Parastoo Farajpoor

Parastoo Farajpoor, Alireza Pourreza, Mohammadreza Narimani et al.

Accurate modeling of leaf spectral reflectance from physiological and biochemical traits is essential for advancing remote sensing applications in plant science and precision agriculture. Widely used radiative transfer models, such as PROSPECT-PRO, rely on generalized trait-reflectance relationships developed from a wide range of species, which may not fully capture the spectral behavior of specific crops like grapevines. In this study, we developed a trait-to-spectra prediction model using a multi-head attention neural network trained on a grapevine-specific dataset that includes 16 leaf traits measured across multiple varieties, growth stages, and years. The model was evaluated using stratified 5-fold cross-validation and achieved an average coefficient of determination (R^2) of 0.84 and normalized root mean squared error (NRMSE) of 1.52 percent, demonstrating high accuracy and generalizability. When compared to PROSPECT-PRO in forward mode, the neural network exhibited lower mean absolute error (MAE), especially in the near-infrared (NIR) and shortwave-infrared (SWIR) regions. These results emphasize the importance of species-specific modeling approaches and show that integrating biochemical and structural traits into data-driven architectures can significantly improve spectral prediction. The proposed model provides a robust framework for generating accurate leaf-level reflectance data, with potential applications in canopy trait retrieval, vineyard monitoring, and remote sensing-driven crop management.

Mohammadreza Narimani, Alireza Pourreza, Parastoo Farajpoor

Field-scale crop maps support supply-chain forecasting and policy, yet statewide crop identification still often depends on retrospective surveys or remote-sensing workflows built around hand-engineered spectral features. Those pipelines can be accurate, but they require repeated preprocessing and often lose robustness across years. This study evaluated whether Google DeepMind's AlphaEarth geospatial embeddings can serve as an analysis-ready alternative for mapping processing tomato systems in California. LandIQ 2018 crop polygons were used to assemble a balanced reference dataset of 4,742 tomato and 4,742 non-tomato fields. For each polygon, 64-band AlphaEarth embedding chips were extracted and aligned with binary masks, then divided into spatially independent training (n = 6,638), validation (n = 1,422), and test (n = 1,424) sets. A U-Net segmentation model was trained on AWS SageMaker using a composite masked binary cross-entropy and soft Dice loss. To complement hard predictions, Monte Carlo dropout was retained at inference and repeated 100 times per chip to estimate predictive mean and variance. On the independent test set, the model achieved 99.19% pixel accuracy, 98.69% precision, 99.40% recall, 99.04% F1 score, 98.11% intersection over union, and 99.02% chip accuracy. Uncertainty maps were consistently highest near field edges and low within field interiors. The results show that AlphaEarth embeddings retain crop-relevant spatial and temporal structure and can support accurate, field-scale tomato mapping without manual feature engineering.

Mohammadreza Narimani, Alireza Pourreza, Ali Moghimi et al.

This study addresses the escalating threat of branched broomrape (Phelipanche ramosa) to California's tomato industry, which supplies over 90 percent of U.S. processing tomatoes. The parasite's largely underground life cycle makes early detection difficult, while conventional chemical controls are costly, environmentally harmful, and often ineffective. To address this, we combined drone-based multispectral imagery with Long Short-Term Memory (LSTM) deep learning networks, using the Synthetic Minority Over-sampling Technique (SMOTE) to handle class imbalance. Research was conducted on a known broomrape-infested tomato farm in Woodland, Yolo County, CA, across five key growth stages determined by growing degree days (GDD). Multispectral images were processed to isolate tomato canopy reflectance. At 897 GDD, broomrape could be detected with 79.09 percent overall accuracy and 70.36 percent recall without integrating later stages. Incorporating sequential growth stages with LSTM improved detection substantially. The best-performing scenario, which integrated all growth stages with SMOTE augmentation, achieved 88.37 percent overall accuracy and 95.37 percent recall. These results demonstrate the strong potential of temporal multispectral analysis and LSTM networks for early broomrape detection. While further real-world data collection is needed for practical deployment, this study shows that UAV-based multispectral sensing coupled with deep learning could provide a powerful precision agriculture tool to reduce losses and improve sustainability in tomato production.

Mohammadreza Narimani, Alireza Pourreza, Ali Moghimi et al.

Branched broomrape (Phelipanche ramosa) is a chlorophyll-deficient parasitic weed that threatens tomato production by extracting nutrients from the host. We investigate early detection using leaf-level spectral reflectance (400-2500 nm) and ensemble machine learning. In a field experiment in Woodland, California, we tracked 300 tomato plants across growth stages defined by growing degree days (GDD). Leaf reflectance was acquired with a portable spectrometer and preprocessed (band denoising, 1 nm interpolation, Savitzky-Golay smoothing, correlation-based band reduction). Clear class differences were observed near 1500 nm and 2000 nm water absorption features, consistent with reduced leaf water content in infected plants at early stages. An ensemble combining Random Forest, XGBoost, SVM with RBF kernel, and Naive Bayes achieved 89% accuracy at 585 GDD, with recalls of 0.86 (infected) and 0.93 (noninfected). Accuracy declined at later stages (e.g., 69% at 1568 GDD), likely due to senescence and weed interference. Despite the small number of infected plants and environmental confounders, results show that proximal sensing with ensemble learning enables timely detection of broomrape before canopy symptoms are visible, supporting targeted interventions and reduced yield losses.

Mohammadreza Narimani, Alireza Pourreza, Ali Moghimi et al.

Branched broomrape (Phelipanche ramosa (L.) Pomel) is a chlorophyll-deficient parasitic plant that threatens tomato production by extracting nutrients from the host, with reported yield losses up to 80 percent. Its mostly subterranean life cycle and prolific seed production (more than 200,000 seeds per plant, viable for up to 20 years) make early detection essential. We present an end-to-end pipeline that uses Sentinel-2 imagery and time-series analysis to identify broomrape-infested tomato fields in California. Regions of interest were defined from farmer-reported infestations, and images with less than 10 percent cloud cover were retained. We processed 12 spectral bands and sun-sensor geometry, computed 20 vegetation indices (e.g., NDVI, NDMI), and derived five plant traits (Leaf Area Index, Leaf Chlorophyll Content, Canopy Chlorophyll Content, Fraction of Absorbed Photosynthetically Active Radiation, and Fractional Vegetation Cover) using a neural network calibrated with ground-truth and synthetic data. Trends in Canopy Chlorophyll Content delineated transplanting-to-harvest periods, and phenology was aligned using growing degree days. Vegetation pixels were segmented and used to train a Long Short-Term Memory (LSTM) network on 18,874 pixels across 48 growing-degree-day time points. The model achieved 88 percent training accuracy and 87 percent test accuracy, with precision 0.86, recall 0.92, and F1 0.89. Permutation feature importance ranked NDMI, Canopy Chlorophyll Content, FAPAR, and a chlorophyll red-edge index as most informative, consistent with the physiological effects of infestation. Results show the promise of satellite-driven time-series modeling for scalable detection of parasitic stress in tomato farms.