Leveraging very-high spatial resolution hyperspectral and thermal UAV imageries for characterizing diurnal indicators of grapevine physiology

Efficient and accurate methods to monitor crop physiological responses help growers better understand crop physiology and improve crop productivity. In recent years, developments in unmanned aerial vehicles (UAV) and sensor technology have enabled image acquisition at very-high spectral, spatial, and temporal resolutions. However, potential applications and limitations of very-high-resolution (VHR) hyperspectral and thermal UAV imaging for characterization of plant diurnal physiology remain largely unknown, due to issues related to shadow and canopy heterogeneity. In this study, we propose a canopy zone-weighting (CZW) method to leverage the potential of VHR (≤9 cm) hyperspectral and thermal UAV imageries in estimating physiological indicators, such as stomatal conductance (Gs) and steady-state fluorescence (Fs). Diurnal flights and concurrent in-situ measurements were conducted during grapevine growing seasons in 2017 and 2018 in a vineyard in Missouri, USA. We used neural net classifier and the Canny edge detection method to extract pure vine canopy from the hyperspectral and thermal images, respectively. Then, the vine canopy was segmented into three canopy zones (sunlit, nadir, and shaded) using K-means clustering based on the canopy shadow fraction and canopy temperature. Common reflectance-based spectral indices, sun-induced chlorophyll fluorescence (SIF), and simplified canopy water stress index (siCWSI) were computed as image retrievals. Using the coefficient of determination (R2) established between the image retrievals from three canopy zones and the in-situ measurements as a weight factor, weighted image retrievals were calculated and their correlation with in-situ measurements was explored. The results showed that the most frequent and the highest correlations were found for Gs and Fs, with CZW-based Photochemical reflectance index (PRI), SIF, and siCWSI (PRICZW, SIFCZW, and siCWSICZW), respectively. When all flights combined for the given field campaign date, PRICZW, SIFCZW, and siCWSICZW significantly improved the relationship with Gs and Fs. The proposed approach takes full advantage of VHR hyperspectral and thermal UAV imageries, and suggests that the CZW method is simple yet effective in estimating Gs and Fs

Effects of green space spatial pattern on land surface temperature: Implications for sustainable urban planning and climate change adaptation

The urban heat island (UHI) refers to the phenomenon of higher atmospheric and surface temperatures occurring in urban areas than in the surrounding rural areas. Mitigation of the UHI effects via the configuration of green spaces and sustainable design of urban environments has become an issue of increasing concern under changing climate. In this paper, the effects of the composition and configuration of green space on land surface temperatures (LST) were explored using landscape metrics including percentage of landscape (PLAND), edge density (ED) and patch density (PD). An oasis city of Aksu in Northwestern China was used as a case study. The metrics were calculated by moving window method based on a green space map derived from Landsat Thematic Mapper (TM) imagery, and LST data were retrieved from Landsat TM thermal band. A normalized mutual information measure was employed to investigate the relationship between LST and the spatial pattern of green space. The results showed that while the PLAND is the most important variable that elicits LST dynamics, spatial configuration of green space also has significant effect on LST. Though, the highest normalized mutual information measure was with the PLAND (0.71), it was found that the ED and PD combination is the most deterministic factors of LST than the unique effects of a single variable or the joint effects of PLAND and PD or PLAND and ED. Normalized mutual information measure estimations between LST and PLAND and ED, PLAND and PD and ED and PD were 0.7679, 0.7650 and 0.7832, respectively. A combination of the three factors PLAND, PD and ED explained much of the variance of LST with a normalized mutual information measure of 0.8694. Results from this study can expand our understanding of the relationship between LST and street trees and vegetation, and provide insights for sustainable urban planning and management under changing climat

