A comparison of different methods for assessing leaf area index in four canopy types

The agreement of Leaf Area Index (LAI) assessments from three indirect methods, i.e. the LAI–2200 Plant Canopy Analyzer, the SS1 SunScan Canopy Analysis System and Digital Hemispherical Photography (DHP) was evaluated for four canopy types, i.e. a short rotation coppice plantation (SRC) with poplar, a Scots pine stand, a Pedunculate oak stand and amaize field. In the SRC and in the maize field, the indirect measurements were compared with direct measurements (litter fall and harvesting). In the low LAI range (0 to 2) the discrepancies of the SS1 were partly explained by the inability to properly account for clumping and the uncertainty of the ellipsoidal leaf angle distribu tion parameter. The higher values for SS1 in the medium (2 to 6) to high (6 to 8) ranges might be explained by gap fraction saturation for LAI–2200 and DHP above certain values. Wood area index –understood as the woody light blocking elements from the canopy with respect to diameter growth– accounted for overestimation by all indirect methods when compared to direct methods in the SRC. The inter-comparison of the three indirect methods in the four canopy types showed a general agreement for all methods in the medium LAI range (2 to 6). LAI–2200 and DHP revealed the best agreement among the indirect methods along the entire range of LAI (0 to 8) in all canopy types. SS1 showed some discrepancies with the LAI–2200 and DHP at low (0 to 2) and high ranges of LAI (6 to 8

Generation of 360 Degree Point Cloud for Characterization of Morphological and Chemical Properties of Maize and Sorghum

Recently, imaged-based high-throughput phenotyping methods have gained popularity in plant phenotyping. Imaging projects the 3D space into a 2D grid causing the loss of depth information and thus causes the retrieval of plant morphological traits challenging. In this study, LiDAR was used along with a turntable to generate a 360-degree point cloud of single plants. A LABVIEW program was developed to control and synchronize both the devices. A data processing pipeline was built to recover the digital surface models of the plants. The system was tested with maize and sorghum plants to derive the morphological properties including leaf area, leaf angle and leaf angular distribution. The results showed a high correlation between the manual measurement and the LiDAR measurements of the leaf area (R2\u3e0.91). Also, Structure from Motion (SFM) was used to generate 3D spectral point clouds of single plants at different narrow spectral bands using 2D images acquired by moving the camera completely around the plants. Seven narrow band (band width of 10 nm) optical filters, with center wavelengths at 530 nm, 570 nm, 660 nm, 680 nm, 720 nm, 770 nm and 970 nm were used to obtain the images for generating a spectral point cloud. The possibility of deriving the biochemical properties of the plants: nitrogen, phosphorous, potassium and moisture content using the multispectral information from the 3D point cloud was tested through statistical modeling techniques. The results were optimistic and thus indicated the possibility of generating a 3D spectral point cloud for deriving both the morphological and biochemical properties of the plants in the future. Advisor: Yufeng G

The Burning Bush: Linking LiDAR-derived Shrub Architecture to Flammability

Light detection and ranging (LiDAR) and terrestrial laser scanning (TLS) sensors are powerful tools for characterizing vegetation structure and for constructing three-dimensional (3D) models of trees, also known as quantitative structural models (QSM). 3D models and structural traits derived from them provide valuable information for biodiversity conservation, forest management, and fire behavior modeling. However, vegetation studies and 3D modeling methodologies often only focus on the forest canopy, with little attention given to understory vegetation. In particular, 3D structural information of shrubs is limited or not included in fire behavior models. Yet, understory vegetation is an important component of forested ecosystems, and has an essential role in determining fire behavior. In this dissertation, I explored the use of TLS data and quantitative structure models to model shrub architecture in three related studies. In the first study, I present a semi-automated methodology for reconstructing architecturally different shrubs from TLS LiDAR. By investigating shrubs with different architectures and point cloud densities, I showed that occlusion, shrub complexity, and shape greatly affect the accuracy of shrub models. In my second study, I assessed the 3D architectural drivers of understory flammability by evaluating the use of architectural metrics derived from the TLS point cloud and 3D reconstructions of the shrubs. I focused on eight species common in the understory of the fire-prone longleaf pine forest ecosystem of the state of Florida, USA. I found a general tendency for each species to be associated with a unique combination of flammability and architectural traits. Novel shrub architectural traits were found to be complementary to the direct use of TLS data and improved flammability predictions. The inherent complexity of shrub architecture and uncertainty in the TLS point cloud make scaling up from an individual shrub to a plot level a challenging task. Therefore, in my third study, I explored the effects of lidar uncertainty on vegetation parameter prediction accuracy. I developed a practical workflow to create synthetic forest stands with varying densities, which were subsequently scanned with simulated terrestrial lidar. This provided data sets quantitatively similar to those created by real-world LiDAR measurements, but with the advantage of exact knowledge of the forest plot parameters, The results showed that the lidar scan location had a large effect on prediction accuracy. Furthermore, occlusion is strongly related to the sampling density and plot complexity. The results of this study illustrate the potential of non-destructive lidar approaches for quantifying shrub architectural traits. TLS, empirical quantitative structural models, and synthetic models provide valuable insights into shrub structure and fire behavior

