Software

CultivarJ: An ImageJ plugin for plant variety testing

For plant variety testing the ImageJ plugin CultivarJ is developed for measuring plant characteristics (phenotyping). The following crops are implemented: flax seeds, flax bolls, pods of pea and beans, cotyledons of sugar beets, carrot and onion. Measured features include length, width and area based on the skeleton, distance transform, and derivative of the outer contour.

Introduction

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 the International 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. Moreover, the results obtained by using image analysis are much more accurate than results of manual measurements. Together with Naktuinbouw we developed a user-friendly image analysis system has been established 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. The following crops are implemented: flax seeds, flax bolls, pods of pea and beans, cotyledons of sugar beets, carrot and onion. Measured features include length, width and area based on the skeleton, distance transform, and derivative of the outer contour. Calibration is done using a calibration disc in a separate part of the image. Identification of the images is done using a QR code label. The software is proven to be very robust, where disturbing factors on the objects, such as small crown leaves are removed automatically. We conclude that ImageJ as popular open source imaging platform is a good choice for implementing an image analysis system for plant variety testing and phenotyping to automatically and reliably measure a large variety of plant characteristics.

Availability

The software is available under a non-profit as well as under a commercial license. Details can be found in the license file after clicking the download button.

CultivarJ.jpg

Version notes

  • 2.3.1 – December 2024 - fixed ambiguity in AnalyzeSkeleton call introduced in ImageJ version 1.51, which effected Bean and Pea analysis