Field-based High-throughput Phenotyping Research Articles

Bagging Improves the Performance of Deep Learning-Based Semantic Segmentation with Limited Labeled Images: A Case Study of Crop Segmentation for High-Throughput Plant Phenotyping.

Advancements in imaging, computer vision, and automation have revolutionized various fields, including field-based high-throughput plant phenotyping (FHTPP). This integration allows for the rapid and accurate measurement of plant traits. Deep Convolutional Neural Networks (DCNNs) have emerged as a powerful tool in FHTPP, particularly in crop segmentation-identifying crops from the background-crucial for trait analysis. However, the effectiveness of DCNNs often hinges on the availability of large, labeled datasets, which poses a challenge due to the high cost of labeling. In this study, a deep learning with bagging approach is introduced to enhance crop segmentation using high-resolution RGB images, tested on the NU-Spidercam dataset from maize plots. The proposed method outperforms traditional machine learning and deep learning models in prediction accuracy and speed. Remarkably, it achieves up to 40% higher Intersection-over-Union (IoU) than the threshold method and 11% over conventional machine learning, with significantly faster prediction times and manageable training duration. Crucially, it demonstrates that even small labeled datasets can yield high accuracy in semantic segmentation. This approach not only proves effective for FHTPP but also suggests potential for broader application in remote sensing, offering a scalable solution to semantic segmentation challenges. This paper is accompanied by publicly available source code.

Field-based high-throughput phenotyping enhances phenomic and genomic predictions for grain yield and plant height across years in maize.

Field-based phenomic prediction employs novel features, like vegetation indices (VIs) from drone images, to predict key agronomic traits in maize, despite challenges in matching biomarker measurement time points across years or environments. This study utilized functional principal component analysis (FPCA) to summarize the variation of temporal VIs, uniquely allowing the integration of this data into phenomic prediction models tested across multiple years (2018-2021) and environments. The models, which included 1 genomic, 2 phenomic, 2 multikernel, and 1 multitrait type, were evaluated in 4 prediction scenarios (CV2, CV1, CV0, and CV00), relevant for plant breeding programs, assessing both tested and untested genotypes in observed and unobserved environments. Two hybrid populations (415 and 220 hybrids) demonstrated the visible atmospherically resistant index's strong temporal correlation with grain yield (up to 0.59) and plant height. The first 2 FPCAs explained 59.3 ± 13.9% and 74.2 ± 9.0% of the temporal variation of temporal data of VIs, respectively, facilitating predictions where flight times varied. Phenomic data, particularly when combined with genomic data, often were comparable to or numerically exceeded the base genomic model in prediction accuracy, particularly for grain yield in untested hybrids, although no significant differences in these models' performance were consistently observed. Overall, this approach underscores the effectiveness of FPCA and combined models in enhancing the prediction of grain yield and plant height across environments and diverse agricultural settings.

Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models.

Incorporating cover crops into cropping systems offers numerous potential benefits, including the reduction of soil erosion, suppression of weeds, decreased nitrogen requirements for subsequent crops, and increased carbon sequestration. The aboveground biomass (AGB) of cover crops strongly influences their performance in delivering these benefits. Despite the significance of AGB, a comprehensive field-based high-throughput phenotyping study to quantify AGB of multiple cover crops in the U.S. Midwest has not been found. This study presents a two-year field experiment carried out in Eastern Nebraska, USA, to estimate AGB of five different cover crop species [canola (Brassica napus L.), rye (Secale cereale L.), triticale (Triticale × Triticosecale L.), vetch (Vicia sativa L.), and wheat (Triticum aestivum L.)] using high-throughput phenotyping and Machine Learning (ML) models. Destructive AGB sampling was performed three times during each spring season in 2022 and 2023. An array of morphological, spectral, thermal, and environmental features from the sensors were utilized as feature inputs of ML models. Moderately strong linear correlations between AGB and the selected features were observed. Four ML models, namely Random Forests Regression (RFR), Support Vector Regression (SVR), Partial Least Squares Regression (PLSR), and Artificial Neural Network (ANN), were investigated. Among the four models, PLSR achieved the highest Coefficient of Determination (R2) of 0.84 and the lowest Root Mean Squared Error (RMSE) of 892 kg/ha (Normalized RMSE (NRMSE) = 8.87%), indicating that PLSR could be the most appropriate method for estimating AGB of multiple cover crop species. Feature importance analysis ranked spectral features like Normalized Difference Red Edge (NDRE), Solar-induced Fluorescence (SIF), Spectral Reflectance at 485 nm (R485), and Normalized Difference Vegetation Index (NDVI) as top model features using PLSR. When utilizing fewer feature inputs, ANN exhibited better prediction performance compared to other models. Using morphological and spectral parameters as input features alone led to a R2 of 0.80 and 0.77 for AGB prediction using ANN, respectively. This study demonstrated the feasibility of high-throughput phenotyping and ML techniques for accurately estimating AGB of multiple cover crop species. Further enhancement of model performance could be achieved through additional destructive sampling conducted across multiple locations and years.

