scholarly journals High-Throughput UAV Image-Based Method Is More Precise Than Manual Rating of Herbicide Tolerance

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Hema S. N. Duddu ◽  
Eric N. Johnson ◽  
Christian J. Willenborg ◽  
Steven J. Shirtliffe
Keyword(s):  
High Throughput ◽  
Human Error ◽  
Vegetation Index ◽  
Block Design ◽  
Vegetation Indices ◽  
Herbicide Tolerance ◽  
Plant Phenotyping ◽  
Study Objective ◽  
Ground Sample ◽  
Visual Rating

The traditional visual rating system is labor-intensive, time-consuming, and prone to human error. Unmanned aerial vehicle (UAV) imagery-based vegetation indices (VI) have potential applications in high-throughput plant phenotyping. The study objective is to determine if UAV imagery provides accurate and consistent estimations of crop injury from herbicide application and its potential as an alternative to visual ratings. The study was conducted at the Kernen Crop Research Farm, University of Saskatchewan in 2016 and 2017. Fababean (Vicia faba L.) crop tolerance to nine herbicide tank mixtures was evaluated with 2 rates distributed in a randomized complete block design (RCBD) with 4 blocks. The trial was imaged using a multispectral camera with a ground sample distance (GSD) of 1.2 cm, one week after the treatment application. Visual ratings of growth reduction and physiological chlorosis were recorded simultaneously with imaging. The optimized soil-adjusted vegetation index (OSAVI) was calculated from the thresholded orthomosaics. The UAV-based vegetation index (OSAVI) produced more precise results compared to visual ratings for both years. The coefficient of variation (CV) of OSAVI was ~1% when compared to 18-43% for the visual ratings. Furthermore, Tukey’s honestly significance difference (HSD) test yielded a more precise mean separation for the UAV-based vegetation index than visual ratings. The significant correlations between OSAVI and the visual ratings from the study suggest that undesirable variability associated with visual assessments can be minimized with the UAV-based approach. UAV-based imagery methods had greater precision than the visual-based ratings for crop herbicide damage. These methods have the potential to replace visual ratings and aid in screening crops for herbicide tolerance.

scholarly journals Automated Hyperspectral Vegetation Index Derivation Using A Hyperparameter Optimization Framework for High-Throughput Plant Phenotyping

2021 ◽  
Author(s):  
Joshua Koh ◽  
Bikram Banerjee ◽  
German Spangenberg ◽  
Surya Kant
Keyword(s):  
High Throughput ◽  
Vegetation Index ◽  
Sugar Content ◽  
Vegetation Indices ◽  
Plant Phenotyping ◽  
Least Squares Regression ◽  
Optimization Framework ◽  
Band Index ◽  
Rapid Generation ◽  
Covering Model

Hyperspectral vegetation indices (VIs) are widely deployed in agriculture remote sensing and plant phenotyping to estimate plant biophysical and biochemical traits. However, existing VIs consist mainly of simple 2-band indices which limits the net performance and often do not generalize well for other traits than they were originally designed for. We present an automated hyperspectral vegetation index (AutoVI) system for the rapid generation of novel 2- to 6-band trait-specific indices in a streamlined process covering model selection, optimization and evaluation driven by the tree parzen estimator algorithm. Its performance was tested in generating novel indices to estimate chlorophyll and sugar contents in wheat. Results show that AutoVI can rapidly generate complex novel VIs (≥4-band index) which correlated strongly (R2 > 0.8) with measured chlorophyll and sugar contents in wheat. AutoVI-derived indices were used as features in simple and stepwise multiple linear regression for chlorophyll and sugar content estimation, and outperformed results achieved with existing 47 VIs and those provided by partial least squares regression. The AutoVI system can deliver novel trait-specific VIs readily adoptable in high-throughput plant phenotyping platforms and should appeal to plant scientists and breeders. A graphical user interface of AutoVI is herein provided.

scholarly journals Biomass estimation of cultivated red algae Pyropia using unmanned aerial platform based multispectral imaging

Plant Methods ◽  
2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Shuai Che ◽  
Guoying Du ◽  
Ning Wang ◽  
Kun He ◽  
Zhaolan Mo ◽  
...  
Keyword(s):  
High Throughput ◽  
Vegetation Index ◽  
Multispectral Imaging ◽  
Vegetation Indices ◽  
Spectral Imaging ◽  
Shielding Effect ◽  
Quadratic Model ◽  
Biomass Estimation ◽  
Marine Aquaculture ◽  
Significant Difference