New sensing methods for scheduling variable rate irrigation to improve water use efficiency and reduce the environmental footprint : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Palmerston North, New Zealand

Figures are re-used under an Attribution 4.0 International (CC BY 4.0) license, or are not copyrighted.Irrigation is the largest user of allocated freshwater, so conservation of water use should begin with improving the efficiency of crop irrigation. Improved irrigation management is necessary for humid areas such as New Zealand in order to produce greater yields, overcome excessive irrigation and eliminate nitrogen losses due to accelerated leaching and/or denitrification. The impact of two different climatic regimes (Hawkes Bay, Manawatū) and soils (free and imperfect drainage) on irrigated pea (Pisum sativum., cv. ‘Ashton’) and barley (Hordeum vulgare., cv. ‘Carfields CKS1’) production was investigated. These experiments were conducted to determine whether variable-rate irrigation (VRI) was warranted. The results showed that both weather conditions and within-field soil variability had a significant effect on the irrigated pea and barley crops (pea yield - 4.15 and 1.75 t/ha; barley yield - 4.0 and 10.3 t/ha for freely and imperfectly drained soils, respectively). Given these results, soil spatial variability was characterised at precision scales using proximal sensor survey systems: to inform precision irrigation practice. Apparent soil electrical conductivity (ECa) data were collected by a Dualem-421S electromagnetic (EM) survey, and the data were kriged into a map and modelled to predict ECa to depth. The ECa depth models were related to soil moisture (θv), and the intrinsic soil differences. The method was used to guide the placement of soil moisture sensors. After quantifying precision irrigation management zones using EM technology, dynamic irrigation scheduling for a VRI system was used to efficiently irrigate a pea crop (Pisum sativum., cv. ‘Massey’) and a French bean crop (Phaseolus vulgaris., cv. ‘Contender’) over one season at the Manawatū site. The effects of two VRI scheduling methods using (i) a soil water balance model and (ii) sensors, were compared. The sensor-based technique irrigated 23–45% less water because the model-based approach overestimated drainage for the slower draining soil. There were no significant crop growth and yield differences between the two approaches, and water use efficiency (WUE) was higher under the scheduling regime based on sensors. ii To further investigate the use of sensor-based scheduling, a new method was developed to assess crop height and biomass for pea, bean and barley crops at high field resolution (0.01 m) using ground-based LiDAR (Light Detection and Ranging) data. The LiDAR multi-temporal, crop height maps can usefully improve crop coefficient estimates in soil water balance models. The results were validated against manually measured plant parameters. A critical component of soil water balance models, and of major importance for irrigation scheduling, is the estimation of crop evapotranspiration (ETc) which traditionally relies on regional climate data and default crop factors based on the day of planting. Therefore, the potential of a simpler, site-specific method for estimation of ETc using in-field crop sensors was investigated. Crop indices (NDVI, and canopy surface temperature, Tc) together with site-specific climate data were used to estimate daily crop water use at the Manawatū and Hawkes Bay sites (2017-2019). These site-specific estimates of daily crop water use were then used to evaluate a calibrated FAO-56 Penman-Monteith algorithm to estimate ETc from barley, pea and bean crops. The modified ETc–model showed a high linear correlation between measured and modelled daily ETc for barley, pea, and bean crops. This indicates the potential value of in-field crop sensing for estimating site-specific values of ETc. A model-based, decision support software system (VRI–DSS) that automates irrigation scheduling to variable soils and multiple crops was then tested at both the Manawatū and Hawkes Bay farm sites. The results showed that the virtual climate forecast models used for this study provided an adequate prediction of evapotranspiration but over predicted rainfall. However, when local data was used with the VRI–DSS system to simulate results, the soil moisture deficit showed good agreement with weekly neutron probe readings. The use of model system-based irrigation scheduling allowed two-thirds of the irrigation water to be saved for the high available water content (AWC) soil. During the season 2018 – 2019, the VRI–DSS was again used to evaluate the level of available soil water (threshold) at which irrigation should be applied to increase WUE and crop water productivity (WP) for spring wheat (Triticum aestivum L., cv. ‘Sensas’) on the sandy loam and silt loam soil zones at the Manawatū site. Two irrigation thresholds (40% and 60% AWC), were investigated in each soil zone along with a rainfed control. Soil water uptake pattern was affected mainly by the soil type rather than irrigation. The soil iii water uptake decreased with soil depth for the sandy loam whereas water was taken up uniformly from all depths of the silt loam. The 60% AWC treatments had greater irrigation water use efficiency (IWUE) than the 40% AWC treatments, indicating that irrigation scheduling using a 60% AWC trigger could be recommended for this soil-crop scenario. Overall, in this study, we have developed new sensor-based methods that can support improved spatial irrigation water management. The findings from this study led to a more beneficial use of agricultural water

