High-throughput phenotyping of plant leaf morphological, physiological, and biochemical traits on multiple scales using optical sensing

Acquisition of plant phenotypic information facilitates plant breeding, sheds light on gene action, and can be applied to optimize the quality of agricultural and forestry products. Because leaves often show the fastest responses to external environmental stimuli, leaf phenotypic traits are indicators of plant growth, health, and stress levels. Combination of new imaging sensors, image processing, and data analytics permits measurement over the full life span of plants at high temporal resolution and at several organizational levels from organs to individual plants to field populations of plants. We review the optical sensors and associated data analytics used for measuring morphological, physiological, and biochemical traits of plant leaves on multiple scales. We summarize the characteristics, advantages and limitations of optical sensing and data-processing methods applied in various plant phenotyping scenarios. Finally, we discuss the future prospects of plant leaf phenotyping research. This review aims to help researchers choose appropriate optical sensors and data processing methods to acquire plant leaf phenotypes rapidly, accurately, and cost-effectively

Modelling spatial variability of coffee (Coffea Arabica L.) crop condition with multispectral remote sensing data.

Doctor of Philosophy in Environmental Science. University of KwaZulu-Natal, Pietermaritzburg, 2017.Abstract available in PDF file

Evaluating the relationship between biomass, percent groundcover and remote sensing indices across six winter cover crop fields in Maryland, United States

AbstractWinter cover crops are an essential part of managing nutrient and sediment losses from agricultural lands. Cover crops lessen sedimentation by reducing erosion, and the accumulation of nitrogen in aboveground biomass results in reduced nutrient runoff. Winter cover crops are planted in the fall and are usually terminated in early spring, making them susceptible to senescence, frost burn, and leaf yellowing due to wintertime conditions. This study sought to determine to what extent remote sensing indices are capable of accurately estimating the percent groundcover and biomass of winter cover crops, and to analyze under what critical ranges these relationships are strong and under which conditions they break down. Cover crop growth on six fields planted to barley, rye, ryegrass, triticale or wheat was measured over the 2012–2013 winter growing season. Data collection included spectral reflectance measurements, aboveground biomass, and percent groundcover. Ten vegetation indices were evaluated using surface reflectance data from a 16-band CROPSCAN sensor. Restricting analysis to sampling dates before the onset of prolonged freezing temperatures and leaf yellowing resulted in increased estimation accuracy. There was a strong relationship between the normalized difference vegetation index (NDVI) and percent groundcover (r2=0.93) suggesting that date restrictions effectively eliminate yellowing vegetation from analysis. The triangular vegetation index (TVI) was most accurate in estimating high ranges of biomass (r2=0.86), while NDVI did not experience a clustering of values in the low and medium biomass ranges but saturated in the higher range (>1500kg/ha). The results of this study show that accounting for index saturation, senescence, and frost burn on leaves can greatly increase the accuracy of estimates of percent groundcover and biomass for winter cover crops

Optimal Exploitation of the Sentinel-2 Spectral Capabilities for Crop Leaf Area Index Mapping

The continuously increasing demand of accurate quantitative high quality information on land surface properties will be faced by a new generation of environmental Earth observation (EO) missions. One current example, associated with a high potential to contribute to those demands, is the multi-spectral ESA Sentinel-2 (S2) system. The present study focuses on the evaluation of spectral information content needed for crop leaf area index (LAI) mapping in view of the future sensors. Data from a field campaign were used to determine the optimal spectral sampling from available S2 bands applying inversion of a radiative transfer model (PROSAIL) with look-up table (LUT) and artificial neural network (ANN) approaches. Overall LAI estimation performance of the proposed LUT approach (LUTN₅₀) was comparable in terms of retrieval performances with a tested and approved ANN method. Employing seven- and eight-band combinations, the LUTN₅₀ approach obtained LAI RMSE of 0.53 and normalized LAI RMSE of 0.12, which was comparable to the results of the ANN. However, the LUTN50 method showed a higher robustness and insensitivity to different band settings. Most frequently selected wavebands were located in near infrared and red edge spectral regions. In conclusion, our results emphasize the potential benefits of the Sentinel-2 mission for agricultural applications

Remote Sensing for Precision Nitrogen Management

This book focuses on the fundamental and applied research of the non-destructive estimation and diagnosis of crop leaf and plant nitrogen status and in-season nitrogen management strategies based on leaf sensors, proximal canopy sensors, unmanned aerial vehicle remote sensing, manned aerial remote sensing and satellite remote sensing technologies. Statistical and machine learning methods are used to predict plant-nitrogen-related parameters with sensor data or sensor data together with soil, landscape, weather and/or management information. Different sensing technologies or different modelling approaches are compared and evaluated. Strategies are developed to use crop sensing data for in-season nitrogen recommendations to improve nitrogen use efficiency and protect the environment