A Three-Dimensional Conceptual Model for Estimating the Above-Ground Biomass of Winter Wheat Using Digital and Multispectral Unmanned Aerial Vehicle Images at Various Growth Stages

The timely and accurate estimation of above-ground biomass (AGB) is crucial for indicating crop growth status, assisting management decisions, and predicting grain yield. Unmanned aerial vehicle (UAV) remote sensing technology is a promising approach for monitoring crop biomass. However, the determination of winter wheat AGB based on canopy reflectance is affected by spectral saturation effects. Thus, constructing a generic model for accurately estimating winter wheat AGB using UAV data is significant. In this study, a three-dimensional conceptual model (3DCM) for estimating winter wheat AGB was constructed using plant height (PH) and fractional vegetation cover (FVC). Compared with both the traditional vegetation index model and the traditional multi-feature combination model, the 3DCM yielded the best accuracy for the jointing stage (based on RGB data: coefficient of determination (R2) = 0.82, normalized root mean square error (nRMSE) = 0.2; based on multispectral (MS) data: R2 = 0.84, nRMSE = 0.16), but the accuracy decreased significantly when the spike organ appeared. Therefore, the spike number (SN) was added to create a new three-dimensional conceptual model (n3DCM). Under different growth stages and UAV platforms, the n3DCM (RGB: R2 = 0.73–0.85, nRMSE = 0.17–0.23; MS: R2 = 0.77–0.84, nRMSE = 0.17–0.23) remarkably outperformed the traditional multi-feature combination model (RGB: R2 = 0.67–0.88, nRMSE = 0.15–0.25; MS: R2 = 0.60–0.77, nRMSE = 0.19–0.26) for the estimation accuracy of the AGB. This study suggests that the n3DCM has great potential in resolving spectral errors and monitoring growth parameters, which could be extended to other crops and regions for AGB estimation and field-based high-throughput phenotyping.

Development and deployment of a big data pipeline for field-based high-throughput cotton phenotyping data

In this study, we propose a big data pipeline for cotton bloom detection using a Lambda architecture, which enables real-time and batch processing of data. Our proposed approach leverages Azure resources such as Data Factory, Event Grids, Rest APIs, and Databricks. This work is the first to develop and demonstrate the implementation of such a pipeline for plant phenotyping through Azure's cloud computing service. The proposed pipeline consists of data preprocessing, object detection using a YOLOv5 neural network model trained through Azure AutoML, and visualization of object detection bounding boxes on output images. The trained model achieves a mean Average Precision (mAP) score of 0.96, demonstrating its high performance for cotton bloom classification. We evaluate our Lambda architecture pipeline using 9,000 images yielding an optimized runtime of 34 minutes. The results illustrate the scalability of the proposed pipeline as a solution for deep learning object detection, with the potential for further expansion through additional Azure processing cores. This work advances the scientific research field by providing a new method for cotton bloom detection on a large dataset and demonstrates the potential of utilizing cloud computing resources, specifically Azure, for efficient and accurate big data processing in precision agriculture.

Phenomic data-driven biological prediction of maize through field-based high-throughput phenotyping integration with genomic data.

