An Efficient Pipeline for Crop Image Extraction and Vegetation Index Derivation Using Unmanned Aerial Systems

2020 ◽  
Vol 63 (4) ◽  
pp. 1133-1146
Author(s):  
Beichen Lyu ◽  
Stuart D. Smith ◽  
Yexiang Xue ◽  
Katy M. Rainey ◽  
Keith Cherkauer
Keyword(s):  
Data Processing ◽  
High Throughput ◽  
Large Scale ◽  
Vegetation Index ◽  
Vegetation Indices ◽  
Unmanned Aerial Systems ◽  
Growth Stages ◽  
Processing Pipeline ◽  
High Throughput Phenotyping ◽  
Aerial Systems

HighlightsThis study addresses two computational challenges in high-throughput phenotyping: scalability and efficiency.Specifically, we focus on extracting crop images and deriving vegetation indices using unmanned aerial systems.To this end, we outline a data processing pipeline, featuring a crop localization algorithm and trie data structure.We demonstrate the efficacy of our approach by computing large-scale and high-precision vegetation indices in a soybean breeding experiment, where we evaluate soybean growth under water inundation and temporal change.Abstract. In agronomy, high-throughput phenotyping (HTP) can provide key information for agronomists in genomic selection as well as farmers in yield prediction. Recently, HTP using unmanned aerial systems (UAS) has shown advantages in both cost and efficiency. However, scalability and efficiency have not been well studied when processing images in complex contexts, such as using multispectral cameras, and when images are collected during early and late growth stages. These challenges hamper further analysis to quantify phenotypic traits for large-scale and high-precision applications in plant breeding. To solve these challenges, our research team previously built a three-step data processing pipeline, which is highly modular. For this project, we present improvements to the previous pipeline to improve canopy segmentation and crop plot localization, leading to improved accuracy in crop image extraction. Furthermore, we propose a novel workflow based on a trie data structure to compute vegetation indices efficiently and with greater flexibility. For each of our proposed changes, we evaluate the advantages by comparison with previous models in the literature or by comparing processing results using both the original and improved pipelines. The improved pipeline is implemented as two MATLAB programs: Crop Image Extraction version 2 (CIE 2.0) and Vegetation Index Derivation version 1 (VID 1.0). Using CIE 2.0 and VID 1.0, we compute canopy coverage and normalized difference vegetation indices (NDVIs) for a soybean phenotyping experiment. We use canopy coverage to investigate excess water stress and NDVIs to evaluate temporal patterns across the soybean growth stages. Both experimental results compare favorably with previous studies, especially for approximation of soybean reproductive stage. Overall, the proposed methodology and implemented experiments provide a scalable and efficient paradigm for applying HTP with UAS to general plant breeding. Keywords: Data processing pipeline, High-throughput phenotyping, Image processing, Soybean breeding, Unmanned aerial systems, Vegetation indices.

scholarly journals Forecasting Yield and Lignocellulosic Composition of Energy Cane Using Unmanned Aerial Systems

Agronomy ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 718 ◽  
Author(s):  
Uriel Cholula ◽  
Jorge A. da Silva ◽  
Thiago Marconi ◽  
J. Alex Thomasson ◽  
Jorge Solorzano ◽  
...  
Keyword(s):  
Vegetation Index ◽  
Management Practices ◽  
Block Design ◽  
Coefficient Of Determination ◽  
Cane Yield ◽  
Unmanned Aerial Systems ◽  
Growth Stages ◽  
Ratoon Crop ◽  
Energy Cane ◽  
Aerial Systems

Crop monitoring and appropriate agricultural management practices of elite germplasm will enhance bioenergy’s efficiency. Unmanned aerial systems (UAS) may be a useful tool for this purpose. The objective of this study was to assess the use of UAS with true color and multispectral imagery to predict the yield and total cellulosic content (TCC) of newly created energy cane germplasm. A trial was established in the growing season of 2016 at the Texas A&M AgriLife Research Center in Weslaco, Texas, where 15 energy cane elite lines and three checks were grown on experimental plots, arranged in a complete block design and replicated four times. Four flights were executed at different growth stages in 2018, at the first ratoon crop, using two multi-rotor UAS: the DJI Phantom 4 Pro equipped with RGB camera and the DJI Matrice 100, equipped with multispectral sensor (SlantRange 3p). Canopy cover, canopy height, NDVI (Normalized Difference Vegetation Index), and ExG (Excess Green Index) were extracted from the images and used to perform a stepwise regression to obtain the yield and TCC models. The results showed a good agreement between the predicted and the measured yields (R2 = 0.88); however, a low coefficient of determination was found between the predicted and the observed TCC (R2 = 0.30). This study demonstrated the potential application of UAS to estimate energy cane yield with high accuracy, enabling plant breeders to phenotype larger populations and make selections with higher confidence.

scholarly journals A Robust Vegetation Index Based on Different UAV RGB Images to Estimate SPAD Values of Naked Barley Leaves

2021 ◽  
Vol 13 (4) ◽  
pp. 686
Author(s):  
Yu Liu ◽  
Kenji Hatou ◽  
Takanori Aihara ◽  
Sakuya Kurose ◽  
Tsutomu Akiyama ◽  
...  
Keyword(s):  
Large Scale ◽  
Vegetation Index ◽  
Smallholder Farmers ◽  
Vegetation Indices ◽  
Ground Level ◽  
High Temporal Resolution ◽  
Growth Stages ◽  
Chlorophyll Contents ◽  
Naked Barley ◽  
Barley Leaves

