{"title":"基于 Mask-RCNN 和无人机图像的油菜群体单株高度高通量表型分析","authors":"Yutao Shen, Xuqi Lu, Mengqi Lyu, Hongyu Zhou, Wenxuan Guan, Lixi Jiang, Yuhong He, Haiyan Cen","doi":"10.1007/s11119-023-10095-9","DOIUrl":null,"url":null,"abstract":"<p>Plant height, a key agronomic trait, affects crop structure, photosynthesis, and thus the final yield and seed quality. The combination of digital cameras on unmanned aerial vehicles (UAVs) and use of structure from motion have enabled high-throughput crop canopy height estimation. However, the focus of prior research has mainly been on plot-level height prediction, neglecting precise estimations for individual plants. This study aims to explore the potential of UAV RGB images with mask region-based convolutional neural network (Mask-RCNN) for high-throughput phenotyping of individual-level height (IH) in oilseed rape at different growth stages. Field-measured height (FH) of nine sampling plants in each subplot of the 150 subplots was obtained by manual measurement after the UAV flight. An instance segmentation model for oilseed rape with data augmentation based on the Mask-RCNN model was developed. The IHs were then used to obtain plot-level height based on individual-level height (PHIH). The results show that Mask-RCNN performed better than the conventional Otsu method with the F1 score increased by 60.8% and 26.6% under high and low weed pressure, respectively. The trained model with data augmentation achieved accurate crop height estimation based on overexposed and underexposed UAV images, indicating the model’s applicability in practical scenarios. The PHIH can be predicted with the determination coefficient (r<sup>2</sup>) of 0.992, root mean square error (RMSE) of 4.03 cm, relative root mean square error (rRMSE) of 7.68%, which outperformed the results in the reported studies, especially in the late bolting stage. The IHs of the whole growth stages of oilseed can be predicted by this method with an r<sup>2</sup> of 0.983, RMSE of 2.60 cm, and rRMSE of 7.14%. Furthermore, this method enabled a comprehensive Genome-wide association study (GWAS) in a 293-accession genetic population. The GWAS identified 200 and 65 statistically significant single nucleotide polymorphisms (SNPs), which were tightly associated with 28 and 11 candidate genes, at the late bolting and flowering stages, respectively. These findings demonstrated that the proposed method is promising for accurate estimations of IHs in oilseed rape as well as exploring the variations within the subplot, thus providing great potential for high-throughput plant phenotyping in crop breeding.</p>","PeriodicalId":20423,"journal":{"name":"Precision Agriculture","volume":null,"pages":null},"PeriodicalIF":5.4000,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"High-throughput phenotyping of individual plant height in an oilseed rape population based on Mask-RCNN and UAV images\",\"authors\":\"Yutao Shen, Xuqi Lu, Mengqi Lyu, Hongyu Zhou, Wenxuan Guan, Lixi Jiang, Yuhong He, Haiyan Cen\",\"doi\":\"10.1007/s11119-023-10095-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Plant height, a key agronomic trait, affects crop structure, photosynthesis, and thus the final yield and seed quality. The combination of digital cameras on unmanned aerial vehicles (UAVs) and use of structure from motion have enabled high-throughput crop canopy height estimation. However, the focus of prior research has mainly been on plot-level height prediction, neglecting precise estimations for individual plants. This study aims to explore the potential of UAV RGB images with mask region-based convolutional neural network (Mask-RCNN) for high-throughput phenotyping of individual-level height (IH) in oilseed rape at different growth stages. Field-measured height (FH) of nine sampling plants in each subplot of the 150 subplots was obtained by manual measurement after the UAV flight. An instance segmentation model for oilseed rape with data augmentation based on the Mask-RCNN model was developed. The IHs were then used to obtain plot-level height based on individual-level height (PHIH). The results show that Mask-RCNN performed better than the conventional Otsu method with the F1 score increased by 60.8% and 26.6% under high and low weed pressure, respectively. The trained model with data augmentation achieved accurate crop height estimation based on overexposed and underexposed UAV images, indicating the model’s applicability in practical scenarios. The PHIH can be predicted with the determination coefficient (r<sup>2</sup>) of 0.992, root mean square error (RMSE) of 4.03 cm, relative root mean square error (rRMSE) of 7.68%, which outperformed the results in the reported studies, especially in the late bolting stage. The IHs of the whole growth stages of oilseed can be predicted by this method with an r<sup>2</sup> of 0.983, RMSE of 2.60 cm, and rRMSE of 7.14%. Furthermore, this method enabled a comprehensive Genome-wide association study (GWAS) in a 293-accession genetic population. The GWAS identified 200 and 65 statistically significant single nucleotide polymorphisms (SNPs), which were tightly associated with 28 and 11 candidate genes, at the late bolting and flowering stages, respectively. These findings demonstrated that the proposed method is promising for accurate estimations of IHs in oilseed rape as well as exploring the variations within the subplot, thus providing great potential for high-throughput plant phenotyping in crop breeding.</p>\",\"PeriodicalId\":20423,\"journal\":{\"name\":\"Precision Agriculture\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.4000,\"publicationDate\":\"2023-12-15\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Precision Agriculture\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.1007/s11119-023-10095-9\",\"RegionNum\":2,\"RegionCategory\":\"农林科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"AGRICULTURE, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Precision Agriculture","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.1007/s11119-023-10095-9","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"AGRICULTURE, MULTIDISCIPLINARY","Score":null,"Total":0}
