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.
| Main Authors: | , , , , |
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| Format: | Article in monograph or in proceedings biblioteca |
| Language: | English |
| Published: |
Centre de Recherche Public Henri Tudor
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| Subjects: | Life Science, |
| Online Access: | https://research.wur.nl/en/publications/an-imagej-based-measurement-setup-for-automated-phenotyping-of-pl |
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| Summary: | 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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