Automated counting of bacterial colony forming units on agar plates.
Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates.A colony counter hardware was designed and a...
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Public Library of Science (PLoS)
2012
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oai:doaj.org-article:8e390d3dc2334c31976045503673e4792021-11-18T07:24:40ZAutomated counting of bacterial colony forming units on agar plates.1932-620310.1371/journal.pone.0033695https://doaj.org/article/8e390d3dc2334c31976045503673e4792012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22448267/?tool=EBIhttps://doaj.org/toc/1932-6203Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates.A colony counter hardware was designed and a novel segmentation algorithm was written in MATLAB. In brief, pre-processing with Top-Hat-filtering to obtain a uniform background was followed by the segmentation step, during which the colony images were extracted from the blood agar and individual colonies were separated. A Bayes classifier was then applied to count the final number of bacterial colonies as some of the colonies could still be concatenated to form larger groups. To assess accuracy and performance of the colony counter, we tested automated colony counting of different agar plates with known CFU numbers of S. pneumoniae, P. aeruginosa and M. catarrhalis and showed excellent performance.Silvio D BruggerChristian BaumbergerMarcel JostWerner JenniUrs BruggerKathrin MühlemannPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33695 (2012) |
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DOAJ |
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EN |
| topic |
Medicine R Science Q |
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Medicine R Science Q Silvio D Brugger Christian Baumberger Marcel Jost Werner Jenni Urs Brugger Kathrin Mühlemann Automated counting of bacterial colony forming units on agar plates. |
| description |
Manual counting of bacterial colony forming units (CFUs) on agar plates is laborious and error-prone. We therefore implemented a colony counting system with a novel segmentation algorithm to discriminate bacterial colonies from blood and other agar plates.A colony counter hardware was designed and a novel segmentation algorithm was written in MATLAB. In brief, pre-processing with Top-Hat-filtering to obtain a uniform background was followed by the segmentation step, during which the colony images were extracted from the blood agar and individual colonies were separated. A Bayes classifier was then applied to count the final number of bacterial colonies as some of the colonies could still be concatenated to form larger groups. To assess accuracy and performance of the colony counter, we tested automated colony counting of different agar plates with known CFU numbers of S. pneumoniae, P. aeruginosa and M. catarrhalis and showed excellent performance. |
| format |
article |
| author |
Silvio D Brugger Christian Baumberger Marcel Jost Werner Jenni Urs Brugger Kathrin Mühlemann |
| author_facet |
Silvio D Brugger Christian Baumberger Marcel Jost Werner Jenni Urs Brugger Kathrin Mühlemann |
| author_sort |
Silvio D Brugger |
| title |
Automated counting of bacterial colony forming units on agar plates. |
| title_short |
Automated counting of bacterial colony forming units on agar plates. |
| title_full |
Automated counting of bacterial colony forming units on agar plates. |
| title_fullStr |
Automated counting of bacterial colony forming units on agar plates. |
| title_full_unstemmed |
Automated counting of bacterial colony forming units on agar plates. |
| title_sort |
automated counting of bacterial colony forming units on agar plates. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/8e390d3dc2334c31976045503673e479 |
| work_keys_str_mv |
AT silviodbrugger automatedcountingofbacterialcolonyformingunitsonagarplates AT christianbaumberger automatedcountingofbacterialcolonyformingunitsonagarplates AT marceljost automatedcountingofbacterialcolonyformingunitsonagarplates AT wernerjenni automatedcountingofbacterialcolonyformingunitsonagarplates AT ursbrugger automatedcountingofbacterialcolonyformingunitsonagarplates AT kathrinmuhlemann automatedcountingofbacterialcolonyformingunitsonagarplates |
| _version_ |
1718423487281889280 |