High-throughput phenotyping (HTP) has expanded the dimensionality of data in plant research; however, HTP has resulted in few novel biological discoveries to date. Field-based HTP (FHTP), using small unoccupied aerial vehicles (UAVs) equipped with imaging sensors, can be deployed routinely to monitor segregating plant population interactions with the environment under biologically meaningful conditions. Here, flowering dates and plant height, important phenological fitness traits, were collected on 520 segregating maize recombinant inbred lines (RILs) in both irrigated and drought stress trials in 2018. Using UAV phenomic, single nucleotide polymorphism (SNP) genomic, as well as combined data, flowering times were predicted using several scenarios. Untested genotypes were predicted with 0.58, 0.59, and 0.41 prediction ability for anthesis, silking, and terminal plant height, respectively, using genomic data, but prediction ability increased to 0.77, 0.76, and 0.58 when phenomic and genomic data were used together. Using the phenomic data in a genome-wide association study, a heat-related candidate gene (GRMZM2G083810; hsp18f) was discovered using temporal reflectance phenotypes belonging to flowering times (both irrigated and drought) trials where heat stress also peaked. Thus, a relationship between plants and abiotic stresses belonging to a specific time of growth was revealed only through use of temporal phenomic data. Overall, this study showed that (i) it is possible to predict complex traits using high dimensional phenomic data between different environments, and (ii) temporal phenomic data can reveal a time-dependent association between genotypes and abiotic stresses, which can help understand mechanisms to develop resilient plants.

High-Throughput Canopy and Belowground Phenotyping of a Set of Peanut CSSLs Detects Lines with Increased Pod Weight and Foliar Disease Tolerance

We deployed field-based high-throughput phenotyping (HTP) techniques to acquire trait data for a subset of a peanut chromosome segment substitution line (CSSL) population. Sensors mounted on an unmanned aerial vehicle (UAV) were used to derive various vegetative indices as well as canopy temperatures. A combination of aerial imaging and manual scoring showed that CSSL 100, CSSL 84, CSSL 111, and CSSL 15 had remarkably low tomato spotted wilt virus (TSWV) incidence, a devastating disease in South Georgia, USA. The four lines also performed well under leaf spot pressure. The vegetative indices showed strong correlations of up to 0.94 with visual disease scores, indicating that aerial phenotyping is a reliable way of selecting under disease pressure. Since the yield components of peanut are below the soil surface, we deployed ground penetrating radar (GPR) technology to detect pods non-destructively. Moderate correlations of up to 0.5 between pod weight and data acquired from GPR signals were observed. Both the manually acquired pod data and GPR variables highlighted the three lines, CSSL 84, CSSL 100, and CSSL 111, as the best-performing lines, with pod weights comparable to the cultivated check Tifguard. Through the combined application of manual and HTP techniques, this study reinforces the premise that chromosome segments from peanut wild relatives may be a potential source of valuable agronomic traits.

High-Throughput Plant Phenotyping (HTPP) in Resource-Constrained Research Programs: A Working Example in Ghana

In this paper, we present a procedure for implementing field-based high-throughput plant phenotyping (HTPP) that can be used in resource-constrained research programs. The procedure relies on opensource tools with the only expensive item being one-off purchase of a drone. It includes acquiring images of the field of interest, stitching the images to get the entire field in one image, calculating and extracting the vegetation indices of the individual plots, and analyzing the extracted indices according to the experimental design. Two populations of groundnut genotypes with different maturities were evaluated for their reaction to early and late leaf spot (ELS, LLS) diseases under field conditions in 2020 and 2021. Each population was made up of 12 genotypes in 2020 and 18 genotypes in 2021. Evaluation of the genotypes was done in four locations in each year. We observed a strong correlation between the vegetation indices and the area under the disease progress curve (AUDPC) for ELS and LLS. However, the strength and direction of the correlation depended upon the time of disease onset, level of tolerance among the genotypes and the physiological traits the vegetation indices were associated with. In 2020, when the disease was observed to have set in late in medium duration population, at the beginning of the seed stage (R5), normalized green-red difference index (NGRDI) and variable atmospheric resistance index (VARI) derived at the beginning pod stage (R3) had a positive relationship with the AUDPC for ELS, and LLS. On the other hand, NGRDI and VARI derived from images taken at R5, and physiological maturity (R7) had negative relationships with AUDPC for ELS, and LLS. In 2021, when the disease was observed to have set in early (at R3) also in medium duration population, a negative relationship was observed between NGRDI and VARI and AUDPC for ELS and LLS, respectively. We found consistently negative relationships of NGRDI and VARI with AUDPC for ELS and LLS, respectively, within the short duration population in both years. Canopy cover (CaC), green area (GA), and greener area (GGA) only showed negative relationships with AUDPC for ELS and LLS when the disease caused yellowing and defoliation. The rankings of some genotypes changed for NGRDI, VARI, CaC, GA, GGA, and crop senescence index (CSI) when lesions caused by the infections of ELS and LLS became severe, although that did not affect groupings of genotypes when analyzed with principal component analysis. Notwithstanding, genotypes that consistently performed well across various reproductive stages with respect to the vegetation indices constituted the top performers when ELS, LLS, haulm, and pod yields were jointly considered.

