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.
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Centre de Recherche Public Henri Tudor
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dig-wur-nl-wurpubs-3985632024-09-23 Kokorian, J. Polder, G. Keurentjes, J.J.B. Vreugdenhil, D. Olortegui Guzman, M.C. Article in monograph or in proceedings Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010 ISBN: 9782919941117 An ImageJ based measurement setup for automated phenotyping of plants 2010 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. en Centre de Recherche Public Henri Tudor application/pdf https://research.wur.nl/en/publications/an-imagej-based-measurement-setup-for-automated-phenotyping-of-pl https://edepot.wur.nl/169770 Life Science Wageningen University & Research |
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Life Science Life Science Kokorian, J. Polder, G. Keurentjes, J.J.B. Vreugdenhil, D. Olortegui Guzman, M.C. An ImageJ based measurement setup for automated phenotyping of plants |
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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. |
format |
Article in monograph or in proceedings |
topic_facet |
Life Science |
author |
Kokorian, J. Polder, G. Keurentjes, J.J.B. Vreugdenhil, D. Olortegui Guzman, M.C. |
author_facet |
Kokorian, J. Polder, G. Keurentjes, J.J.B. Vreugdenhil, D. Olortegui Guzman, M.C. |
author_sort |
Kokorian, J. |
title |
An ImageJ based measurement setup for automated phenotyping of plants |
title_short |
An ImageJ based measurement setup for automated phenotyping of plants |
title_full |
An ImageJ based measurement setup for automated phenotyping of plants |
title_fullStr |
An ImageJ based measurement setup for automated phenotyping of plants |
title_full_unstemmed |
An ImageJ based measurement setup for automated phenotyping of plants |
title_sort |
imagej based measurement setup for automated phenotyping of plants |
publisher |
Centre de Recherche Public Henri Tudor |
url |
https://research.wur.nl/en/publications/an-imagej-based-measurement-setup-for-automated-phenotyping-of-pl |
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