Image analysis semi-automatic system for colony-forming-unit counting

Pedro Miguel Rodrigues*, Jorge Luís, Freni Kekhasharú Tavaria

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


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.
Original languageEnglish
Article number271
Number of pages20
Issue number7
Publication statusPublished - Jul 2022


  • Colony forming units
  • Enumeration
  • Image processing
  • Petri-plates


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