An assessment of background removal approaches for improved estimation of rice leaf nitrogen concentration with unmanned aerial vehicle multispectral imagery at various observation times

Background effect is a crucial limitation for the monitoring of leaf nitrogen concentration (LNC) in crops with unmanned aerial vehicle (UAV) multispectral imagery. Some background removal approaches have been developed for improve the estimation of LNC, but their performances are not compared in one study and it is unclear whether they are sensitive to the observation time of UAV imagery. This study evaluated three background removal approaches, i.e., the soil-adjusted vegetation index (SAVI) approach, the green pixel vegetation index approach (GPVI) and abundance adjusted vegetation index (AAVI), for estimating rice LNC from UAV-based multispectral imagery at individual and across growth stages as well as different observation times of the day. The red edge chlorophyll index (CIre) was chosen as the common basis for the last two approaches. In particular, the AAVI approach was refined with a higher number of endmembers and automated endmember extraction, and further evaluated for assessing the effect of separating sunlit components from shaded components of the canopy. Our results demonstrated that the vegetation indices (VIs) for off-noon observation times showed better relationships with LNC than those for noon at individual and across growth stages. Compared to both SAVI and CIre-green, the AACIre for all pixels (AACIre-all) exhibited the weakest sensitivity to observation time and yielded the best relationships for single-stage (jointing: r2=0.70, booting: r2=0.76, heading: r2=0.70) and across-stage (r2=0.66) models. Among the AAVIs derived from three categories of pixels, the AACIre-sunlit (R2 =0.90, RMSE=0.17%, Bias=0.03%) outperformed AACIre-all (R2 =0.85, RMSE=0.23%, Bias=0.08%) and then AACIre-shaded (R2 =0.38, RMSE=0.49%, Bias=0.40%) remarkably for the estimation accuracy of LNC. This study suggests that the refined AAVI approach has great value in reducing the background effect for more accurate monitoring of growth parameters and could be extended to other crops and regions for improved precision crop management and field-based high-throughput phenotyping.

Recent Advances for Drought Stress Tolerance in Maize (Zea mays L.): Present Status and Future Prospects.

Drought stress has severely hampered maize production, affecting the livelihood and economics of millions of people worldwide. In the future, as a result of climate change, unpredictable weather events will become more frequent hence the implementation of adaptive strategies will be inevitable. Through utilizing different genetic and breeding approaches, efforts are in progress to develop the drought tolerance in maize. The recent approaches of genomics-assisted breeding, transcriptomics, proteomics, transgenics, and genome editing have fast-tracked enhancement for drought stress tolerance under laboratory and field conditions. Drought stress tolerance in maize could be considerably improved by combining omics technologies with novel breeding methods and high-throughput phenotyping (HTP). This review focuses on maize responses against drought, as well as novel breeding and system biology approaches applied to better understand drought tolerance mechanisms and the development of drought-tolerant maize cultivars. Researchers must disentangle the molecular and physiological bases of drought tolerance features in order to increase maize yield. Therefore, the integrated investments in field-based HTP, system biology, and sophisticated breeding methodologies are expected to help increase and stabilize maize production in the face of climate change.

Phenomic data-facilitated rust and senescence prediction in maize using machine learning algorithms

Current methods in measuring maize (Zea mays L.) southern rust (Puccinia polyspora Underw.) and subsequent crop senescence require expert observation and are resource-intensive and prone to subjectivity. In this study, unoccupied aerial system (UAS) field-based high-throughput phenotyping (HTP) was employed to collect high-resolution aerial imagery of elite maize hybrids planted in the 2020 and 2021 growing seasons, with 13 UAS flights obtained from 2020 and 17 from 2021. In total, 36 vegetation indices (VIs) were extracted from mosaicked aerial images that served as temporal phenomic predictors for southern rust scored in the field and senescence as scored using UAS-acquired mosaic images. Temporal best linear unbiased predictors (TBLUPs) were calculated using a nested model that treated hybrid performance as nested within flights in terms of rust and senescence. All eight machine learning regressions tested (ridge, lasso, elastic net, random forest, support vector machine with radial and linear kernels, partial least squares, and k-nearest neighbors) outperformed a general linear model with both higher prediction accuracies (92–98%) and lower root mean squared error (RMSE) for rust and senescence scores (linear model RMSE ranged from 65.8 to 2396.5 across all traits, machine learning regressions RMSE ranged from 0.3 to 17.0). UAS-acquired VIs enabled the discovery of novel early quantitative phenotypic indicators of maize senescence and southern rust before being detectable by expert annotation and revealed positive correlations between grain filling time and yield (0.22 and 0.44 in 2020 and 2021), with practical implications for precision agricultural practices.