Remote Sensing of Biophysical Parameters

Vegetation plays an essential role in the study of the environment through plant respiration and photosynthesis. Therefore, the assessment of the current vegetation status is critical to modeling terrestrial ecosystems and energy cycles. Canopy structure (LAI, fCover, plant height, biomass, leaf angle distribution) and biochemical parameters (leaf pigmentation and water content) have been employed to assess vegetation status and its dynamics at scales ranging from kilometric to decametric spatial resolutions thanks to methods based on remote sensing (RS) data.Optical RS retrieval methods are based on the radiative transfer processes of sunlight in vegetation, determining the amount of radiation that is measured by passive sensors in the visible and infrared channels. The increased availability of active RS (radar and LiDAR) data has fostered their use in many applications for the analysis of land surface properties and processes, thanks to their insensitivity to weather conditions and the ability to exploit rich structural and texture information. Optical and radar data fusion and multi-sensor integration approaches are pressing topics, which could fully exploit the information conveyed by both the optical and microwave parts of the electromagnetic spectrum.This Special Issue reprint reviews the state of the art in biophysical parameters retrieval and its usage in a wide variety of applications (e.g., ecology, carbon cycle, agriculture, forestry and food security)

Evaluation of Terrestrial Laser Scanning and Ground Penetrating Radar for Field-Based High-Throughput Phenotyping in Wheat Breeding

Targeted adaptive physiological trait introgression, a method by which breeders seek to introduce specific characteristics into breeding germplasm in a specific and targeted manner, is one of the primary methods breeders are using to develop cultivars optimized for performance and yield under heat and drought conditions. In traditional breeding platforms, this is carried out in a stepwise fashion, with the crossing of parental lines and the phenotype-driven selection of offspring. As with other adaptive physiological traits, rapid field-based high-throughput phenotyping of early season aboveground biomass and ideal root architecture is limited by our inability to accurately and nondestructively characterize these important traits. Terrestrial laser scanning (TLS) and ground penetrating radar (GPR) have the potential to fill this gap by non-invasively estimating biomass and mapping three-dimensional above- and below-ground vegetation. The research objective was to evaluate the use of TLS to estimate aboveground wheat (Triticum aestivum L.) biomass. Linear regressions comparing mean canopy height and total plot forage yield for each experimental plot across four replications was poorly correlated (R^2 0.08). Mean plot normalized difference vegetation index measurements were evaluated against total plot forage biomass with limited correlation (R^2 0.036). The mean value of the TLS elevation points had the highest correlation with both plot (R^20.09458) and sub plot (R^2 0.37984) forage yield as compared to traditional platforms. GPR is a remote sensing technology that has been successfully used in the evaluation of coarse tree root biomass. Incorporating GPR into current crop phenotyping methodologies could potentially provide a long awaited solution to the current inability to efficiently phenotype roots under realistic field conditions. Here, the utility of using GPR to estimate root biomass of wheat was evaluated. GPR ability to predict root presence and absence was tested and GPR was able to differentiate root mass from soil significantly (α = 0.95, t = 1.96022). Linear regression between Log10 of the mean GPR amplitude return at the 0-3 ns range was compared with agronomic breeding traits. Overall increased amplitude was observed in plots scoring higher with regard to overall yield and yield components

