An ImageJ based measurement setup for automated phenotyping of plants

J. Kokorian, G. Polder, J.J.B. Keurentjes, D. Vreugdenhil, M.C. Olortegui Guzman

Research output: Chapter in Book/Report/Conference proceedingConference paperAcademic


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.
Original languageEnglish
Title of host publicationProceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010
EditorsA. Jahnen, C. Moll
Place of PublicationLuxembourg
PublisherCentre de Recherche Public Henri Tudor
ISBN (Print)9782919941117
Publication statusPublished - 2010
EventImageJ User and Developer Conference, Luxembourg, Luxembourg -
Duration: 27 Oct 201029 Oct 2010


ConferenceImageJ User and Developer Conference, Luxembourg, Luxembourg


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