The timing and duration of flowering are key agronomic traits that are often associated with the ability of a variety to escape abiotic stress such as heat and drought. Flowering information is valuable in both plant breeding and agricultural production management. Visual assessment, the standard protocol used for phenotyping flowering, is a low-throughput and subjective method. In this study, we evaluated multiple imaging sensors (RGB and multiple multispectral cameras), image resolution (proximal/remote sensing at 1.6 to 30 m above ground level/AGL), and image processing (standard and unsupervised learning) techniques in monitoring flowering intensity of four cool-season crops (canola, camelina, chickpea, and pea) to enhance the accuracy and efficiency in quantifying flowering traits. The features (flower area, percentage of flower area with respect to canopy area) extracted from proximal (1.6–2.2 m AGL) RGB and multispectral (with near infrared, green and blue band) image data were strongly correlated (r up to 0.89) with visual rating scores, especially in pea and canola. The features extracted from unmanned aerial vehicle integrated RGB image data (15–30 m AGL) could also accurately detect and quantify large flowers of winter canola (r up to 0.84), spring canola (r up to 0.72), and pea (r up to 0.72), but not camelina or chickpea flowers. When standard image processing using thresholds and unsupervised machine learning such as k-means clustering were utilized for flower detection and feature extraction, the results were comparable. In general, for applicability of imaging for flower detection, it is recommended that the image data resolution (i.e., ground sampling distance) is at least 2–3 times smaller than that of the flower size. Overall, this study demonstrates the feasibility of utilizing imaging for monitoring flowering intensity in multiple varieties of evaluated crops. Full article

Heat stress and resulting sunburn is a major abiotic stress in perineal specialty crops. For example, such stress to the maturing fruits on apple tree canopies can cause several physiological disorders that result in considerable crop losses and reduced marketability of the produce. Thus, there is a critical technological need to effectively monitor the abiotic stress under field conditions for timely actuation of remedial measures. Fruit surface temperature (FST) is one of the stress indicators that can reliably be used to predict apple fruit sunburn susceptibility. This study was therefore focused on development and in-field testing of a mobile FST monitoring tool that can be used for real-time crop stress monitoring. The tool integrates a smartphone connected thermal-Red-Green-Blue (RGB) imaging sensor and a custom developed application (‘AppSense 1.0’) for apple fruit sunburn prediction. This tool is configured to acquire and analyze imagery data onboard the smartphone to estimate FST. The tool also utilizes geolocation-specific weather data to estimate weather-based FST using an energy balance modeling approach. The ‘AppSense 1.0’ application, developed to work in the Android operating system, allows visual display, annotation and real-time sharing of the imagery, weather data and pertinent FST estimates. The developed tool was evaluated in orchard conditions during the 2019 crop production season on the Gala, Fuji, Red delicious and Honeycrisp apple cultivars. Overall, results showed no significant difference (t₁₁₀ = 0.51, p = 0.6) between the mobile FST monitoring tool outputs, and ground truth FST data collected using a thermal probe which had accuracy of ±0.4 °C. Upon further refinements, such tool could aid growers in real-time apple fruit sunburn susceptibility prediction and assist in more effective actuation of apple fruit sunburn preventative measures. This tool also has the potential to be customized for in-field monitoring of the heat stressors in some of the sun-exposed perennial and annual specialty crops at produce maturation. Full article

The dimensions of phenotyping parameters such as the thickness of rice play an important role in rice quality assessment and phenotyping research. The objective of this study was to propose an automatic method for extracting rice thickness. This method was based on the principle of binocular stereovision but avoiding the problem that it was difficult to directly match the corresponding points for 3D reconstruction due to the lack of texture of rice. Firstly, the shape features of edge, instead of texture, was used to match the corresponding points of the rice edge. Secondly, the height of the rice edge was obtained by way of space intersection. Finally, the thickness of rice was extracted based on the assumption that the average height of the edges of multiple rice is half of the thickness of rice. According to the results of the experiments on six kinds of rice or grain, errors of thickness extraction were no more than the upper limit of 0.1 mm specified in the national industry standard. The results proved that edge features could be used to extract rice thickness and validated the effectiveness of the thickness extraction algorithm we proposed, which provided technical support for the extraction of phenotyping parameters for crop researchers. Full article

