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Updated: Jan 20, 2026
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Harvesting and Disaggregation: An Overlooked Step in Biofilm Methods Research
Published on: April 22, 2022
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Structure and Fluorescence Intensity Measurements in Biofilms
Bertrand Cinquin1, Filipa Lopes2
1Laboratoire de Biologie et Pharmaceutique Appliquée, ENS Saclay, Cachan, France. bcinquin@ens-paris-saclay.fr.
Methods in Molecular Biology (Clifton, N.J.)
|August 22, 2019
Summary
A new ImageJ tool, BIAM, quantifies fluorescent signal intensity and biofilm architecture from confocal laser scanning microscopy data. This advances biofilm research by enabling detailed analysis of development and gene expression.
Area of Science:
- Microbiology
- Biophysics
- Image Analysis
Background:
- Confocal laser scanning microscopy (CLSM) is crucial for in situ biofilm research.
- Existing tools effectively analyze biofilm architecture but lack depth-specific fluorescence quantification.
- Accurate measurement of fluorescence intensity across biofilm depth is needed.
Purpose of the Study:
- To introduce BIAM (Biofilm Intensity and Architecture Measurement), an ImageJ-based tool.
- To enable simultaneous extraction of biofilm structure and fluorescence intensity from CLSM data.
- To address the need for quantitative analysis of fluorescence signals within biofilm depth.
Main Methods:
- Development of a novel tool within the ImageJ open-source software.
- Utilizing CLSM data as input for analysis.
- Extracting both structural and fluorescence intensity information from 3D biofilm images.
Main Results:
- BIAM successfully extracts structural and fluorescence intensity data from CLSM images.
- The tool provides quantitative measurements of fluorescence signal over biofilm depth.
- BIAM offers a solution for a previously unmet analytical need in biofilm research.
Conclusions:
- BIAM is a significant advancement for biofilm research.
- The tool facilitates deeper understanding of biofilm development, differentiation, and gene expression.
- BIAM aids in evaluating the impact of external molecules on biofilm phenotypes.
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