Abstract Background Pyropia is an economically advantageous genus of red macroalgae, which has been cultivated in the coastal areas of East Asia for over 300 years. Realizing estimation of macroalgae biomass in a high-throughput way would great benefit their cultivation management and research on breeding and phenomics. However, the conventional method is labour-intensive, time-consuming, manually destructive, and prone to human error. Nowadays, high-throughput phenotyping using unmanned aerial vehicle (UAV)-based spectral imaging is widely used for terrestrial crops, grassland, and forest, but no such application in marine aquaculture has been reported. Results In this study, multispectral images of cultivated Pyropia yezoensis were taken using a UAV system in the north of Haizhou Bay in the midwestern coast of Yellow Sea. The exposure period of P. yezoensis was utilized to prevent the significant shielding effect of seawater on the reflectance spectrum. The vegetation indices of normalized difference vegetation index (NDVI), ratio vegetation index (RVI), difference vegetation index (DVI) and normalized difference of red edge (NDRE) were derived and indicated no significant difference between the time that P. yezoensis was completely exposed to the air and 1 h later. The regression models of the vegetation indices and P. yezoensis biomass per unit area were established and validated. The quadratic model of DVI (Biomass = − 5.550DVI2 + 105.410DVI + 7.530) showed more accuracy than the other index or indices combination, with the highest coefficient of determination (R2), root mean square error (RMSE), and relative estimated accuracy (Ac) values of 0.925, 8.06, and 74.93%, respectively. The regression model was further validated by consistently predicting the biomass with a high R2 value of 0.918, RMSE of 8.80, and Ac of 82.25%. Conclusions This study suggests that the biomass of Pyropia can be effectively estimated using UAV-based spectral imaging with high accuracy and consistency. It also implied that multispectral aerial imaging is potential to assist digital management and phenomics research on cultivated macroalgae in a high-throughput way.

scholarly journals Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Wang ◽  
Fangdong Liu ◽  
Xiaoshuai Hao ◽  
Wubin Wang ◽  
Guangnan Xing ◽  
...  
Keyword(s):  
High Throughput ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Block Design ◽  
Physiological Traits ◽  
Growth And Yield ◽  
Genetic Changes ◽  
Soybean Germplasm

The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05–0.18 and 1.20–4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2–4 and 2–6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.

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 Relationship between vegetation indices and agronomic performance of maize varieties under different nitrogen rates

2020 ◽  
Vol 36 (5) ◽  
Author(s):  
Marcela da Silva Flores ◽  
Willian Meniti Paschoalete ◽  
Fabio Henrique Rojo Baio ◽  
Cid Naudi Silva Campos ◽  
Ariane de Andréa Pantaleão ◽  
...  
Keyword(s):  
Plant Height ◽  
Precision Agriculture ◽  
Vegetation Index ◽  
Block Design ◽  
Vegetation Indices ◽  
Agronomic Performance ◽  
N Content ◽  
Maize Varieties ◽  
Leaf N Content ◽  
Leaf N

Precision agriculture is a set of techniques that assist the monitoring of the agronomic performance of the maize crop by using vegetation indices. This study aimed to verify the relationship between vegetation indices, plant height, leaf N content, and grain yield of three maize varieties, grown under high and low N as topdressing. The experiment was carried out at the Fundação de Apoio à Pesquisa Agropecuária de Chapadão (Fundação Chapadão), located in the municipality of Chapadão do Sul, during the 2017/2018 season. The experiment consisted of a randomized block design with four replications, arranged in a 3x2 split-plot scheme. The first factor (plots) corresponded to three open-pollinated maize varieties (BRS 4103, BRS Gorotuba, and SCS 154), and the second factor (subplots) consisted of two N rates applied as topdressing (80 and 160 kg- 1). All the evaluated variables showed varieties x N interaction. Vegetation indices in maize varieties were influenced by the N rate applied as topdressing. Normalized Difference Vegetation Index (NDVI) and Soil-adjusted Vegetation Index (SAVI) showed a higher correlation with plant height. At the same time, Normalized Difference Red Edge (NDRE) had a stronger association with leaf N content.

