title: Automated counting of bacterial colony forming units on agar plates.
abstract: 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.
authors.affiliation: Institute for Infectious Diseases, University of Bern, Bern, Switzerland. silvio.brugger@ifik.unibe.ch
authors.forename: Silvio D
authors.initials: SD
authors.lastname: Brugger
authors.forename: Christian
authors.initials: C
authors.lastname: Baumberger
authors.forename: Marcel
authors.initials: M
authors.lastname: Jost
authors.forename: Werner
authors.initials: W
authors.lastname: Jenni
authors.forename: Urs
authors.initials: U
authors.lastname: Brugger
authors.forename: Kathrin
authors.initials: K
authors.lastname: Mühlemann
mesh_terms: D000362:Agar / Q000737:chemistry*; D000465:Algorithms; D001331:Automation; D001419:Bacteria / Q000166:cytology* / Q000378:metabolism; D001499:Bayes Theorem; D002452:Cell Count / Q000295:instrumentation / Q000379:methods*; D002478:Cells, Cultured; D015169:Colony Count, Microbial; D003114:Colony-Forming Units Assay / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*
chemical_list: D000362:Agar