QUANTIFYING GRASSLAND NON-PHOTOSYNTHETIC VEGETATION BIOMASS USING REMOTE SENSING DATA

Non-photosynthetic vegetation (NPV) refers to vegetation that cannot perform a photosynthetic function. NPV, including standing dead vegetation and surface plant litter, plays a vital role in maintaining ecosystem function through controlling carbon, water and nutrient uptake as well as natural fire frequency and intensity in diverse ecosystems such as forest, savannah, wetland, cropland, and grassland. Due to its ecological importance, NPV has been selected as an indicator of grassland ecosystem health by the Alberta Public Lands Administration in Canada. The ecological importance of NPV has driven considerable research on quantifying NPV biomass with remote sensing approaches in various ecosystems. Although remote images, especially hyperspectral images, have demonstrated potential for use in NPV estimation, there has not been a way to quantify NPV biomass in semiarid grasslands where NPV biomass is affected by green vegetation (PV), bare soil and biological soil crust (BSC). The purpose of this research is to find a solution to quantitatively estimate NPV biomass with remote sensing approaches in semiarid mixed grasslands. Research was conducted in Grasslands National Park (GNP), a parcel of semiarid mixed prairie grassland in southern Saskatchewan, Canada. Multispectral images, including newly operational Landsat 8 Operational Land Imager (OLI) and Sentinel-2A Multi-spectral Instrument (MSIs) images and fine Quad-pol Radarsat-2 images were used for estimating NPV biomass in early, middle, and peak growing seasons via a simple linear regression approach. The results indicate that multispectral Landsat 8 OLI and Sentinel-2A MSIs have potential to quantify NPV biomass in peak and early senescence growing seasons. Radarsat-2 can also provide a solution for NPV biomass estimation. However, the performance of Radarsat-2 images is greatly affected by incidence angle of the image acquisition. This research filled a critical gap in applying remote sensing approaches to quantify NPV biomass in grassland ecosystems. NPV biomass estimates and approaches for estimating NPV biomass will contribute to grassland ecosystem health assessment (EHA) and natural resource (i.e. land, soil, water, plant, and animal) management

Monitoring Crop Carotenoids Concentration by Remote Sensing

Assessment of carotenoids (Car) content provides a valuable insight into clarifying the mechanisms of plant photoprotection and light-adaption and is critical for stress diagnoses in plants. Due to their small proportion in the overall total pigment content and to the overlapping of spectral absorption features with chlorophylls (Chl) in the blue region of the spectrum, accurate estimation of Car content in plants, from remotely sensed data, is challenging. Previous studies made progress in Car content estimation at both the leaf and canopy level with remote sensing techniques. However, established spectral indices and methods for Car estimation in most studies that generally rely on specific and limited measured data might lack predictive accuracy for Car estimation and lack sensitivity to low or high Car content in various species and at different growth stages. In this chapter, a new carotenoid index (CARI) was proposed for foliar Car assessment with abundant simulated leaf data and various measured leaf reflectances. Detailed analysis on the mechanism, formation and performance of the new spectral index on Car retrieval was presented. Analysis results suggested that accurate nondestructive estimation of foliar Car content with CARI could be achieved at the leaf scale, through remote sensing techniques

Characterizing crop productivity under heat stress using MODIS data

Stress caused by high temperatures is a critical limiting factor of crop growth and development. Although remote sensing has been used to investigate the impacts of high temperatures on crops, its ability to detect heat stress independently of other stressors and assess its effects on gross primary production (GPP) estimation is unclear. This study developed an innovative approach to distinguish crop heat stress periods from normal growth conditions in croplands independent of water stress and light limitation. Multispectral broad bands and spectral vegetation indices (VIs) derived from MODIS for 78 periods of heat stress were used to assess the sensitivity of canopy reflectance to heat stress and its impacts on GPP. Results reveal that heat stress significantly increased the reflectance in the red band. VIs, in general, enhanced the detection of heat-induced spectral variations, and exhibited sufficient skill in distinguishing crops under heat stress and normal conditions. Three visible-based indices (the Visible Atmospherically Resistant Index, the Green Leaf Index, and the Normalized Green–Red Difference Index) exhibited the highest discriminability (p-value < 0.01 in the Mann–Whitney U test), while the Enhanced Vegetation Index displayed the highest accuracy in GPP estimation (R2 = 0.62, RMSE = 5.49, RRMSE = 0.35) under heat conditions. Overall, the isolation of heat stress impact on crop growth has important implications for advancing large-scale crop modeling and climate change studies, for example, incorporating the suggested VIs into temperature response simulations within crop models