scholarly journals Sustainability Trait Modeling of Field-Grown Switchgrass (Panicum virgatum) Using UAV-Based Imagery

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2726
Author(s):  
Yaping Xu ◽  
Vivek Shrestha ◽  
Cristiano Piasecki ◽  
Benjamin Wolfe ◽  
Lance Hamilton ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Data Collection ◽  
High Throughput ◽  
Panicum Virgatum ◽  
Vegetation Index ◽  
Lignin Content ◽  
Vegetation Indices ◽  
Rust Disease ◽  
Bioenergy Feedstock ◽  
First Time

Unmanned aerial vehicles (UAVs) provide an intermediate scale of spatial and spectral data collection that yields increased accuracy and consistency in data collection for morphological and physiological traits than satellites and expanded flexibility and high-throughput compared to ground-based data collection. In this study, we used UAV-based remote sensing for automated phenotyping of field-grown switchgrass (Panicum virgatum), a leading bioenergy feedstock. Using vegetation indices calculated from a UAV-based multispectral camera, statistical models were developed for rust disease caused by Puccinia novopanici, leaf chlorophyll, nitrogen, and lignin contents. For the first time, UAV remote sensing technology was used to explore the potentials for multiple traits associated with sustainable production of switchgrass, and one statistical model was developed for each individual trait based on the statistical correlation between vegetation indices and the corresponding trait. Also, for the first time, lignin content was estimated in switchgrass shoots via UAV-based multispectral image analysis and statistical analysis. The UAV-based models were verified by ground-truthing via correlation analysis between the traits measured manually on the ground-based with UAV-based data. The normalized difference red edge (NDRE) vegetation index outperformed the normalized difference vegetation index (NDVI) for rust disease and nitrogen content, while NDVI performed better than NDRE for chlorophyll and lignin content. Overall, linear models were sufficient for rust disease and chlorophyll analysis, but for nitrogen and lignin contents, nonlinear models achieved better results. As the first comprehensive study to model switchgrass sustainability traits from UAV-based remote sensing, these results suggest that this methodology can be utilized for switchgrass high-throughput phenotyping in the field.

scholarly journals UAV-Based Multispectral Phenotyping for Disease Resistance to Accelerate Crop Improvement under Changing Climate Conditions

2020 ◽  
Vol 12 (15) ◽  
pp. 2445
Author(s):  
Walter Chivasa ◽  
Onisimo Mutanga ◽  
Chandrashekhar Biradar
Keyword(s):  
Plant Breeding ◽  
High Throughput ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Crop Improvement ◽  
Data Availability ◽  
Data Driven ◽  
Plant Phenotyping ◽  
Variety Selection ◽  
Chlorophyll Index

Accelerating crop improvement for increased yield and better adaptation to changing climatic conditions is an issue of increasing urgency in order to satisfy the ever-increasing global food demand. However, the major bottleneck is the absence of high-throughput plant phenotyping methods for rapid and cost-effective data-driven variety selection and release in plant breeding. Traditional phenotyping methods that rely on trained experts are slow, costly, labor-intensive, subjective, and often require destructive sampling. We explore ways to improve the efficiency of crop phenotyping through the use of unmanned aerial vehicle (UAV)-based multispectral remotely sensed data in maize (Zea mays L.) varietal response to maize streak virus (MSV) disease. Twenty-five maize varieties grown in a trial with three replications were evaluated under artificial MSV inoculation. Ground scoring for MSV infection was carried out at mid-vegetative, flowering, and mid-grain filling on a scale of 1 (resistant) to 9 (susceptible). UAV-derived spectral data were acquired at these three different phenological stages in multispectral bands corresponding to Green (0.53–0.57 μm), Red (0.64–0.68 μm), Rededge (0.73–0.74 μm), and Near-Infrared (0.77–0.81 μm). The imagery captured was stitched together in Pix4Dmapper, which generates two types of multispectral orthomosaics: the NoAlpha and the transparent mosaics for each band. The NoAlpha imagery was used as input into QGIS to extract reflectance data. Six vegetation indices were derived for each variety: normalized difference vegetation index (NDVI), green normalized difference vegetation index (GNDVI), Rededge NDVI (NDVIrededge), Simple Ratio (SR), green Chlorophyll Index (CIgreen), and Rededge Chlorophyll Index (CIrededge). The Random Forest (RF) classifier was used to evaluate UAV-derived spectral and VIs with and without variable optimization. Correlations between the UAV-derived data and manual MSV scores were significant (R = 0.74–0.84). Varieties were classified into resistant, moderately resistant, and susceptible with overall classification accuracies of 77.3% (Kappa = 0.64) with optimized and 68.2% (Kappa = 0.51) without optimized variables, representing an improvement of ~13.3% due to variable optimization. The RF model selected GNDVI, CIgreen, CIrededge, and the Red band as the most important variables for classification. Mid-vegetative was the most ideal phenological stage for accurate varietal phenotyping and discrimination using UAV-derived multispectral data with RF under artificial MSV inoculation. The results provide a rapid UAV-based remote sensing solution that offers a step-change towards data availability at high spatial (submeter) and temporal (daily/weekly) resolution in varietal analysis for quick and robust high-throughput plant phenotyping, important for timely and unbiased data-driven variety selection and release in plant breeding programs, especially as climate change accelerates.

