Updated 27 Aug 2015
This is an image analysis program developed at Pacific Northwest National Laboratory by Curtis Larimer, Eric Winder, Robert Jeters, Ian Nettleship, R. Shane Addleman, and George Bonheyo
Contact email@example.com with questions
Brief description of Biofilm Growth Intensity program -
The accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. The aim of this program is to use image analysis to enhance contrast of early stage biofouling. This program executes an algorithm developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field.
A new method of image analysis using multilevel thresholding was developed to rapidly measure fouling in digital photographs. The analysis evaluates biofilm growth intensity (BGI) on sample coupons and assigns a simple, easy-to-understand value between zero and 100 that represents an absolute score for fouling intensity over the entire coupon. Measuring BGI allows direct, quantifiable, and robust comparison of fouling on different coupons. BGI is not just a measure of areal coverage of fouling: it also includes information about the density and thickness of surface growth.
Disclaimer This program is primarily designed to run within the Matlab runtime, which is available for Windows, Mac, and Linux. Please use this program at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.
This software was developed at Pacific Northwest National Laboratories (PNNL), which is operated for the US Department of Energy by Battelle Memorial Institute under contract DE AC06-76RLO 1830. The work was supported by the Chemical Imaging Initiative-Laboratory Directed Research and Development (CII-LDRD) program. A portion of the work presented here was also supported by the Wind and Water Power Program under the Office of Energy Efficiency and Renewable Energy, US Department of Energy. The work was also supported by a grant from the Intelligence Community Postdoctoral Research Fellowship Program. All statements of fact, opinion, or analysis expressed are those of the author and do not reflect the official positions or views of the Intelligence Community or any other U.S. Government agency. Nothing in the contents should be construed as asserting or implying U.S. Government authentication of information or Intelligence Community endorsement of the author’s views.
Curtis Larimer (2023). curtislarimer/Biofilm-Growth-Intensity (https://github.com/curtislarimer/Biofilm-Growth-Intensity), GitHub. Retrieved .
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
- Sciences > Biological and Health Sciences > Biomedical Imaging >
- Sciences > Physics > Biological Physics >
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!Start Hunting!
Discover Live Editor
Create scripts with code, output, and formatted text in a single executable document.
Versions that use the GitHub default branch cannot be downloaded