An ImageJ based measurement setup for automated phenotyping of plants

The objective of plant phenotyping studies is to understand the relationship between a plant’s genotype and phenotype. In our study we focus on the leaf morphology of Arabidopsis seedlings. Our experimental setup consists of a table of 0.9 m × 3.8 m with a matrix of about 1500 small cubes of rockwool, each containing an Arabidopsis seedling with a di¿erent genotype. The table is equipped with an automated supply for water and nutrients. The entire setup is placed in a climate-chamber with carefully controlled lighting and atmospheric conditions. We will present a fully automated measurement system that monitors the development of each individual seedling by high resolution time-lapse photography. ImageJ is used to analyze the photographs. We will discuss the challenges concerning the image processing involved, including the automatic calibration of the image di- mensions by marker recognition, segmentation of the photograph into regions that contain the individual plants, and the measurement of the leaf shape and area.