Advances in field-based high-throughput photosynthetic phenotyping.

Gas exchange techniques revolutionized plant research and advanced understanding, including associated fluxes and efficiencies, of photosynthesis, photorespiration, and respiration of plants from cellular to ecosystem scales. These techniques remain the gold standard for inferring photosynthetic rates and underlying physiology/biochemistry, although their utility for high-throughput phenotyping (HTP) of photosynthesis is limited both by the number of gas exchange systems available and the number of personnel available to operate the equipment. Remote sensing techniques have long been used to assess ecosystem productivity at coarse spatial and temporal resolutions, and advances in sensor technology coupled with advanced statistical techniques are expanding remote sensing tools to finer spatial scales and increasing the number and complexity of phenotypes that can be extracted. In this review, we outline the photosynthetic phenotypes of interest to the plant science community and describe the advances in high-throughput techniques to characterize photosynthesis at spatial scales useful to infer treatment or genotypic variation in field-based experiments or breeding trials. We will accomplish this objective by presenting six lessons learned thus far through the development and application of proximal/remote sensing-based measurements and the accompanying statistical analyses. We will conclude by outlining what we perceive as the current limitations, bottlenecks, and opportunities facing HTP of photosynthesis.

Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes.

Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.

Temporal Vegetation Indices and Plant Height from Remotely Sensed Imagery Can Predict Grain Yield and Flowering Time Breeding Value in Maize via Machine Learning Regression

Unoccupied aerial system (UAS; i.e., drone equipped with sensors) field-based high-throughput phenotyping (HTP) platforms are used to collect high quality images of plant nurseries to screen genetic materials (e.g., hybrids and inbreds) throughout plant growth at relatively low cost. In this study, a set of 100 advanced breeding maize (Zea mays L.) hybrids were planted at optimal (OHOT trial) and delayed planting dates (DHOT trial). Twelve UAS surveys were conducted over the trials throughout the growing season. Fifteen vegetative indices (VIs) and the 99th percentile canopy height measurement (CHMs) were extracted from processed UAS imagery (orthomosaics and point clouds) which were used to predict plot-level grain yield, days to anthesis (DTA), and silking (DTS). A novel statistical approach utilizing a nested design was fit to predict temporal best linear unbiased predictors (TBLUP) for the combined temporal UAS data. Our results demonstrated machine learning-based regressions (ridge, lasso, and elastic net) had from 4- to 9-fold increases in the prediction accuracies and from 13- to 73-fold reductions in root mean squared error (RMSE) compared to classical linear regression in prediction of grain yield or flowering time. Ridge regression performed best in predicting grain yield (prediction accuracy = ~0.6), while lasso and elastic net regressions performed best in predicting DTA and DTS (prediction accuracy = ~0.8) consistently in both trials. We demonstrated that predictor variable importance descended towards the terminal stages of growth, signifying the importance of phenotype collection beyond classical terminal growth stages. This study is among the first to demonstrate an ability to predict yield in elite hybrid maize breeding trials using temporal UAS image-based phenotypes and supports the potential benefit of phenomic selection approaches in estimating breeding values before harvest.

Development of a Mobile Platform for Field-Based High-Throughput Wheat Phenotyping

Designing and implementing an affordable High-Throughput Phenotyping Platform (HTPP) for monitoring crops’ features in different stages of their growth can provide valuable information for crop-breeders to study possible correlation between genotypes and phenotypes. Conducting automatic field measurements can improve crop productions. In this research, we have focused on development of a mechatronic system, hardware and software, for a mobile, field-based HTPP for autonomous crop monitoring for wheat field. The system can measure canopy’s height, temperature, and vegetation indices and is able to take high quality photos of crops. The system includes. developed software for data and image acquisition. The main contribution of this study is autonomous, reliable, and fast data collection for wheat and similar crops.

Bottlenecks and opportunities in field-based high-throughput phenotyping for heat and drought stress.

