex
- W1965460969
- Cited by
- 579
- References
- 58
- FWCI
- 10.33
- Type
- journal article
- Language
- en
- Open access
- closed
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