Increases in Vein Length Compensate for Leaf Area Lost to Lobing in Grapevine

Premise:Leaf lobing and leaf size vary considerably across and within species,including among grapevines (Vitisspp.), some of the best‐studied leaves. Weexamined the relationship between leaf lobing and leaf area across grapevinepopulations that varied in extent of leaf lobing.Methods:We used homologous landmarking techniques to measure 2632 leavesacross 2 years in 476 unique, genetically distinct grapevines fromfive biparentalcrosses that vary primarily in the extent of lobing. We determined to what extent leafarea explained variation in lobing, vein length, and vein to blade ratio.Results:Although lobing was the primary source of variation in shape across theleaves we measured, leaf area varied only slightly as a function of lobing. Rather, leafarea increases as a function of total major vein length, total branching vein length, andvein to blade ratio. These relationships are stronger for more highly lobed leaves, withthe residuals for each model differing as a function of distal lobing.Conclusions:For leaves with different extents of lobing but the same area, the morehighly lobed leaves have longer veins and higher vein to blade ratios, allowing themto maintain similar leaf areas despite increased lobing. Thesefindings show howmore highly lobed leaves may compensate for what would otherwise result in areduced leaf area, allowing for increasedphotosynthetic capacity through similarleaf siz

Effects of Ambient Ozone on Soybean Biophysical Variables and Mineral Nutrient Accumulation

The effects of increasing ambient ozone (O3) concentrations on food security has become a major concern as the demand for agricultural productivity is projected to increase significantly over the next several decades. In this contribution, the responses of common soybean genotypes (AK-HARROW, PI88788, DWIGHT, PANA, and WILLIAMS82) to ambient O3 are characterized using hyperspectral data and foliar biophysical, mineral nutrient concentrations and soybean yield. Specifically, leaf reflectance spectra measured at different growth stages and canopy layers were used to examine the spectral indices that were most strongly correlated with leaf physiological status. The effects of elevated O3 on six important nutrients (K, Ca, Mg, Fe, Mn and Cu) were evaluated by analyzing the variations in nutrient concentrations at two critical growth stages with increasing ambient O3 concentration using Partial Least Square Regression (PLSR). Lastly, the identified best spectral indices and the robust nutrient prediction models were extrapolated to the entire growth period to explore their ability to track the effects of ambient O3 concentrations on soybean physiology and nutrient uptake. The results showed that fluorescence yield (ΔF/Fm’) and photochemical quenching (qP) appear to be good indicators of soybean physiological responses to O3 stress that are echoed by the harvest index (HI). Newly identified normalized difference spectral index (NDSI) [R416, R2371] always had the highest correlation (R2 > 0.6) with ΔF/Fm’, qP and electron transport rate (ETR, μmol m−2 s−1) compared to the published indices. Additionally, there were significant and broad spectral regions in visible and near infrared region that were well-correlated with ΔF/Fm’ and selected NDSIs that were applicable to satellite observations. The results of nutrient modeling using PLSR explained 54–87% of the variance in nutrient concentrations, and the predicted mineral nutrient accumulation throughout the growing season reflected the responses of ozone tolerant and sensitive genotypes well. NDSI [R416, R2371] demonstrated great potential in regard to its sensitivity in tracking plant physiological responses to changing ambient O3 concentrations. The outcome of this research has potential implications for development of space-based observation of large-scale crop responses to O3 damage, as well as for biotechnological breeding efforts to improve ozone tolerance under future climate scenarios

Dual Activation Function-Based Extreme Learning Machine (ELM) for Estimating Grapevine Berry Yield and Quality

Reliable assessment of grapevine productivity is a destructive and time-consuming process. In addition, the mixed effects of grapevine water status and scion-rootstock interactions on grapevine productivity are not always linear. Despite the potential opportunity of applying remote sensing and machine learning techniques to predict plant traits, there are still limitations to previously studied techniques for vine productivity due to the complexity of the system not being adequately modeled. During the 2014 and 2015 growing seasons, hyperspectral reflectance spectra were collected using a handheld spectroradiometer in a vineyard designed to investigate the effects of irrigation level (0%, 50%, and 100%) and rootstocks (1103 Paulsen, 3309 Couderc, SO4 and Chambourcin) on vine productivity. To assess vine productivity, it is necessary to measure factors related to fruit ripeness and not just yield, as an over cropped vine may produce high-yield but poor-quality fruit. Therefore, yield, Total Soluble Solids (TSS), Titratable Acidity (TA) and the ratio TSS/TA (maturation index, IMAD) were measured. A total of 20 vegetation indices were calculated from hyperspectral data and used as input for predictive model calibration. Prediction performance of linear/nonlinear multiple regression methods and Weighted Regularized Extreme Learning Machine (WRELM) were compared with our newly developed WRELM-TanhRe. The developed method is based on two activation functions: hyperbolic tangent (Tanh) and rectified linear unit (ReLU). The results revealed that WRELM and WRELM-TanhRe outperformed the widely used multiple regression methods when model performance was tested with an independent validation dataset. WRELM-TanhRe produced the highest prediction accuracy for all the berry yield and quality parameters (R2 of 0.522–0.682 and RMSE of 2–15%), except for TA, which was predicted best with WRELM (R2 of 0.545 and RMSE of 6%). The results demonstrate the value of combining hyperspectral remote sensing and machine learning methods for improving of berry yield and quality prediction

