Early detection of grapevine viral diseases is critical for early interventions in order to prevent the disease from spreading to the entire vineyard. Hyperspectral remote sensing can potentially detect and quantify viral diseases in a nondestructive manner. This study utilized hyperspectral imagery at the plant level to identify and classify grapevines inoculated with the newly discovered DNA virus grapevine vein-clearing virus (GVCV) at the early asymptomatic stages. An experiment was set up at a test site at South Farm Research Center, Columbia, MO, USA (38.92 N, −92.28 W), with two grapevine groups, namely healthy and GVCV-infected, while other conditions were controlled. Images of each vine were captured by a SPECIM IQ 400–1000 nm hyperspectral sensor (Oulu, Finland). Hyperspectral images were calibrated and preprocessed to retain only grapevine pixels. A statistical approach was employed to discriminate two reflectance spectra patterns between healthy and GVCV vines. Disease-centric vegetation indices (VIs) were established and explored in terms of their importance to the classification power. Pixel-wise (spectral features) classification was performed in parallel with image-wise (joint spatial–spectral features) classification within a framework involving deep learning architectures and traditional machine learning. The results showed that: (1) the discriminative wavelength regions included the 900–940 nm range in the near-infrared (NIR) region in vines 30 days after sowing (DAS) and the entire visual (VIS) region of 400–700 nm in vines 90 DAS; (2) the normalized pheophytization index (NPQI), fluorescence ratio index 1 (FRI1), plant senescence reflectance index (PSRI), anthocyanin index (AntGitelson), and water stress and canopy temperature (WSCT) measures were the most discriminative indices; (3) the support vector machine (SVM) was effective in VI-wise classification with smaller feature spaces, while the RF classifier performed better in pixel-wise and image-wise classification with larger feature spaces; and (4) the automated 3D convolutional neural network (3D-CNN) feature extractor provided promising results over the 2D convolutional neural network (2D-CNN) in learning features from hyperspectral data cubes with a limited number of samples.

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 (G_s) 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). G_s resulted in being a proxy of water stress. Therefore, the partial least squares regression (PLSR) method was utilized to develop a predictive model for G_s. Our results showed that the PLSR model was inferior to the NDSI in G_s 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 G_s. The VIP analysis confirmed that the yellow band improves the prediction ability of hyperspectral reflectance factor data in G_s estimation. The findings of this study demonstrate the potential of hyperspectral spectroscopy data in motoring plant stress response.

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.

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.

Soil salinization is one of the most widespread soil degradation processes on Earth, especially in arid and semi-arid areas. The salinized soil in arid to semi-arid Xinjiang Uyghur Autonomous Region in China accounts for 31% of the area of cultivated land, and thus it is pivotal for the sustainable agricultural development of the area to identify reliable and cost-effective methodologies to monitor the spatial and temporal variations in soil salinity. This objective was accomplished over the study area (Keriya River Basin, northwestern China) by adopting technologies that heavily rely on, and integrate information contained in, a readily available suite of remote sensing datasets. The following procedures were conducted: (1) a selective principle component analysis (S-PCA) fusion image was generated using Phased Array Type L-band SAR (PALSAR) backscattering coefficient (σ°) and Landsat Enhanced Thematic Mapper Plus (ETM+) multispectral image of Keriya River Basin; and (2) a support vector machines (SVM) classification method was employed to classify land cover types with a focus on mapping salinized soils; (3) a cross-validation method was adopted to identify the optimum classification parameters, and obtain an optimal SVM classification model; (4) Radarsat-2 (C band) and PALSAR polarimetric images were used to analyze polarimetric backscattering behaviors in relation to the variation in soil salinization; (5) a decision tree (DT) scheme for multi-source optical and polarimetric SAR data integration was proposed to improve the estimation and monitoring accuracies of soil salinization; and (6) detailed field observations and ground truthing were used for validation of the adopted methodology, and quantity and allocation disagreement measures were applied to assess classification outcome. Results showed that the fusion of passive reflective and active microwave remote sensing data provided an effective tool in detecting soil salinization. Overall accuracy of the adopted SVM classifier with optimal parameters for fused image of ETM+ and PALSAR data was 91.25% with a Kappa coefficient of 0.89, which was further improved by the DT data integration and classification method yielding an accuracy of 93.01% with a Kappa coefficient of 0.92 and lower disagreement of quantity and allocation.