Using sensors and electronic systems for characterization of plant traits provides valuable digital inputs to support complex analytical modeling in genetics research. In field applications, frequent sensor deployment enables the study of the dynamics of these traits and their interaction with the environment. This study focused on implementing lidar (light detection and ranging) technology to generate 2D displacement data at high spatial resolution and extract plant architectural parameters, namely canopy height and cover, in a diverse population of 252 maize (Zea mays L.) genotypes. A prime objective was to develop the mechanical and electrical subcomponents for field deployment from a ground vehicle. Data reduction approaches were implemented for efficient same-day post-processing to generate by-plot statistics. The lidar system was successfully deployed six times in a span of 42 days. Lidar data accuracy was validated through independent measurements in a subset of 75 experimental units. Manual and lidar-derived canopy height measurements were compared resulting in root mean square error (RMSE) = 0.068 m and r² = 0.81. Subsequent genome-wide association study (GWAS) analyses for quantitative trait locus (QTL) identification and comparisons of genetic correlations and heritabilities for manual and lidar-based traits showed statistically significant associations. Low-cost, field-ready lidar of computational simplicity make possible timely phenotyping of diverse populations in multiple environments. Full article

It is well known that timely crop growth monitoring and accurate crop yield estimation at a fine scale is of vital importance for agricultural monitoring and crop management. Crop growth models have been widely used for crop growth process description and yield prediction. In particular, the accurate simulation of important state variables, such as leaf area index (LAI) and root zone soil moisture (SM), is of great importance for yield estimation. Data assimilation is a useful tool that combines a crop model and external observations (often derived from remote sensing data) to improve the simulated crop state variables and consequently model outputs like crop total biomass, water use and grain yield. In spite of its effectiveness, applying data assimilation for monitoring crop growth at the regional scale in China remains challenging, due to the lack of high spatiotemporal resolution satellite data that can match the small field sizes which are typical for agriculture in China. With the accessibility of freely available images acquired by Sentinel satellites, it becomes possible to acquire data at high spatiotemporal resolution (10–30 m, 5–6 days), which offers attractive opportunities to characterize crop growth. In this study, we assimilated remotely sensed LAI and SM into the Word Food Studies (WOFOST) model to estimate winter wheat yield using an ensemble Kalman filter (EnKF) algorithm. The LAI was calculated from Sentinel-2 using a lookup table method, and the SM was calculated from Sentinel-1 and Sentinel-2 based on a change detection approach. Through validation with field data, the inverse error was 10% and 35% for LAI and SM, respectively. The open-loop wheat yield estimation, independent assimilations of LAI and SM, and a joint assimilation of LAI + SM were tested and validated using field measurement observation in the city of Hengshui, China, during the 2016–2017 winter wheat growing season. The results indicated that the accuracy of wheat yield simulated by WOFOST was significantly improved after joint assimilation at the field scale. Compared to the open-loop estimation, the yield root mean square error (RMSE) with field observations was decreased by 69 kg/ha for the LAI assimilation, 39 kg/ha for the SM assimilation and 167 kg/ha for the joint LAI + SM assimilation. Yield coefficients of determination (R²) of 0.41, 0.65, 0.50, and 0.76 and mean relative errors (MRE) of 4.87%, 4.32%, 4.45% and 3.17% were obtained for open-loop, LAI assimilation alone, SM assimilation alone and joint LAI + SM assimilation, respectively. The results suggest that LAI was the first-choice variable for crop data assimilation over SM, and when both LAI and SM satellite data are available, the joint data assimilation has a better performance because LAI and SM have interacting effects. Hence, joint assimilation of LAI and SM from Sentinel-1 and Sentinel-2 at a 20 m resolution into the WOFOST provides a robust method to improve crop yield estimations. However, there is still bias between the key soil moisture in the root zone and the Sentinel-1 C band retrieved SM, especially when the vegetation cover is high. By active and passive microwave data fusion, it may be possible to offer a higher accuracy SM for crop yield prediction. Full article

