Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law
Beer's Law explains how light attenuates into thick specimens, including thick biofilms. We use a Bayesian optimality criterion, the maximum of the posterior probability distribution, and computationally efficiently fit Beer's Law to the 3D intensity data collected from thick living biofil...
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ftmontanastateu:oai:scholarworks.montana.edu:1/16457 2023-05-15T13:55:57+02:00 Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law Parker, Albert E. Christen, J. A. Lorenz, Lindsey A. Smith, Heidi J. 2020-05 application/pdf https://scholarworks.montana.edu/xmlui/handle/1/16457 en_US eng Parker, A.E., Christen, J.A., Lorenz, L., & Smith, H. (2020). Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law. Journal of Microbiological Methods, 174, 105943. https://doi.org/10.1016/j.mimet.2020.105943 0167-7012 https://scholarworks.montana.edu/xmlui/handle/1/16457 © This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/ CC-BY-NC-ND Article 2020 ftmontanastateu 2022-06-06T07:24:11Z Beer's Law explains how light attenuates into thick specimens, including thick biofilms. We use a Bayesian optimality criterion, the maximum of the posterior probability distribution, and computationally efficiently fit Beer's Law to the 3D intensity data collected from thick living biofilms by a confocal scanning laser microscope. Using this approach the top surface of the biofilm and an optimal image threshold can be estimated. Biofilm characteristics, such as bio-volumes, can be calculated from this surface. Results from the Bayesian approach are compared to other approaches including the method of maximum likelihood or simply counting bright pixels. Uncertainty quantification (i.e., error bars) can be provided for the parameters of interest. This approach is applied to confocal images of stained biofilms of a common lab strain of Pseudomonas aeruginosa, stained biofilms of Janthinobacterium isolated from the Antarctic, and biofilms of Staphylococcus aureus that have been genetically modified to fluoresce green. Article in Journal/Newspaper Antarc* Antarctic Montana State University (MSU): ScholarWorks Antarctic The Antarctic |
institution |
Open Polar |
collection |
Montana State University (MSU): ScholarWorks |
op_collection_id |
ftmontanastateu |
language |
English |
description |
Beer's Law explains how light attenuates into thick specimens, including thick biofilms. We use a Bayesian optimality criterion, the maximum of the posterior probability distribution, and computationally efficiently fit Beer's Law to the 3D intensity data collected from thick living biofilms by a confocal scanning laser microscope. Using this approach the top surface of the biofilm and an optimal image threshold can be estimated. Biofilm characteristics, such as bio-volumes, can be calculated from this surface. Results from the Bayesian approach are compared to other approaches including the method of maximum likelihood or simply counting bright pixels. Uncertainty quantification (i.e., error bars) can be provided for the parameters of interest. This approach is applied to confocal images of stained biofilms of a common lab strain of Pseudomonas aeruginosa, stained biofilms of Janthinobacterium isolated from the Antarctic, and biofilms of Staphylococcus aureus that have been genetically modified to fluoresce green. |
format |
Article in Journal/Newspaper |
author |
Parker, Albert E. Christen, J. A. Lorenz, Lindsey A. Smith, Heidi J. |
spellingShingle |
Parker, Albert E. Christen, J. A. Lorenz, Lindsey A. Smith, Heidi J. Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
author_facet |
Parker, Albert E. Christen, J. A. Lorenz, Lindsey A. Smith, Heidi J. |
author_sort |
Parker, Albert E. |
title |
Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
title_short |
Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
title_full |
Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
title_fullStr |
Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
title_full_unstemmed |
Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law |
title_sort |
optimal surface estimation and thresholding of confocal microscope images of biofilms using beer's law |
publishDate |
2020 |
url |
https://scholarworks.montana.edu/xmlui/handle/1/16457 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
Parker, A.E., Christen, J.A., Lorenz, L., & Smith, H. (2020). Optimal surface estimation and thresholding of confocal microscope images of biofilms using Beer's Law. Journal of Microbiological Methods, 174, 105943. https://doi.org/10.1016/j.mimet.2020.105943 0167-7012 https://scholarworks.montana.edu/xmlui/handle/1/16457 |
op_rights |
© This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/ |
op_rightsnorm |
CC-BY-NC-ND |
_version_ |
1766262945862385664 |