New onion module for ImageJ plugin for plant variety testing

Published on
March 17, 2014

For plant variety testing many plant characteristics need to be measured to assess distinctness between varieties and uniformity and stability of a variety. The characteristics are described in guidelines and protocols for each crop. These guidelines are established by international organisations such as the Union for the Protection of New Varieties of Plants (UPOV) and the Community Plant Variety Office (CPVO).

Several characteristics, related to shape and form are tedious to measure by hand and should be measured in an objective and reproducible way. The use of image analysis leads to a significant decrease of time needed for measuring the characteristics (phenotyping). Moreover, the results obtained by using image analysis are much more accurate than results of manual measurements. Together with Naktuinbouw a user friendly image analysis system has been established in the past for recording and analysis of images using a standard camera. This software is implemented as an plugin for the popular opensource image processing package ImageJ.

UPOV characteristics can be measured for flax, beans, sugar beets and carrots. Recently the plugin is extended with a module to measure onion varieties. Using first - and second order derivatives of the outer contour of the onion bulb a number of important UPOV features can be measured. A new feature of the plugin is the possibility to group shapes of different varieties using K-Means clustering on the average contour of each variety. This feature gives insight in how varieties differ from each other and acts as a valuable phenotyping tool for breeders and plant variety testing.

Foto internetbericht Gerrit Polder.png