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Automatic detection and morphological delineation of bacteriophages in electron microscopy images
Kaunas University of Technology, Kaunas, Lithuania.
Halmstad University, School of Information Technology, Halmstad Embedded and Intelligent Systems Research (EIS), CAISR - Center for Applied Intelligent Systems Research. Kaunas University of Technology, Kaunas, Lithuania.ORCID iD: 0000-0003-2185-8973
Kaunas University of Technology, Kaunas, Lithuania.
Kaunas University of Technology, Kaunas, Lithuania.
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2015 (English)In: Computers in Biology and Medicine, ISSN 0010-4825, E-ISSN 1879-0534, Vol. 64, 101-116 p.Article in journal (Refereed) Published
Abstract [en]

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. © 2015 Elsevier Ltd.

Place, publisher, year, edition, pages
Kidlington: Pergamon Press, 2015. Vol. 64, 101-116 p.
Keyword [en]
Bacteriophage, Vb-AphaS- CL131, Aphanizomenon flos-aquae, Cyanophage, Cyanobacteria, Electron microscopy, Pattern recognition, Random forest, Open active contours, Bland–Altman
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:hh:diva-29083DOI: 10.1016/j.compbiomed.2015.06.015ISI: 000361412500010PubMedID: 26164031Scopus ID: 2-s2.0-84936882280OAI: oai:DiVA.org:hh-29083DiVA: diva2:844113
Note

Funding for this work was provided by a grant (No. LEK-09/2012) from the Research Council of Lithuania under National Research Programme “Ecosystems in Lithuania: Climate Change and Human Impact”.

Available from: 2015-08-03 Created: 2015-08-03 Last updated: 2016-11-24Bibliographically approved

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CiteExportLink to record
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Citation style
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