A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms

Abstract Biofilms are surface-attached microbial communities whose architecture can be captured with confocal microscopy. Manual or automatic thresholding of acquired images is often needed to help distinguish biofilm biomass from background noise. However, manual thresholding is subjective and curr...

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Autores principales:	Ting L. Luo, Marisa C. Eisenberg, Michael A. L. Hayashi, Carlos Gonzalez-Cabezas, Betsy Foxman, Carl F. Marrs, Alexander H. Rickard
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a4dea36ed02c464d90ccebb189d9b4e1
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spelling	oai:doaj.org-article:a4dea36ed02c464d90ccebb189d9b4e12021-12-02T15:08:29ZA Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms10.1038/s41598-018-31012-52045-2322https://doaj.org/article/a4dea36ed02c464d90ccebb189d9b4e12018-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-31012-5https://doaj.org/toc/2045-2322Abstract Biofilms are surface-attached microbial communities whose architecture can be captured with confocal microscopy. Manual or automatic thresholding of acquired images is often needed to help distinguish biofilm biomass from background noise. However, manual thresholding is subjective and current automatic thresholding methods can lead to loss of meaningful data. Here, we describe an automatic thresholding method designed for confocal fluorescent signal, termed the biovolume elasticity method (BEM). We evaluated BEM using confocal image stacks of oral biofilms grown in pooled human saliva. Image stacks were thresholded manually and automatically with three different methods; Otsu, iterative selection (IS), and BEM. Effects on biovolume, surface area, and number of objects detected indicated that the BEM was the least aggressive at removing signal, and provided the greatest visual and quantitative acuity of single cells. Thus, thresholding with BEM offers a sensitive, automatic, and tunable method to maintain biofilm architectural properties for subsequent analysis.Ting L. LuoMarisa C. EisenbergMichael A. L. HayashiCarlos Gonzalez-CabezasBetsy FoxmanCarl F. MarrsAlexander H. RickardNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-14 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ting L. Luo Marisa C. Eisenberg Michael A. L. Hayashi Carlos Gonzalez-Cabezas Betsy Foxman Carl F. Marrs Alexander H. Rickard A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
description	Abstract Biofilms are surface-attached microbial communities whose architecture can be captured with confocal microscopy. Manual or automatic thresholding of acquired images is often needed to help distinguish biofilm biomass from background noise. However, manual thresholding is subjective and current automatic thresholding methods can lead to loss of meaningful data. Here, we describe an automatic thresholding method designed for confocal fluorescent signal, termed the biovolume elasticity method (BEM). We evaluated BEM using confocal image stacks of oral biofilms grown in pooled human saliva. Image stacks were thresholded manually and automatically with three different methods; Otsu, iterative selection (IS), and BEM. Effects on biovolume, surface area, and number of objects detected indicated that the BEM was the least aggressive at removing signal, and provided the greatest visual and quantitative acuity of single cells. Thus, thresholding with BEM offers a sensitive, automatic, and tunable method to maintain biofilm architectural properties for subsequent analysis.
format	article
author	Ting L. Luo Marisa C. Eisenberg Michael A. L. Hayashi Carlos Gonzalez-Cabezas Betsy Foxman Carl F. Marrs Alexander H. Rickard
author_facet	Ting L. Luo Marisa C. Eisenberg Michael A. L. Hayashi Carlos Gonzalez-Cabezas Betsy Foxman Carl F. Marrs Alexander H. Rickard
author_sort	Ting L. Luo
title	A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
title_short	A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
title_full	A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
title_fullStr	A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
title_full_unstemmed	A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms
title_sort	sensitive thresholding method for confocal laser scanning microscope image stacks of microbial biofilms
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/a4dea36ed02c464d90ccebb189d9b4e1
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A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms

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