Crop-type identification is very important in agricultural regions. Most researchers in this area have focused on exploring the ability of synthetic-aperture radar (SAR) sensors to identify crops. This paper uses multi-source (Sentinel-1, Sentinel-2, and Landsat-8) and multi-temporal data to identify crop types. The change detection method was used to analyze spectral and indices information in time series. Significant differences in crop growth status during the growing season were found. Then, three obviously differentiated time features were extracted. Three advanced machine learning algorithms (Support Vector Machine, Artificial Neural Network, and Random Forest, RF) were used to identify the crop types. The results showed that the detection of (Vertical-vertical) VV, (Vertical-horizontal) VH, and Cross Ratio (CR) changes was effective for identifying land cover. Moreover, the red-edge changes were obviously different according to crop growth periods. Sentinel-2 and Landsat-8 showed different normalized difference vegetation index (NDVI) changes also. By using single remote sensing data to classify crops, Sentinel-2 produced the highest overall accuracy (0.91) and Kappa coefficient (0.89). The combination of Sentinel-1, Sentinel-2, and Landsat-8 data provided the best overall accuracy (0.93) and Kappa coefficient (0.91). The RF method had the best performance in terms of identity classification. In addition, the indices feature dominated the classification results. The combination of phenological period information with multi-source remote sensing data can be used to explore a crop area and its status in the growing season. The results of crop classification can be used to analyze the density and distribution of crops. This study can also allow to determine crop growth status, improve crop yield estimation accuracy, and provide a basis for crop management. Full article

Optical sensors have shown high capabilities to improve the detection and monitoring of plant disease development. This study was designed to compare the feasibility of different sensors to characterize Fusarium head blight (FHB) caused by Fusarium graminearum and Fusarium culmorum. Under controlled conditions, time-series measurements were performed with infrared thermography (IRT), chlorophyll fluorescence imaging (CFI), and hyperspectral imaging (HSI) starting 3 days after inoculation (dai). IRT allowed the visualization of temperature differences within the infected spikelets beginning 5 dai. At the same time, a disorder of the photosynthetic activity was confirmed by CFI via maximal fluorescence yields of spikelets (Fm) 5 dai. Pigment-specific simple ratio PSSRa and PSSRb derived from HSI allowed discrimination between Fusarium-infected and non-inoculated spikelets 3 dai. This effect on assimilation started earlier and was more pronounced with F. graminearum. Except the maximum temperature difference (MTD), all parameters derived from different sensors were significantly correlated with each other and with disease severity (DS). A support vector machine (SVM) classification of parameters derived from IRT, CFI, or HSI allowed the differentiation between non-inoculated and infected spikelets 3 dai with an accuracy of 78, 56 and 78%, respectively. Combining the IRT-HSI or CFI-HSI parameters improved the accuracy to 89% 30 dai. Full article

Field pea cultivars are constantly improved through breeding programs to enhance biotic and abiotic stress tolerance and increase seed yield potential. In pea breeding, the Above Ground Biomass (AGBM) is assessed due to its influence on seed yield, canopy closure, and weed suppression. It is also the primary yield component for peas used as a cover crop and/or grazing. Measuring AGBM is destructive and labor-intensive process. Sensor-based phenotyping of such traits can greatly enhance crop breeding efficiency. In this research, high resolution RGB and multispectral images acquired with unmanned aerial systems were used to assess phenotypes in spring and winter pea breeding plots. The Green Red Vegetation Index (GRVI), Normalized Difference Vegetation Index (NDVI), Normalized Difference Red Edge Index (NDRE), plot volume, canopy height, and canopy coverage were extracted from RGB and multispectral information at five imaging times (between 365 to 1948 accumulated degree days/ADD after 1 May) in four winter field pea experiments and at three imaging times (between 1231 to 1648 ADD) in one spring field pea experiment. The image features were compared to ground-truth data including AGBM, lodging, leaf type, days to 50% flowering, days to physiological maturity, number of the first reproductive node, and seed yield. In two of the winter pea experiments, a strong correlation between image features and seed yield was observed at 1268 ADD (flowering). An increase in correlation between image features with the phenological traits such as days to 50% flowering and days to physiological maturity was observed at about 1725 ADD in these winter pea experiments. In the spring pea experiment, the plot volume estimated from images was highly correlated with ground truth canopy height (r = 0.83) at 1231 ADD. In two other winter pea experiments and the spring pea experiment, the GRVI and NDVI features were significantly correlated with AGBM at flowering. When selected image features were used to develop a least absolute shrinkage and selection operator model for AGBM estimation, the correlation coefficient between the actual and predicted AGBM was 0.60 and 0.84 in the winter and spring pea experiments, respectively. A SPOT-6 satellite image (1.5 m resolution) was also evaluated for its applicability to assess biomass and seed yield. The image features extracted from satellite imagery showed significant correlation with seed yield in two winter field pea experiments, however, the trend was not consistent. In summary, the study supports the potential of using unmanned aerial system-based imaging techniques to estimate biomass and crop performance in pea breeding programs. Full article