Flowering and grain-filling stages are highly sensitive to heat and drought stress exposure, leading to significant loss in crop yields. Therefore, phenotyping to enhance resilience to these abiotic stresses is critical for sustaining genetic gains in crop improvement programs. However, traditional methods for screening traits related to these stresses are slow, laborious, and often expensive. Remote sensing provides opportunities to introduce low-cost, less biased, high-throughput phenotyping methods to capture large genetic diversity to facilitate enhancement of stress resilience in crops. This review focuses on four key physiological traits and processes that are critical in understanding crop responses to drought and heat stress during reproductive and grain-filling periods. Specifically, these traits include: (i) time of day of flowering, to escape these stresses during flowering; (ii) optimizing photosynthetic efficiency; (iii) storage and translocation of water-soluble carbohydrates; and (iv) yield and yield components to provide in-season yield estimates. Moreover, we provide an overview of current advances in remote sensing in capturing these traits, and discuss the limitations with existing technology as well as future direction of research to develop high-throughput phenotyping approaches. In the future, phenotyping these complex traits will require sensor advancement, high-quality imagery combined with machine learning methods, and efforts in transdisciplinary science to foster integration across disciplines.

Measuring Stem Diameter of Sorghum Plants in the Field Using a High-Throughput Stereo Vision System

HighlightsA custom-built camera module named PhenoStereo was developed for high-throughput field-based plant phenotyping.Novel integration of strobe lights facilitated application of PhenoStereo in various environmental conditions.Image-derived stem diameters were found to have high correlations with ground truth, which outperformed any previously reported sensing approach.PhenoStereo showed promising potential to characterize a broad spectrum of plant phenotypes.Abstract. The stem diameter of sorghum plants is an important trait for evaluation of stalk strength and biomass potential, but it is a challenging sensing task to automate in the field due to the complexity of the imaging object and the environment. In recent years, stereo vision has offered a viable three-dimensional (3D) solution due to its high spatial resolution and wide selection of camera modules. However, the performance of in-field stereo imaging for plant phenotyping is adversely affected by textureless regions, occlusion of plants, variable outdoor lighting, and wind conditions. In this study, a portable stereo imaging module named PhenoStereo was developed for high-throughput field-based plant phenotyping. PhenoStereo features a self-contained embedded design, which makes it capable of capturing images at 14 stereoscopic frames per second. In addition, a set of customized strobe lights is integrated to overcome lighting variations and enable the use of high shutter speed to overcome motion blur. PhenoStereo was used to acquire a set of sorghum plant images, and an automated point cloud data processing pipeline was developed to automatically extract the stems and then quantify their diameters via an optimized 3D modeling process. The pipeline employed a mask region convolutional neural network (Mask R-CNN) for detecting stalk contours and a semi-global block matching (SGBM) stereo matching algorithm for generating disparity maps. The correlation coefficient (r) between the image-derived stem diameters and the ground truth was 0.97 with a mean absolute error (MAE) of 1.44 mm, which outperformed any previously reported sensing approach. These results demonstrate that, with proper customization, stereo vision can be an effective sensing method for field-based plant phenotyping using high-fidelity 3D models reconstructed from stereoscopic images. Based on the results from sorghum plant stem diameter sensing, this proposed stereo sensing approach can likely be extended to characterize a broad range of plant phenotypes, such as the leaf angle and tassel shape of maize plants and the seed pods and stem nodes of soybean plants. Keywords: Field-based high-throughput phenotyping, Point cloud, Stem diameter, Stereo vision.

Improved Accuracy of High-Throughput Phenotyping From Unmanned Aerial Systems by Extracting Traits Directly From Orthorectified Images.