Remote Sensing Based Spatial Statistics to Document Tropical Rainforest Transition Pathways

In this paper, grid cell based spatial statistics were used to quantify the drivers of land-cover and land-use change (LCLUC) and habitat degradation in a tropical rainforest in Madagascar. First, a spectral database of various land-cover and land-use information was compiled using multi-year field campaign data and photointerpretation of satellite images. Next, residential areas were extracted from IKONOS-2 and GeoEye-1 images using object oriented feature extraction (OBIA). Then, Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) data were used to generate land-cover and land-use maps from 1990 to 2011, and LCLUC maps were developed with decadal intervals and converted to 100 m vector grid cells. Finally, the causal associations between LCLUC were quantified using ordinary least square regression analysis and Moran’s I, and a forest disturbance index derived from the time series Landsat data were used to further confirm LCLUC drivers. The results showed that (1) local spatial statistical approaches were most effective at quantifying the drivers of LCLUC, and (2) the combined threats of habitat degradation in and around the reserve and increasing encroachment of invasive plant species lead to the expansion of shrubland and mixed forest within the former primary forest, which was echoed by the forest disturbance index derived from the Landsat data

Early Detection of Plant Physiological Responses to Different Levels of Water Stress Using Reflectance Spectroscopy

Early detection of water stress is critical for precision farming for improving crop productivity and fruit quality. To investigate varying rootstock and irrigation interactions in an open agricultural ecosystem, different irrigation treatments were implemented in a vineyard experimental site either: (i) nonirrigated (NIR); (ii) with full replacement of evapotranspiration (FIR); or (iii) intermediate irrigation (INT, 50% replacement of evapotranspiration). In the summers 2014 and 2015, we collected leaf reflectance factor spectra of the vineyard using field spectroscopy along with grapevine physiological parameters. To comprehensively analyze the field-collected hyperspectral data, various band combinations were used to calculate the normalized difference spectral index (NDSI) along with 26 various indices from the literature. Then, the relationship between the indices and plant physiological parameters were examined and the strongest relationships were determined. We found that newly-identified NDSIs always performed better than the indices from the literature, and stomatal conductance (Gs) was the plant physiological parameter that showed the highest correlation with NDSI(R603,R558) calculated using leaf reflectance factor spectra (R2 = 0.720). Additionally, the best NDSI(R685,R415) for non-photochemical quenching (NPQ) was determined (R2 = 0.681). Gs resulted in being a proxy of water stress. Therefore, the partial least squares regression (PLSR) method was utilized to develop a predictive model for Gs. Our results showed that the PLSR model was inferior to the NDSI in Gs estimation (R2 = 0.680). The variable importance in the projection (VIP) was then employed to investigate the most important wavelengths that were most effective in determining Gs. The VIP analysis confirmed that the yellow band improves the prediction ability of hyperspectral reflectance factor data in Gs estimation. The findings of this study demonstrate the potential of hyperspectral spectroscopy data in motoring plant stress response

Quantifying Leaf Chlorophyll Concentration of Sorghum from Hyperspectral Data Using Derivative Calculus and Machine Learning