A reasonable plant type is an essential factor for improving canopy structure, ensuring a reasonable expansion of the leaf area index and obtaining a high-quality spatial distribution of light. It is of great significance in promoting effective selection of the ecological breeding index and production practices for maize. In this study, a method for calculating the phenotypic traits of the maize canopy in three-dimensional (3D) space was proposed, focusing on the problems existing in traditional measurement methods in maize morphological structure research, such as their complex procedures and relatively large error margins. Specifically, the whole maize plant was first scanned with a FastSCAN hand-held scanner to obtain 3D point cloud data for maize. Subsequently, the raw point clouds were simplified by the grid method, and the effect of noise on the quality of the point clouds in maize canopies was further denoised by bilateral filtering. In the last step, the 3D structure of the maize canopy was reconstructed. In accordance with the 3D reconstruction of the maize canopy, the phenotypic traits of the maize canopy, such as plant height, stem diameter and canopy breadth, were calculated by means of a fitting sphere and a fitting cylinder. Thereafter, multiple regression analysis was carried out, focusing on the calculated data and the actual measured data to verify the accuracy of the calculation method proposed in this study. The corresponding results showed that the calculated values of plant height, stem diameter and plant width based on 3D scanning were highly correlated with the actual measured data, and the determinant coefficients R² were 0.9807, 0.8907 and 0.9562, respectively. In summary, the method proposed in this study can accurately measure the phenotypic traits of maize. Significantly, these research findings provide technical support for further research on the phenotypic traits of other crops and on variety breeding. Full article

Rapid and effective acquisition of crop growth information is a crucial step of precision agriculture for making in-season management decisions. Active canopy sensor GreenSeeker (Trimble Navigation Limited, Sunnyvale, CA, USA) is a portable device commonly used for non-destructively obtaining crop growth information. This study intended to expand the applicability of GreenSeeker in monitoring growth status and predicting grain yield of winter wheat (Triticum aestivum L.). Four field experiments with multiple wheat cultivars and N treatments were conducted during 2013–2015 for obtaining canopy normalized difference vegetation index (NDVI) and ratio vegetation index (RVI) synchronized with four agronomic parameters: leaf area index (LAI), leaf dry matter (LDM), leaf nitrogen concentration (LNC), and leaf nitrogen accumulation (LNA). Duration models based on NDVI and RVI were developed to monitor these parameters, which indicated that NDVI and RVI explained 80%, 68–70%, 10–12%, and 67–73% of the variability in LAI, LDM, LNC and LNA, respectively. According to the validation results, the relative root mean square error (RRMSE) were all <0.24 and the relative error (RE) were all <23%. Considering the variation among different wheat cultivars, the newly normalized vegetation indices rNDVI (NDVI vs. the NDVI for the highest N rate) and rRVI (RVI vs. the RVI for the highest N rate) were calculated to predict the relative grain yield (RY, the yield vs. the yield for the highest N rate). rNDVI and rRVI explained 77–85% of the variability in RY, the RRMSEs were both <0.13 and the REs were both <6.3%. The result demonstrates the feasibility of monitoring growth parameters and predicting grain yield of winter wheat with portable GreenSeeker sensor. Full article

As one of the key crop traits, plant height is traditionally evaluated manually, which can be slow, laborious and prone to error. Rapid development of remote and proximal sensing technologies in recent years allows plant height to be estimated in more objective and efficient fashions, while research regarding direct comparisons between different height measurement methods seems to be lagging. In this study, a ground-based multi-sensor phenotyping system equipped with ultrasonic sensors and light detection and ranging (LiDAR) was developed. Canopy heights of 100 wheat plots were estimated five times during a season by the ground phenotyping system and an unmanned aircraft system (UAS), and the results were compared to manual measurements. Overall, LiDAR provided the best results, with a root-mean-square error (RMSE) of 0.05 m and an R² of 0.97. UAS obtained reasonable results with an RMSE of 0.09 m and an R² of 0.91. Ultrasonic sensors did not perform well due to our static measurement style. In conclusion, we suggest LiDAR and UAS are reliable alternative methods for wheat height evaluation. Full article

