title: COVASIAM: an image analysis method that allows detection of confluent microbial colonies and colonies of various sizes for automated counting.
abstract: In this work we introduce the confluent and various sizes image analysis method (COVASIAM), an automated colony count technique that uses digital imaging technology for detection and separation of confluent microbial colonies and colonies of various sizes growing on petri dishes. The proposed method takes advantage of the optical properties of the surfaces of most microbial colonies. Colonies in the petri dish are epi-illuminated in order to direct the reflection of concentrated light coming from a halogen lamp towards an image-sensing device. In conjunction, a multilevel threshold algorithm is proposed for colony separation and counting. These procedures improved the quantification of colonies showing confluence or differences in size. We tested COVASIAM with a sample set of microorganisms that form colonies with contrasting physical properties: Saccharomyces cerevisiae, Aspergillus nidulans, Escherichia coli, Azotobacter vinelandii, Pseudomonas aeruginosa, and Rhizobium etli. These physical properties range from smooth to hairy, from bright to opaque, and from high to low convexities. COVASIAM estimated an average of 95.47% (sigma = 8.55%) of the manually counted colonies, while an automated method based on a single-threshold segmentation procedure estimated an average of 76% (sigma = 16.27) of the manually counted colonies. This method can be easily transposed to almost every image-processing analyzer since the procedures to compile it are generically standard.
authors.affiliation: Laboratorio de Procesamiento de Imágenes, Centro de Instrumentos, UNAM, México Distrito Federal, Mexico. corkidi@sgima.ibt.unam.mx
authors.forename: G
authors.initials: G
authors.lastname: Corkidi
authors.forename: R
authors.initials: R
authors.lastname: Diaz-Uribe
authors.forename: J L
authors.initials: JL
authors.lastname: Folch-Mallol
authors.forename: J
authors.initials: J
authors.lastname: Nieto-Sotelo
mesh_terms: D001233:Aspergillus nidulans / Q000302:isolation & purification; D016948:Azotobacter vinelandii / Q000302:isolation & purification; D015169:Colony Count, Microbial / Q000295:instrumentation / Q000379:methods*; D004926:Escherichia coli / Q000302:isolation & purification; D005069:Evaluation Studies as Topic; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods*; D011550:Pseudomonas aeruginosa / Q000302:isolation & purification; D012231:Rhizobium / Q000302:isolation & purification; D012441:Saccharomyces cerevisiae / Q000302:isolation & purification