Chlorophyll content in plant leaves is an essential indicator of the growth condition and the fertilization management effect of naked barley crops. The soil plant analysis development (SPAD) values strongly correlate with leaf chlorophyll contents. Unmanned Aerial Vehicles (UAV) can provide an efficient way to retrieve SPAD values on a relatively large scale with a high temporal resolution. But the UAV mounted with high-cost multispectral or hyperspectral sensors may be a tremendous economic burden for smallholder farmers. To overcome this shortcoming, we investigated the potential of UAV mounted with a commercial digital camera for estimating the SPAD values of naked barley leaves. We related 21 color-based vegetation indices (VIs) calculated from UAV images acquired from two flight heights (6.0 m and 50.0 m above ground level) in four different growth stages with SPAD values. Our results indicated that vegetation extraction and naked barley ears mask could improve the correlation between image-calculated vegetation indices and SPAD values. The VIs of ‘L*,’ ‘b*,’ ‘G − B’ and ‘2G − R − B’ showed significant correlations with SPAD values of naked barley leaves at both flight heights. The validation of the regression model showed that the index of ‘G-B’ could be regarded as the most robust vegetation index for predicting the SPAD values of naked barley leaves for different images and different flight heights. Our study demonstrated that the UAV mounted with a commercial camera has great potentiality in retrieving SPAD values of naked barley leaves under unstable photography conditions. It is significant for farmers to take advantage of the cheap measurement system to monitor crops.

scholarly journals Application of unmanned aerial systems for high throughput phenotyping of large wheat breeding nurseries

Plant Methods ◽  
2016 ◽  
Vol 12 (1) ◽  
Author(s):  
Atena Haghighattalab ◽  
Lorena González Pérez ◽  
Suchismita Mondal ◽  
Daljit Singh ◽  
Dale Schinstock ◽  
...  
Keyword(s):  
High Throughput ◽  
Wheat Breeding ◽  
Unmanned Aerial Systems ◽  
High Throughput Phenotyping ◽  
Aerial Systems

scholarly journals Quantifying Effects of Excess Water Stress at Early Soybean Growth Stages Using Unmanned Aerial Systems

2021 ◽  
Vol 13 (15) ◽  
pp. 2911
Author(s):  
Stuart D. Smith ◽  
Laura C. Bowling ◽  
Katy M. Rainey ◽  
Keith A. Cherkauer
Keyword(s):  
Water Stress ◽  
High Throughput ◽  
Low Cost ◽  
Unmanned Aerial Systems ◽  
Above Ground Biomass ◽  
Development Stages ◽  
High Throughput Data ◽  
Processing Pipeline ◽  
Excess Water ◽  
Aerial Systems

Low-gradient agricultural areas prone to in-field flooding impact crop development and yield potential, resulting in financial losses. Early identification of the potential reduction in yield from excess water stress at the plot scale provides stakeholders with the high-throughput information needed to assess risk and make responsive economic management decisions as well as future investments. The objective of this study is to analyze and evaluate the application of proximal remote sensing from unmanned aerial systems (UAS) to detect excess water stress in soybean and predict the potential reduction in yield due to this excess water stress. A high-throughput data processing pipeline is developed to analyze multispectral images captured at the early development stages (R4–R5) from a low-cost UAS over two radiation use efficiency experiments in West–Central Indiana, USA. Above-ground biomass is estimated remotely to assess the soybean development by considering soybean genotype classes (High Yielding, High Yielding under Drought, Diversity, all classes) and transferring estimated parameters to a replicate experiment. Digital terrain analysis using the Topographic Wetness Index (TWI) is used to objectively compare plots more susceptible to inundation with replicate plots less susceptible to inundation. The results of the study indicate that proximal remote sensing estimates above-ground biomass at the R4–R5 stage using adaptable and transferable methods, with a calculated percent bias between 0.8% and 14% and root mean square error between 72 g/m2 and 77 g/m2 across all genetic classes. The estimated biomass is sensitive to excess water stress with distinguishable differences identified between the R4 and R5 development stages; this translates into a reduction in the percent of expected yield corresponding with observations of in-field flooding and high TWI. This study demonstrates transferable methods to estimate yield loss due to excess water stress at the plot level and increased potential to provide crop status assessments to stakeholders prior to harvest using low-cost UAS and a high-throughput data processing pipeline.

High throughput phenotyping of tomato spot wilt disease in peanuts using unmanned aerial systems and multispectral imaging

2017 ◽  
Vol 20 (3) ◽  
pp. 4-12 ◽  
Author(s):  
Aaron Patrick ◽  
Sara Pelham ◽  
Albert Culbreath ◽  
C. Corely Holbrook ◽  
Ignacio Jose De Godoy ◽  
...  
Keyword(s):  
High Throughput ◽  
Multispectral Imaging ◽  
Wilt Disease ◽  
Unmanned Aerial Systems ◽  
High Throughput Phenotyping ◽  
Aerial Systems

scholarly journals High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

2021 ◽  
Vol 22 (15) ◽  
pp. 8266
Author(s):  
Minsu Kim ◽  
Chaewon Lee ◽  
Subin Hong ◽  
Song Lim Kim ◽  
Jeong-Ho Baek ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Large Scale ◽  
Crop Yields ◽  
Plant Traits ◽  
Rapid Development ◽  
Plant Responses ◽  
Phenotypic Data ◽  
Agricultural Technologies ◽  
High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

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