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dc.contributor.authorBeyenal, Haluk
dc.contributor.authorDonovan, C.
dc.contributor.authorLewandowski, Zbigniew
dc.contributor.authorHarkin, Gary
dc.date.accessioned2017-07-26T22:46:52Z
dc.date.available2017-07-26T22:46:52Z
dc.date.issued2004-12
dc.identifier.citationBeyenal H, Donovan C, Lewandowski Z, Harkin G, "Three-dimensional biofilm structure quantification," J Microbiol Methods, 2004 59:395-413en_US
dc.identifier.issn0167-7012
dc.identifier.urihttps://scholarworks.montana.edu/xmlui/handle/1/13417
dc.description.abstractQuantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions. This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy, energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at site prior to publication of the paper.en_US
dc.titleThree-dimensional biofilm structure quantificationen_US
dc.typeArticleen_US
mus.citation.extentfirstpage395en_US
mus.citation.extentlastpage413en_US
mus.citation.issue3en_US
mus.citation.journaltitleJournal of Microbiological Methodsen_US
mus.citation.volume59en_US
mus.identifier.categoryEngineering & Computer Scienceen_US
mus.identifier.doi10.1016/j.mimet.2004.08.003en_US
mus.relation.collegeCollege of Engineeringen_US
mus.relation.departmentCenter for Biofilm Engineering.en_US
mus.relation.departmentChemical & Biological Engineering.en_US
mus.relation.departmentChemical Engineering.en_US
mus.relation.universityMontana State University - Bozemanen_US
mus.relation.researchgroupCenter for Biofilm Engineering.en_US
mus.data.thumbpage3en_US


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