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A novel algorithm for the determination of bacterial cell volumes that is unbiased by cell morphology


Zeder, M; Kohler, E; Zeder, L; Pernthaler, J (2011). A novel algorithm for the determination of bacterial cell volumes that is unbiased by cell morphology. Microscopy and Microanalysis, 17(5):799-809.

Abstract

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto-and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e. g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manner.

The determination of cell volumes and biomass offers a means of comparing the standing stocks of auto-and heterotrophic microbes of vastly different sizes for applications including the assessment of the flux of organic carbon within aquatic ecosystems. Conclusions about the importance of particular genotypes within microbial communities (e. g., of filamentous bacteria) may strongly depend on whether their contribution to total abundance or to biomass is regarded. Fluorescence microscopy and image analysis are suitable tools for determining bacterial biomass that moreover hold the potential to replace labor-intensive manual measurements by fully automated approaches. However, the current approaches to calculate bacterial cell volumes from digital images are intrinsically biased by the models that are used to approximate the morphology of the cells. Therefore, we developed a generic contour based algorithm to reconstruct the volumes of prokaryotic cells from two-dimensional representations (i.e., microscopic images) irrespective of their shape. Geometric models of commonly encountered bacterial morphotypes were used to verify the algorithm and to compare its performance with previously described approaches. The algorithm is embedded in a freely available computer program that is able to process both raw (8-bit grayscale) and thresholded (binary) images in a fully automated manner.

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7 citations in Web of Science®
6 citations in Scopus®
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Contributors:Inst Plant Biol, Dept Limnol, UZH, Max Planck Inst Marine Microbiol, Dept Mol Ecol, D-28359 Bremen, Germany , Technobiol GmbH, CH-6033 Buchrain, Switzerland
Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:580 Plants (Botany)
Language:English
Date:1 October 2011
Deposited On:05 Mar 2012 14:08
Last Modified:05 Apr 2016 15:40
Publisher:Cambridge University Press
ISSN:1431-9276
Additional Information:Copyright: Cambridge University Press.
Publisher DOI:10.1017/S1431927611012104
PubMed ID:21910938
Permanent URL: http://doi.org/10.5167/uzh-59993

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