Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images

Abstract Quantifying biofilm formation on surfaces is challenging because traditional microbiological methods, such as total colony-forming units (CFUs), often rely on manual counting. These are laborious, resource intensive techniques, more susceptible to human error. Confocal laser scanning micros...

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Autores principales:	Sophie E. Mountcastle, Nina Vyas, Victor M. Villapun, Sophie C. Cox, Sara Jabbari, Rachel L. Sammons, Richard M. Shelton, A. Damien Walmsley, Sarah A. Kuehne
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/636b47d961724f49943cd012bcbcd36d
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spelling	oai:doaj.org-article:636b47d961724f49943cd012bcbcd36d2021-12-02T15:55:18ZBiofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images10.1038/s41522-021-00214-72055-5008https://doaj.org/article/636b47d961724f49943cd012bcbcd36d2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00214-7https://doaj.org/toc/2055-5008Abstract Quantifying biofilm formation on surfaces is challenging because traditional microbiological methods, such as total colony-forming units (CFUs), often rely on manual counting. These are laborious, resource intensive techniques, more susceptible to human error. Confocal laser scanning microscopy (CLSM) is a high-resolution technique that allows 3D visualisation of biofilm architecture. In combination with a live/dead stain, it can be used to quantify biofilm viability on both transparent and opaque surfaces. However, there is little consensus on the appropriate methodology to apply in confocal micrograph processing. In this study, we report the development of an image analysis approach to repeatably quantify biofilm viability and surface coverage. We also demonstrate its use for a range of bacterial species and translational applications. This protocol has been created with ease of use and accessibility in mind, to enable researchers who do not specialise in computational techniques to be confident in applying these methods to analyse biofilm micrographs. Furthermore, the simplicity of the method enables the user to adapt it for their bespoke needs. Validation experiments demonstrate the automated analysis is robust and accurate across a range of bacterial species and an improvement on traditional microbiological analysis. Furthermore, application to translational case studies show the automated method is a reliable measurement of biomass and cell viability. This approach will ensure image analysis is an accessible option for those in the microbiology and biomaterials field, improve current detection approaches and ultimately support the development of novel strategies for preventing biofilm formation by ensuring comparability across studies.Sophie E. MountcastleNina VyasVictor M. VillapunSophie C. CoxSara JabbariRachel L. SammonsRichard M. SheltonA. Damien WalmsleySarah A. KuehneNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbial ecology QR100-130
spellingShingle	Microbial ecology QR100-130 Sophie E. Mountcastle Nina Vyas Victor M. Villapun Sophie C. Cox Sara Jabbari Rachel L. Sammons Richard M. Shelton A. Damien Walmsley Sarah A. Kuehne Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
description	Abstract Quantifying biofilm formation on surfaces is challenging because traditional microbiological methods, such as total colony-forming units (CFUs), often rely on manual counting. These are laborious, resource intensive techniques, more susceptible to human error. Confocal laser scanning microscopy (CLSM) is a high-resolution technique that allows 3D visualisation of biofilm architecture. In combination with a live/dead stain, it can be used to quantify biofilm viability on both transparent and opaque surfaces. However, there is little consensus on the appropriate methodology to apply in confocal micrograph processing. In this study, we report the development of an image analysis approach to repeatably quantify biofilm viability and surface coverage. We also demonstrate its use for a range of bacterial species and translational applications. This protocol has been created with ease of use and accessibility in mind, to enable researchers who do not specialise in computational techniques to be confident in applying these methods to analyse biofilm micrographs. Furthermore, the simplicity of the method enables the user to adapt it for their bespoke needs. Validation experiments demonstrate the automated analysis is robust and accurate across a range of bacterial species and an improvement on traditional microbiological analysis. Furthermore, application to translational case studies show the automated method is a reliable measurement of biomass and cell viability. This approach will ensure image analysis is an accessible option for those in the microbiology and biomaterials field, improve current detection approaches and ultimately support the development of novel strategies for preventing biofilm formation by ensuring comparability across studies.
format	article
author	Sophie E. Mountcastle Nina Vyas Victor M. Villapun Sophie C. Cox Sara Jabbari Rachel L. Sammons Richard M. Shelton A. Damien Walmsley Sarah A. Kuehne
author_facet	Sophie E. Mountcastle Nina Vyas Victor M. Villapun Sophie C. Cox Sara Jabbari Rachel L. Sammons Richard M. Shelton A. Damien Walmsley Sarah A. Kuehne
author_sort	Sophie E. Mountcastle
title	Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
title_short	Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
title_full	Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
title_fullStr	Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
title_full_unstemmed	Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images
title_sort	biofilm viability checker: an open-source tool for automated biofilm viability analysis from confocal microscopy images
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/636b47d961724f49943cd012bcbcd36d
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_version_	1718385395535708160

Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images

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