Quantitative image analysis of microbial communities with BiofilmQ

2021/01/04 by Raimo Hartmann, Hannah Jeckel, Eric Jelli +17 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Cell Image Analysis Techniques #Microbial Community Ecology and Physiology #Bacterial biofilms and quorum sensing

paper · pdf · doi:10.1038/s41564-020-00817-4

openalex publication_date 2021/01/04 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ-a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

Citations

• Picture Thresholding Using an Iterative Selection Method
• A Threshold Selection Method from Gray-Level Histograms

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Discussions

• Mark has superb computer skills thus a bit of intruction from Knut Drescher's group, he could built a pipeline for analysis of the biofilm images including BiofilmQ (doi.org/10.1038/s415...) [5/n] [bsky, 0 points, 1 comments]