The development of high-throughput genotyping and phenotyping has provided access to many tools to accelerate plant breeding programs. Unmanned Aerial Systems (UAS)-based remote sensing is being broadly implemented for field-based high-throughput phenotyping due to its low cost and the capacity to rapidly cover large breeding populations. The Structure-from-Motion photogrammetry processes aerial images taken from multiple perspectives over a field to an orthomosaic photo of a complete field experiment, allowing spectral or morphological trait extraction from the canopy surface for each individual field plot. However, some phenotypic information observable in each raw aerial image seems to be lost to the orthomosaic photo, probably due to photogrammetry processes such as pixel merging and blending. To formally assess this, we introduced a set of image processing methods to extract phenotypes from orthorectified raw aerial images and compared them to the negative control of extracting the same traits from processed orthomosaic images. We predict that standard measures of accuracy in terms of the broad-sense heritability of the remote sensing spectral traits will be higher using the orthorectified photos than with the orthomosaic image. Using three case studies, we therefore compared the broad-sense heritability of phenotypes in wheat breeding nurseries including, (1) canopy temperature from thermal imaging, (2) canopy normalized difference vegetation index (NDVI), and (3) early-stage ground cover from multispectral imaging. We evaluated heritability estimates of these phenotypes extracted from multiple orthorectified aerial images via four statistical models and compared the results with heritability estimates of these phenotypes extracted from a single orthomosaic image. Our results indicate that extracting traits directly from multiple orthorectified aerial images yielded increased estimates of heritability for all three phenotypes through proper modeling, compared to estimation using traits extracted from the orthomosaic image. In summary, the image processing methods demonstrated in this study have the potential to improve the quality of the plant trait extracted from high-throughput imaging. This, in turn, can enable breeders to utilize phenomics technologies more effectively for improved selection.

Integrated Puncture Score: force\u2013displacement weighted rind penetration tests improve stalk lodging resistance estimations in maize

BackgroundStalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Rind penetration resistance tests have been used by plant scientists and breeders to estimate the stalk lodging resistance of maize for nearly a hundred years. However, the rind puncture method has two key limitations: (1) the predictive power of the test decreases significantly when measuring elite or pre-commercial hybrids, and (2) using rind penetration measurements as a breeding metric does not necessarily create stronger stalks. In this study, we present a new rind penetration method called the Integrated Puncture Score, which uses a modified rind penetration testing protocol and a physics-based model to provide a robust measure of stalk lodging resistance.ResultsTwo datasets, one with a diverse array of maize hybrids and one with only elite hybrids, were evaluated by comparing traditional rind penetration testing and the Integrated Puncture Score method to measurements of stalk bending strength. When evaluating the diverse set of hybrids, both methods were good predictors of stalk bending strength (R2 values of 0.67). However, when evaluating elite hybrids, the Integrated Puncture Score had an R2 value of 0.74 whereas the traditional method had an R2 value of 0.48. Additionally, the Integrated Puncture Score was able to differentiate between the strongest and weakest hybrids in the elite hybrid data set whereas the traditional rind penetration method was not. Additional experiments revealed strong evidence in favor of the data aggregation steps utilized to compute the Integrated Puncture Score.ConclusionsThis study presents a new method for evaluating rind penetration resistance that highly correlates with stalk bending strength and can possibly be used as a breeding index for assessing stalk lodging resistance. This research lays the foundation required to develop a field-based high-throughput phenotyping device for stalk lodging resistance.

Development and evaluation of a self-propelled electric platform for high-throughput field phenotyping in wheat breeding trials

The use of high-throughput phenotyping systems in crop research offers a powerful alternative to traditional methods for understanding plant behaviours. These systems provide a rapid, consistent, repeatable, non-destructive and objective sampling method to quantify complex and previously unobtainable traits at relatively fine resolutions. In this study, a field-based high-throughput phenotyping solution for wheat was developed using a sensor suite mounted on a self-propelled electric platform. A 2D LiDAR was used to scan wheat plots from overhead, while an odometry system was used as a local navigation system to determine the precise plot/plant/scan location. Accurate 3D models of the scanned wheat plots were reconstructed based on the recorded LiDAR and odometry data. Seven plots of different wheat cultivars were scanned to calculate the canopy height using LiDAR data, and these results were compared with manual ground truth measurements. Additionally, in each of these seven plots, the NDVI and PRI spectral indices were calculated using low-cost spectral reflectance sensors (SRSs) and an expensive visible/near-infrared (VIS/NIR) spectral analysis system used for reference purposes. The results of the validation showed good agreement between the LiDAR and manual wheat plant height measurements with an R2 of 0.73 and RMSE = 2.63 cm for three days of campaign measurements. A statistically significant linear correlation was observed between the NDVI values obtained with the reference spectrometer and the low-cost SRS; the coefficients of determination were R2 = 0.69 for day 1 and R2 = 0.81 for day 2, suggesting a similar degree of accuracy among both sensing systems. The developed platform and the obtained wheat phenotyping results demonstrated the suitability of the system for acquiring reliable data under field conditions while maintaining a constant low speed and stability during field deployment. The adaptability of the platform to the structure of the crop and the repeatability of data collection throughout the growing season make the system suitable for integration into commercial breeding programmes.