title: Automatic detection and morphological delineation of bacteriophages in electron microscopy images.
abstract: Automatic detection, recognition and geometric characterization of bacteriophages in electron microscopy images was the main objective of this work. A novel technique, combining phase congruency-based image enhancement, Hough transform-, Radon transform- and open active contours with free boundary conditions-based object detection was developed to detect and recognize the bacteriophages associated with infection and lysis of cyanobacteria Aphanizomenon flos-aquae. A random forest classifier designed to recognize phage capsids provided higher than 99% accuracy, while measurable phage tails were detected and associated with a correct capsid with 81.35% accuracy. Automatically derived morphometric measurements of phage capsids and tails exhibited lower variability than the ones obtained manually. The technique allows performing precise and accurate quantitative (e.g. abundance estimation) and qualitative (e.g. diversity and capsid size) measurements for studying the interactions between host population and different phages that infect the same host.
authors.affiliation: Department of Electric Power Systems, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania. Electronic address: adas.gelzinis@ktu.lt.
authors.forename: A
authors.initials: A
authors.lastname: Gelzinis
authors.affiliation: Department of Electric Power Systems, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania; Intelligent Systems Laboratory, Centre for Applied Intelligent Systems Research, Halmstad University, Kristian IV:s väg 3, Box 823, S-30118 Halmstad, Sweden. Electronic address: antanas.verikas@hh.se.
authors.forename: A
authors.initials: A
authors.lastname: Verikas
authors.affiliation: Department of Electric Power Systems, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania; Department Information Systems, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania. Electronic address: evaldas.vaiciukynas@ktu.lt.
authors.forename: E
authors.initials: E
authors.lastname: Vaiciukynas
authors.affiliation: Department of Electric Power Systems, Kaunas University of Technology, Studentu 50, LT-51368 Kaunas, Lithuania. Electronic address: marija.bacauskiene@ktu.lt.
authors.forename: M
authors.initials: M
authors.lastname: Bacauskiene
authors.affiliation: Marine Science and Technology Center, Klaipeda University, H. Manto 84, LT-92294 Klaipeda, Lithuania; Open Access Centre for Nature Research, Nature Research Centre, Akademijos str. 2, LT-08412 Vilnius, Lithuania. Electronic address: sigitas.sulcius@jmtc.ku.lt.
authors.forename: S
authors.initials: S
authors.lastname: Sulcius
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Lithuania. Electronic address: eugenijus.simoliunas@bchi.vu.lt.
authors.forename: E
authors.initials: E
authors.lastname: Simoliunas
authors.affiliation: Laboratory of Plant Viruses, Nature Research Centre, Institute of Botany, Mokslininku 12, LT-08662 Vilnius, Lithuania. Electronic address: juozas.staniulis@botanika.lt.
authors.forename: J
authors.initials: J
authors.lastname: Staniulis
authors.affiliation: Marine Science and Technology Center, Klaipeda University, H. Manto 84, LT-92294 Klaipeda, Lithuania; Laboratory of Algology and Microbial Ecology, Nature Research Centre, Mokslininku 12, LT-08662 Vilnius, Lithuania. Electronic address: ricardas.paskauskas@jmtc.ku.lt.
authors.forename: R
authors.initials: R
authors.lastname: Paskauskas
mesh_terms: D000465:Algorithms; D046890:Aphanizomenon / Q000821:virology; D001435:Bacteriophages / Q000145:classification / Q000648:ultrastructure*; D002213:Capsid / Q000145:classification / Q000648:ultrastructure*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008854:Microscopy, Electron / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*
keywords: Aphanizomenon flos-aquae; Bacteriophage; Bland–Altman; Cyanobacteria; Cyanophage; Electron microscopy; Open active contours; Pattern recognition; Random forest; Vb-AphaS- CL131