引用次数: 0
摘要
株高是一项重要的农艺性状,影响作物结构、光合作用,进而影响最终产量和种子品质。结合无人机上的数码相机和运动结构的使用,实现了高通量作物冠层高度估计。然而,以往的研究主要集中在样地高度的预测上,忽略了对单株植物的精确估计。本研究旨在探索基于掩模区域的卷积神经网络(mask - rcnn)的无人机RGB图像在油菜不同生育期个体水平身高(IH)高通量表型分析中的潜力。在无人机飞行后,通过人工测量获得150个子样地中每个子样地9个样地的实测高度。提出了一种基于Mask-RCNN模型的数据增强油菜实例分割模型。然后利用his获得基于个人水平高度(phh)的样地高度。结果表明,在高、低杂草压力下,Mask-RCNN的F1分数分别提高了60.8%和26.6%,优于传统的Otsu方法。经过数据增强训练后的模型能够基于过曝光和欠曝光的无人机图像准确估计作物高度,表明该模型在实际场景中的适用性。PHIH预测的决定系数(r2)为0.992,均方根误差(RMSE)为4.03 cm,相对均方根误差(rRMSE)为7.68%,优于文献报道的结果,特别是在抽苔后期。该方法可预测油籽各生育期的his, r2为0.983,RMSE为2.60 cm, rRMSE为7.14%。此外,该方法能够在293个遗传群体中进行全面的全基因组关联研究(GWAS)。GWAS在抽穗期和开花期分别鉴定出200个和65个具有统计学意义的单核苷酸多态性(snp),分别与28个和11个候选基因密切相关。这些结果表明,该方法有望准确估计油菜的his,并探索亚区内的变化,从而为作物育种中的高通量植物表型分析提供了巨大的潜力。
High-throughput phenotyping of individual plant height in an oilseed rape population based on Mask-RCNN and UAV images
Plant height, a key agronomic trait, affects crop structure, photosynthesis, and thus the final yield and seed quality. The combination of digital cameras on unmanned aerial vehicles (UAVs) and use of structure from motion have enabled high-throughput crop canopy height estimation. However, the focus of prior research has mainly been on plot-level height prediction, neglecting precise estimations for individual plants. This study aims to explore the potential of UAV RGB images with mask region-based convolutional neural network (Mask-RCNN) for high-throughput phenotyping of individual-level height (IH) in oilseed rape at different growth stages. Field-measured height (FH) of nine sampling plants in each subplot of the 150 subplots was obtained by manual measurement after the UAV flight. An instance segmentation model for oilseed rape with data augmentation based on the Mask-RCNN model was developed. The IHs were then used to obtain plot-level height based on individual-level height (PHIH). The results show that Mask-RCNN performed better than the conventional Otsu method with the F1 score increased by 60.8% and 26.6% under high and low weed pressure, respectively. The trained model with data augmentation achieved accurate crop height estimation based on overexposed and underexposed UAV images, indicating the model’s applicability in practical scenarios. The PHIH can be predicted with the determination coefficient (r2) of 0.992, root mean square error (RMSE) of 4.03 cm, relative root mean square error (rRMSE) of 7.68%, which outperformed the results in the reported studies, especially in the late bolting stage. The IHs of the whole growth stages of oilseed can be predicted by this method with an r2 of 0.983, RMSE of 2.60 cm, and rRMSE of 7.14%. Furthermore, this method enabled a comprehensive Genome-wide association study (GWAS) in a 293-accession genetic population. The GWAS identified 200 and 65 statistically significant single nucleotide polymorphisms (SNPs), which were tightly associated with 28 and 11 candidate genes, at the late bolting and flowering stages, respectively. These findings demonstrated that the proposed method is promising for accurate estimations of IHs in oilseed rape as well as exploring the variations within the subplot, thus providing great potential for high-throughput plant phenotyping in crop breeding.
期刊介绍:
Precision Agriculture promotes the most innovative results coming from the research in the field of precision agriculture. It provides an effective forum for disseminating original and fundamental research and experience in the rapidly advancing area of precision farming.
There are many topics in the field of precision agriculture; therefore, the topics that are addressed include, but are not limited to:
Natural Resources Variability: Soil and landscape variability, digital elevation models, soil mapping, geostatistics, geographic information systems, microclimate, weather forecasting, remote sensing, management units, scale, etc.
Managing Variability: Sampling techniques, site-specific nutrient and crop protection chemical recommendation, crop quality, tillage, seed density, seed variety, yield mapping, remote sensing, record keeping systems, data interpretation and use, crops (corn, wheat, sugar beets, potatoes, peanut, cotton, vegetables, etc.), management scale, etc.
Engineering Technology: Computers, positioning systems, DGPS, machinery, tillage, planting, nutrient and crop protection implements, manure, irrigation, fertigation, yield monitor and mapping, soil physical and chemical characteristic sensors, weed/pest mapping, etc.
Profitability: MEY, net returns, BMPs, optimum recommendations, crop quality, technology cost, sustainability, social impacts, marketing, cooperatives, farm scale, crop type, etc.
Environment: Nutrient, crop protection chemicals, sediments, leaching, runoff, practices, field, watershed, on/off farm, artificial drainage, ground water, surface water, etc.
Technology Transfer: Skill needs, education, training, outreach, methods, surveys, agri-business, producers, distance education, Internet, simulations models, decision support systems, expert systems, on-farm experimentation, partnerships, quality of rural life, etc.