Journal article
Three-dimensional biofilm structure quantification
Journal of microbiological methods, Vol.59(3), pp.395-413
2004
Handle:
https://hdl.handle.net/2376/100686
PMID: 15488282
Abstract
Quantitative 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
www.erc.montana.edu site prior to publication of the paper.
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Details
- Title
- Three-dimensional biofilm structure quantification
- Creators
- Haluk Beyenal - Center for Biofilm Engineering, P.O. Box 173980, Room 366 EPS, Montana State University, Bozeman, MT 59717-3980, United StatesConrad Donovan - Center for Biofilm Engineering, P.O. Box 173980, Room 366 EPS, Montana State University, Bozeman, MT 59717-3980, United StatesZbigniew Lewandowski - Center for Biofilm Engineering, P.O. Box 173980, Room 366 EPS, Montana State University, Bozeman, MT 59717-3980, United StatesGary Harkin - Computer Science Department, Montana State University, Bozeman, MT 59717, United States
- Publication Details
- Journal of microbiological methods, Vol.59(3), pp.395-413
- Academic Unit
- Chemical Engineering and Bioengineering, School of
- Publisher
- Elsevier B.V
- Identifiers
- 99900546659001842
- Language
- English
- Resource Type
- Journal article