ArticleScientific reports2018
A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Artificial Intelligence-Empowered Single-Cell Phenotyping for Rapid, Automated Pathogen Diagnostics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm.Microbial ecology · 2026Article
- Effect of biofilm physical characteristics on their susceptibility to antibiotics: impacts of low-frequency ultrasound.NPJ biofilms and microbiomes · 2024Article
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- Characteristics of paraspinal muscle fat infiltration in asymptomatic Chinese adults: a cross-sectional study.Quantitative imaging in medicine and surgery · 2023Article
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- Automated analysis of mitochondrial dimensions in mesenchymal stem cells: Current methods and future perspectives.Heliyon · 2023Review
- In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities.Journal of applied microbiology · 2022Review
- DNase inhibits early biofilm formation inFrontiers in cellular and infection microbiology · 2022Article
- Biofilm viability checker: An open-source tool for automated biofilm viability analysis from confocal microscopy images.NPJ biofilms and microbiomes · 2021Article
- Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidence.Frontiers in microbiology · 2021Article
- High cell densities favor lysogeny: induction of an H20 prophage is repressed by quorum sensing and enhances biofilm formation in Vibrio anguillarum.The ISME journal · 2020Article
- Testing Anti-Biofilm Polymeric Surfaces: Where to Start?International journal of molecular sciences · 2019Review
- The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease.Journal of molecular biology · 2019Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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