Plant vigor is an important trait of field crops at early growth stages, influencing weed suppression, nutrient and water use efficiency and plant growth. High-throughput techniques for its evaluation are required and are promising for nutrient management in early growth stages and for detecting promising breeding material in plant phenotyping. However, spectral sensing for assessing early plant vigor in crops is limited by the strong soil background reflection. Digital imaging may provide a low-cost, easy-to-use alternative. Therefore, image segmentation for retrieving canopy cover was applied in a trial with three cultivars of winter wheat (Triticum aestivum L.) grown under two nitrogen regimes and in three sowing densities during four early plant growth stages (Zadok’s stages 14–32) in 2017. Imaging-based canopy cover was tested in correlation analysis for estimating dry weight, nitrogen uptake and nitrogen content. An active Greenseeker sensor and various established and newly developed vegetation indices and spectral unmixing from a passive hyperspectral spectrometer were used as alternative approaches and additionally tested for retrieving canopy cover. Before tillering (until Zadok’s stage 20), correlation coefficients for dry weight and nitrogen uptake with canopy cover strongly exceeded all other methods and remained on higher levels (R² > 0.60***) than from the Greenseeker measurements until tillering. From early tillering on, red edge based indices such as the NDRE and a newly extracted normalized difference index (736 nm; ~794 nm) were identified as best spectral methods for both traits whereas the Greenseeker and spectral unmixing correlated best with canopy cover. RGB-segmentation could be used as simple low-cost approach for very early growth stages until early tillering whereas the application of multispectral sensors should consider red edge bands for subsequent stages. Full article

Global wheat production reached 754.8 million tons in 2017, according to the FAO database. While wheat is considered as a staple food for many populations across the globe, mapping wheat could be an effective tool to achieve the SDG2 sustainable development goal—End Hunger and Secure Food Security. In Lebanon, this crop is supported financially, and sometimes technically, by the Lebanese government. However, there is a lack of statistical databases, at both national and regional scales, as well as critical information much needed in the subsidy and compensation system. In this context, this study proposes an innovative approach, named Simple and Effective Wheat Mapping Approach (SEWMA), to map the winter wheat areas grown in the Bekaa plain, the primary wheat production area in Lebanon, in the years of 2016 and 2017. The proposed methodology is a tree-like approach relying on the Normalized Difference Vegetation Index (NDVI) values of four-month period that coincides with several phenological stages of wheat (i.e., tillering, stem extension, heading, flowering and ripening). The usage of the freely available Sentinel-2 imageries, with a high spatial (10 m) and temporal (5 days) resolutions, was necessary, particularly due to the small sized and overlapped plots encountered in the study area. Concerning the wheat areas, results show that there was a decrease from 11,063 ± 1309 ha in 2016 to 7605 ± 1184 in 2017. When SEWMA was applied using 2016 ground truth data, the overall accuracy reached 87.0% on 2017 data, whereas, when implemented using 2017 ground truth data, the overall accuracy was 82.6% on 2016 data. The novelty resides in executing early classification output (up to six weeks before harvest) as well as distinguishing wheat from other winter cereal crops with similar NDVI yearly profiles (i.e., barley and triticale). SEWMA offers a simple, yet effective and budget-saving approach providing early-season classification information, very crucial to decision support systems and the Lebanese government concerning, but not limited to, food production, trade, management and agricultural financial support. Full article

Accurate estimation of terrestrial photosynthesis has broad scientific and societal impacts. Measurements of photosynthesis can be used to assess plant health, quantify crop yield, and determine the largest CO₂ flux in the carbon cycle. Long-term and continuous monitoring of vegetation optical properties can provide valuable information about plant physiology. Recent developments of the remote sensing of solar-induced chlorophyll fluorescence (SIF) and vegetation spectroscopy have shown promising results in using this information to quantify plant photosynthetic activities and stresses at the ecosystem scale. However, there are few automated systems that allow for unattended observations over months to years. Here we present FluoSpec 2, an automated system for collecting irradiance and canopy radiance that has been deployed in various ecosystems in the past years. The instrument design, calibration, and tests are recorded in detail. We discuss the future directions of this field spectroscopy system. A network of SIF sensors, FluoNet, is established to measure the diurnal and seasonal variations of SIF in several ecosystems. Automated systems such as FluoSpec 2 can provide unique information on ecosystem functioning and provide important support to the satellite remote sensing of canopy photosynthesis. Full article