Transformer-Based hyperspectral image analysis for phenotyping drought tolerance in blueberries

Drought-induced stress significantly impacted blueberry production due to the plants’ inefficient water regulation mechanisms to maintain yield and fruit quality under drought stress. Traditional methods of manual phenotyping for drought stress are not only time-consuming but also labor-intensive. To address the need for accurate and large-scale assessment of drought tolerance, we developed a high-throughput phenotyping (HTP) system to capture hyperspectral images of blueberry plants under drought conditions. A novel transformer-based model, LWC-former was introduced to predict leaf water content (LWC) utilizing spectral reflectance from hyperspectral images obtained from the developed HTP system. The LWC-former transformed the spectral reflectance into patch representations and embedded these patches into a lower dimensional to address multicollinearity issues. These patches were then passed to the transformer encoder to learn distributed features, followed by a regression head to predict LWC. To train the model, spectral reflectance data were extracted from hyperspectral images and pre-processed using log(1/R), mean scatter correction (MSC), and mean centering (MC). The results showed that our model achieved a coefficient of determination (R²) of 0.81 on the test dataset. The performance of the proposed model was also compared with TabTransformer, DeepRWC, multilayer perceptron (MLP), partial least squares regression (PLSR), support vector regression (SVR), and random forest (RF), achieving R² values of 0.65, 0.73, 0.71, 0.47, and 0.58, respectively. The results demonstrated that LWC-former outperformed other deep learning and statistical-based models. The high-throughput phenotyping system effectively facilitated large-scale data collection, while the LWC-former model addressed multicollinearity issues, significantly improving the prediction of LWC. These results demonstrate the potential of our approach for large-scale drought tolerance assessment in blueberries.