title: HyphArea--automated analysis of spatiotemporal fungal patterns.
abstract: In phytopathology quantitative measurements are rarely used to assess crop plant disease symptoms. Instead, a qualitative valuation by eye is often the method of choice. In order to close the gap between subjective human inspection and objective quantitative results, the development of an automated analysis system that is capable of recognizing and characterizing the growth patterns of fungal hyphae in micrograph images was developed. This system should enable the efficient screening of different host-pathogen combinations (e.g., barley-Blumeria graminis, barley-Rhynchosporium secalis) using different microscopy technologies (e.g., bright field, fluorescence). An image segmentation algorithm was developed for gray-scale image data that achieved good results with several microscope imaging protocols. Furthermore, adaptability towards different host-pathogen systems was obtained by using a classification that is based on a genetic algorithm. The developed software system was named HyphArea, since the quantification of the area covered by a hyphal colony is the basic task and prerequisite for all further morphological and statistical analyses in this context. By means of a typical use case the utilization and basic properties of HyphArea could be demonstrated. It was possible to detect statistically significant differences between the growth of an R. secalis wild-type strain and a virulence mutant.
authors.affiliation: Fraunhofer-Institute for Factory Operation and Automation (IFF), Biosystems Engineering, Sandtorstrasse 22, Magdeburg, Germany. tobias.baum@iff.fraunhofer.de
authors.forename: Tobias
authors.initials: T
authors.lastname: Baum
authors.forename: Aura
authors.initials: A
authors.lastname: Navarro-Quezada
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Knogge
authors.forename: Dimitar
authors.initials: D
authors.lastname: Douchkov
authors.forename: Patrick
authors.initials: P
authors.lastname: Schweizer
authors.forename: Udo
authors.initials: U
authors.lastname: Seiffert
mesh_terms: D001203:Ascomycota / Q000472:pathogenicity*; D001467:Hordeum / Q000166:cytology* / Q000382:microbiology*; D008856:Microscopy, Fluorescence; D010935:Plant Diseases / Q000382:microbiology*; D012984:Software