Leaf chlorophyll concentration (LCC) is an important indicator of plant health, vigor, physiological status, productivity, and nutrient deficiencies. Hyperspectral spectroscopy at leaf level has been widely used to estimate LCC accurately and non-destructively. This study utilized leaf-level hyperspectral data with derivative calculus and machine learning to estimate LCC of sorghum. We calculated fractional derivative (FD) orders starting from 0.2 to 2.0 with 0.2 order increments. Additionally, 43 common vegetation indices (VIs) were calculated from leaf spectral reflectance factor to make comparisons with reflectance-based data. Within the modeling pipeline, three feature selection methods were assessed: Pearson's correlation coefficient (PCC), partial least squares based variable importance in the projection (VIP), and random forest-based mean decrease impurity (MDI). Finally, we used partial least squares regression (PLSR), random forest regression (RFR), support vector regression (SVR), and extreme learning regression (ELR) to estimate the LCC of sorghum. Results showed that: (1) increasing derivative order can show improved model performance until certain order for reflectance-based analysis; however, it is inconclusive to state that a particular order is optimal for estimating LCC of sorghum; (2) VI-based modeling outperformed derivative augmented reflectance factor-based modeling; (3) mean decrease impurity was found effective in selecting sensitive features from large feature space (reflectance-based analysis), whereas simple Pearson's correlation coefficient worked better with smaller feature space (VI-based analysis); and (4) SVR outperformed all other models within reflectance-based analysis; alternatively, ELR with VIs from original reflectance yielded slightly better results compared to all other models.Advanced Research Projects Agency - EnergyOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Dynamics of land surface temperature (LST) in response to land use and land cover (LULC) changes in the Weigan and Kuqa river oasis, Xinjiang, China

Land use and land cover (LULC) changes caused by human activities have strong influences on regional environment. Land surface temperate plays an important role in studying the impact of LULC changes on regional environment. In this paper, remotely sensed thermal infrared data were used to assess land surface temperature (LST) in the Weigan and Kuqa river oasis, Xingjiang, one of the important agricultural areas in the northwestern China. The present study deals with the extraction of LST and the relationship between LULC changes using Landsat 5 TM acquired on September 25, 1989, and September 6, 2011. The results indicate that the surface temperature of water body, bare land, and desert changed significantly between 1989 and 2011. In general, the LST was lower in 1989 than in 2011. There were no lower, higher, and highest temperature zones in 1989. However, the minimum temperature was 10.7 °C in 1989 and 15.8 °C in 2011. The maximum temperature was 29.3 °C in 1989 and 41.8 °C in 2011. Regarding the LULC types, the desert features in the Gobi Desert warmed more quickly than the oasis. So, the temperature of the oasis was lower than the surrounded areas, resulting in a so-called “cold island” phenomenon. Oasis cold island effect index (OCIEI) shows that stability of oasis had rising trend from 1989 to 2011. In addition, the impact of LULC changes on LST was analyzed and the driving forces were also analyzed from 1977 to 2011. This study is significant for further understanding of the energy exchange status of soil-plant-atmospheric system and the regional heat distribution in arid and semi-arid areas of the northwest China

Field-scale crop yield prediction using multi-temporal WorldView-3 and PlanetScope satellite data and deep learning

Agricultural management at field-scale is critical for improving yield to address global food security, as providing enough food for the world\u27s growing population has become a wicked problem for both scientists and policymakers. County- or regional-scale data do not provide meaningful information to farmers who are interested in field-scale yield forecasting for effective and timely field management. No studies directly utilized raw satellite imagery for field-scale yield prediction using deep learning. The objectives of this paper were twofold: (1) to develop a raw imagery-based deep learning approach for field-scale yield prediction, (2) investigate the contribution of in-season multitemporal imagery for grain yield prediction with hand-crafted features and WorldView-3 (WV) and PlanetScope (PS) imagery as the direct input, respectively. Four WV-3 and 25 PS imagery collected during the growing season of soybean were utilized. Both 2-dimensional (2D) and 3-dimensional (3D) convolution neural network (CNN) architectures were developed that integrated spectral, spatial, temporal information contained in the satellite data. For comparison, hundreds of carefully selected spectral, spatial, textural, and temporal features that are optimal for crop growth monitoring were extracted and fed into the same deep learning model. Our results demonstrated that (1) deep learning was able to predict yield directly using raw satellite imagery to the extent that was comparable to feature-fed deep learning approaches; (2) both 2D and 3D CNN models were able to explain nearly 90% variance in field-scale yield; (3) limited number of WV-3 outperformed multi-temporal PS data collected during entire growing season mainly attributed to RedEdge and SWIR bands available with WV-3; and (4) 3D CNN increased the prediction power of PS data compared to 2D CNN due to its ability to digest temporal features extracted from PS data