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Updated: Sep 3, 2025
Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome
Published on: January 13, 2023
Image Analysis Semi-Automatic System for Colony-Forming-Unit Counting
Pedro Miguel Rodrigues1, Jorge Luís1, Freni Kekhasharú Tavaria1
1CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua de Diogo Botelho 1327, 4169-005 Porto, Portugal.
Background:
Accurate quantitative analysis of microorganisms is recognized as an essential tool for gauging safety and quality in microbiology settings in a wide range of fields. The enumeration process of viable microorganisms via traditional culturing techniques are methodically convenient and cost-effective, conferring high applicability worldwide. However, manual counting can be time-consuming, laborious and imprecise. Furthermore, particular cases require an urgent and accurate response for effective processing.
Methods:
To reduce time limitations and discrepancies, this work introduces an image processing method capable of semi-automatically quantifying the number of colony forming units (CFUs). This rapid enumeration technique enables the technician to provide an expeditious assessment of the microbial load of a given sample. To test and validate the system, three bacterial species were cultured, and a labeled database was created, with subsequent image acquisition.
Results:
The system demonstrated acceptable classification measures; the mean values of Accuracy, Recall and F-measure were: (1) 95%, 95% and 0.95 for E. coli; (2) 91%, 91% and 0.90 for P. aeruginosa; and (3) 84%, 86% and 0.85 for S. aureus.
Conclusions:
Evidence related to the time-saving potential of the system was achieved; the time spent on quantification tasks of plates with a high number of colonies might be reduced to a half and occasionally to a third.