scholarly journals Sensor based calibration study for in-season nitrogen management of winter wheat in Turkey

2020 ◽  
Vol 6 (2) ◽  
pp. 204-211
Author(s):  
Erdinc Savasli ◽  
Oguz Onder ◽  
Cemal Cekic ◽  
Hasan Mufit Kalayci ◽  
Ramis Dayioglu ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Vegetation Index ◽  
Agricultural Research ◽  
Nitrogen Nutrition ◽  
Stem Elongation ◽  
Block Design ◽  
Vegetation Indices ◽  
Nutrition Status ◽  
Growth Stages ◽  
Yield Estimation

The aims of this study were to compare the responses of four winter wheat cultivars to nitrogen fertilization with vegetation indices calculated using spectral reflection (GreenSeeker hand-held sensor) and to estimate in-season yield (INSEY) using the vegetation indices. The field experiment was conducted at Transitional Zone Agricultural Research Institute of Eskisehir province, Turkey in 2007-2008, 2008-2009 and 2009-2010 growing seasons. The experimental layout was a 2factor factorial in the randomized complete block design. Nitrogen rates were 0, 40, 80, 120, 160 and 200 kg N ha-1. Vegetation Index (NDVI) was obtained at growth stages of Zadoks 24 (tillering stage), Zadoks stage 30 (stem elongation), Zadoks stage 31 (the first node is visible) and Zadoks stage 32 (the second node is visible). The results revealed that Zadoks stage 30 was the most realistic reading time. NDVI had the advantage of providing information on biomass, in addition to nitrogen nutrition status of crops, enabling in-season yield estimation possible. Therefore, NDVI based calibration equations were preferred for testing in the fields of actual farmers for the last year of study. A comparison of the system with traditional farmer applications indicated that yield estimation obtained by the new system was quite similar yields with 13.2 kg ha-1 less N in the spring (ZD 3.0), showing its economically promising value. Asian J. Med. Biol. Res. June 2020, 6(2): 204-211

HEALTHINESS OF OIL PALM PLANTATION TOWARDS SUSTAINABILITY OF ENVIRONMENT

2020 ◽  
Vol 7 (1) ◽  
pp. 21
Author(s):  
Faradina Marzukhi ◽  
Nur Nadhirah Rusyda Rosnan ◽  
Md Azlin Md Said
Keyword(s):  
Oil Palm ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Satellite Image ◽  
Vegetation Indices ◽  
Soil Nutrient ◽  
Oil Palm Plantation ◽  
Sustainable Environment ◽  
Moisture Analysis ◽  
The Relationship

The aim of this study is to analyse the relationship between vegetation indices of Normalized Difference Vegetation Index (NDVI) and soil nutrient of oil palm plantation at Felcra Nasaruddin Bota in Perak for future sustainable environment. The satellite image was used and processed in the research. By Using NDVI, the vegetation index was obtained which varies from -1 to +1. Then, the soil sample and soil moisture analysis were carried in order to identify the nutrient values of Nitrogen (N), Phosphorus (P) and Potassium (K). A total of seven soil samples were acquired within the oil palm plantation area. A regression model was then made between physical condition of the oil palms and soil nutrients for determining the strength of the relationship. It is hoped that the risk map of oil palm healthiness can be produced for various applications which are related to agricultural plantation.

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