High-throughput volumetric reconstruction for 3D wheat plant architecture studies
For many tiller crops, the plant architecture (PA), including the plant fresh weight, plant height, number of tillers, tiller angle and stem diameter, significantly affects the grain yield. In this study, we propose a method based on volumetric reconstruction for high-throughput three-dimensional (3...
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doaj-1b061d84c2fb4f6b96a85d36433edfbb2020-11-24T23:05:52ZengWorld Scientific PublishingJournal of Innovative Optical Health Sciences1793-54581793-72052016-09-01951650037-11650037-1310.1142/S179354581650037110.1142/S1793545816500371High-throughput volumetric reconstruction for 3D wheat plant architecture studiesWei Fang0Hui Feng1Wanneng Yang2Lingfeng Duan3Guoxing Chen4Lizhong Xiong5Qian Liu6Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Rd. Wuhan 430074, P. R. ChinaBritton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Rd. Wuhan 430074, P. R. ChinaBritton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Rd. Wuhan 430074, P. R. ChinaCollege of Engineering, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaMOA Key Laboratory of Crop Ecophysiology and Farming, System in the Middle Reaches of the Yangtze River, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaNational Key Laboratory of Crop Genetic, Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P. R. ChinaBritton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Rd. Wuhan 430074, P. R. ChinaFor many tiller crops, the plant architecture (PA), including the plant fresh weight, plant height, number of tillers, tiller angle and stem diameter, significantly affects the grain yield. In this study, we propose a method based on volumetric reconstruction for high-throughput three-dimensional (3D) wheat PA studies. The proposed methodology involves plant volumetric reconstruction from multiple images, plant model processing and phenotypic parameter estimation and analysis. This study was performed on 80 Triticum aestivum plants, and the results were analyzed. Comparing the automated measurements with manual measurements, the mean absolute percentage error (MAPE) in the plant height and the plant fresh weight was 2.71% (1.08cm with an average plant height of 40.07cm) and 10.06% (1.41g with an average plant fresh weight of 14.06g), respectively. The root mean square error (RMSE) was 1.37cm and 1.79g for the plant height and plant fresh weight, respectively. The correlation coefficients were 0.95 and 0.96 for the plant height and plant fresh weight, respectively. Additionally, the proposed methodology, including plant reconstruction, model processing and trait extraction, required only approximately 20s on average per plant using parallel computing on a graphics processing unit (GPU), demonstrating that the methodology would be valuable for a high-throughput phenotyping platform.http://www.worldscientific.com/doi/pdf/10.1142/S1793545816500371Three-dimensionalvolumetric reconstructionplant architecturegraphics processing unithigh-throughput |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Wei Fang Hui Feng Wanneng Yang Lingfeng Duan Guoxing Chen Lizhong Xiong Qian Liu |
spellingShingle |
Wei Fang Hui Feng Wanneng Yang Lingfeng Duan Guoxing Chen Lizhong Xiong Qian Liu High-throughput volumetric reconstruction for 3D wheat plant architecture studies Journal of Innovative Optical Health Sciences Three-dimensional volumetric reconstruction plant architecture graphics processing unit high-throughput |
author_facet |
Wei Fang Hui Feng Wanneng Yang Lingfeng Duan Guoxing Chen Lizhong Xiong Qian Liu |
author_sort |
Wei Fang |
title |
High-throughput volumetric reconstruction for 3D wheat plant architecture studies |
title_short |
High-throughput volumetric reconstruction for 3D wheat plant architecture studies |
title_full |
High-throughput volumetric reconstruction for 3D wheat plant architecture studies |
title_fullStr |
High-throughput volumetric reconstruction for 3D wheat plant architecture studies |
title_full_unstemmed |
High-throughput volumetric reconstruction for 3D wheat plant architecture studies |
title_sort |
high-throughput volumetric reconstruction for 3d wheat plant architecture studies |
publisher |
World Scientific Publishing |
series |
Journal of Innovative Optical Health Sciences |
issn |
1793-5458 1793-7205 |
publishDate |
2016-09-01 |
description |
For many tiller crops, the plant architecture (PA), including the plant fresh weight, plant height, number of tillers, tiller angle and stem diameter, significantly affects the grain yield. In this study, we propose a method based on volumetric reconstruction for high-throughput three-dimensional (3D) wheat PA studies. The proposed methodology involves plant volumetric reconstruction from multiple images, plant model processing and phenotypic parameter estimation and analysis. This study was performed on 80 Triticum aestivum plants, and the results were analyzed. Comparing the automated measurements with manual measurements, the mean absolute percentage error (MAPE) in the plant height and the plant fresh weight was 2.71% (1.08cm with an average plant height of 40.07cm) and 10.06% (1.41g with an average plant fresh weight of 14.06g), respectively. The root mean square error (RMSE) was 1.37cm and 1.79g for the plant height and plant fresh weight, respectively. The correlation coefficients were 0.95 and 0.96 for the plant height and plant fresh weight, respectively. Additionally, the proposed methodology, including plant reconstruction, model processing and trait extraction, required only approximately 20s on average per plant using parallel computing on a graphics processing unit (GPU), demonstrating that the methodology would be valuable for a high-throughput phenotyping platform. |
topic |
Three-dimensional volumetric reconstruction plant architecture graphics processing unit high-throughput |
url |
http://www.worldscientific.com/doi/pdf/10.1142/S1793545816500371 |
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