An ImageJ based measurement setup for automated phenotyping of plants

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

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 proceeding › Conference paper › Academic

Abstract

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 language	English
Title of host publication	Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010
Editors	A. Jahnen, C. Moll
Place of Publication	Luxembourg
Publisher	Centre de Recherche Public Henri Tudor
Pages	178-182
ISBN (Print)	9782919941117
Publication status	Published - 2010
Event	ImageJ User and Developer Conference, Luxembourg, Luxembourg - Duration: 27 Oct 2010 → 29 Oct 2010

Conference/symposium

Conference/symposium	ImageJ User and Developer Conference, Luxembourg, Luxembourg
Period	27/10/10 → 29/10/10

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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https://edepot.wur.nl/169770

Cite this

Kokorian, J., Polder, G., Keurentjes, J. J. B., Vreugdenhil, D., & Olortegui Guzman, M. C. (2010). An ImageJ based measurement setup for automated phenotyping of plants. In A. Jahnen, & C. Moll (Eds.), Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010 (pp. 178-182). Centre de Recherche Public Henri Tudor. https://edepot.wur.nl/169770

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title = "An ImageJ based measurement setup for automated phenotyping of plants",

abstract = "The objective of plant phenotyping studies is to understand the relationship between a plant{\textquoteright}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.",

author = "J. Kokorian and G. Polder and J.J.B. Keurentjes and D. Vreugdenhil and {Olortegui Guzman}, M.C.",

year = "2010",

language = "English",

isbn = "9782919941117",

pages = "178--182",

editor = "A. Jahnen and C. Moll",

booktitle = "Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010",

publisher = "Centre de Recherche Public Henri Tudor",

note = "ImageJ User and Developer Conference, Luxembourg, Luxembourg ; Conference date: 27-10-2010 Through 29-10-2010",

}

Kokorian, J, Polder, G , Keurentjes, JJB, Vreugdenhil, D & Olortegui Guzman, MC 2010, An ImageJ based measurement setup for automated phenotyping of plants. in A Jahnen & C Moll (eds), Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010. Centre de Recherche Public Henri Tudor, Luxembourg, pp. 178-182, ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27/10/10. <https://edepot.wur.nl/169770>

An ImageJ based measurement setup for automated phenotyping of plants. / Kokorian, J.; Polder, G.; Keurentjes, J.J.B. et al.
Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010. ed. / A. Jahnen; C. Moll. Luxembourg: Centre de Recherche Public Henri Tudor, 2010. p. 178-182.

Research output: Chapter in Book/Report/Conference proceeding › Conference paper › Academic

TY - GEN

T1 - An ImageJ based measurement setup for automated phenotyping of plants

AU - Kokorian, J.

AU - Polder, G.

AU - Keurentjes, J.J.B.

AU - Vreugdenhil, D.

AU - Olortegui Guzman, M.C.

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

M3 - Conference paper

SN - 9782919941117

SP - 178

EP - 182

BT - Proceedings of the ImageJ User and Developer Conference, Luxembourg, Luxembourg, 27-29 October 2010

A2 - Jahnen, A.

A2 - Moll, C.

PB - Centre de Recherche Public Henri Tudor

CY - Luxembourg

T2 - ImageJ User and Developer Conference, Luxembourg, Luxembourg

Y2 - 27 October 2010 through 29 October 2010

ER -

An ImageJ based measurement setup for automated phenotyping of plants

Abstract

Conference/symposium

UN SDGs

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