Terrestrial laser scanning for crop monitoring. Capturing 3D data of plant height for estimating biomass at field scale

Terrestrial laser scanning (TLS) is a young remote sensing method, but the trustworthiness of such measurements offers great potential for accurate surveying. TLS allows non-experts to rapidly acquire 3D data of high density. Generally, this acquisition of accurate geoinformation is increasingly desired in various fields, however this study focuses on the application of TLS for crop monitoring. The increasing cost and efficiency pressure on agriculture induced the emergence of site specific crop management, which requires a comprehensive knowledge about the plant development. An important parameter to evaluate this development or rather the actual plant status is the amount of plant biomass, which is however directly only determinable with destructive sampling. With the aim of avoiding destructive measurements, interest is increasingly directed towards non-contact remote sensing surveys. Nowadays, different approaches address biomass estimations based on other parameters, such as vegetation indices (VIs) from spectral data or plant height. Since the plants are not taken it is feasible to perform several measurements across a field and across the growing season. Hence, the change of spatial and temporal patterns can be monitored. This study applies TLS for objectively measuring and monitoring plant height as estimator for biomass at field scale. Overall 35 TLS campaigns were carried out at three sites over four growing seasons. In each campaign a 3D point cloud, covering the surface of the field, was obtained and interpolated to a crop surface model (CSM). A CSM represents the crop canopy in a very high spatial resolution on a specific date. By subtracting a digital terrain model (DTM) of the bare ground from each CSM, plant heights were calculated pixel-wise. Manual measurements aligned well with the TLS data and demonstrated the main benefit of CSMs: the highly detailed acquisition of the entire crop surface. The plant height data were used to estimate biomass with empirically developed biomass regression models (BRMs). Validation analyses against destructive measurements were carried out to confirm the results. The spatial and temporal transferability of crop-specific BRMs was shown. In one case study, the estimations from plant height and six VIs were compared and the benefit of fusing both parameters was investigated. The analyses were based on the TLS-derived CSMs and spectral data measured with a field spectrometer. The important role of plant height as a robust estimator was shown in contrast to a varying performance of BRMs based on the VIs. A major benefit through the fusion of both parameters in multivariate BRMs could not be concluded in this study. Nevertheless, further research should address this fusion, with regard to the capability of VIs to assess information about the vegetation cover or biochemical and biophysical parameters

Individual maize location and height estimation in field from UAV-borne LiDAR and RGB images

Crop height is an essential parameter used to monitor overall crop growth, forecast crop yield, and estimate crop biomass in precision agriculture. However, individual maize segmentation is the prerequisite for precision field monitoring, which is a challenging task because the maize stalks are usually occluded by leaves between adjacent plants, especially when they grow up. In this study, we proposed a novel method that combined seedling detection and clustering algorithms to segment individual maize plants from UAV-borne LiDAR and RGB images. As seedlings emerged, the images collected by an RGB camera mounted on a UAV platform were processed and used to generate a digital orthophoto map. Based on this orthophoto, the location of each maize seedling was identified by extra-green detection and morphological filtering. A seed point set was then generated and used as input for the clustering algorithm. The fuzzy C-means clustering algorithm was used to segment individual maize plants. We computed the difference between the maximum elevation value of the LiDAR point cloud and the average elevation value of the bare digital terrain model (DTM) at each corresponding area for individual plant height estimation. The results revealed that our height estimation approach test on two cultivars produced the accuracy with R2 greater than 0.95, with the mean square error (RMSE) of 4.55 cm, 3.04 cm, and 3.29 cm, as well as the mean absolute percentage error (MAPE) of 3.75%, 0.91%, and 0.98% at three different growth stages, respectively. Our approach, utilizing UAV-borne LiDAR and RGB cameras, demonstrated promising performance for estimating maize height and its field position

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