Comparative classification of spectrally overlapping Allium seed genotypes using Vis–NIR spectroscopy and hyperspectral imaging with chemometric, machine, and deep learning models

Accurate identification of Allium seed genotypes is essential for cultivar authentication, breeding, and fraud prevention, yet remains challenging due to morphological similarities. This study evaluates the potential of a visible and near-infrared (Vis-NIR) spectrometer and a hyperspectral camera for non-destructive classification of seven closely related Allium genotypes, including shallot, red, white, and yellow onions, bon-sorkh, and two leek varieties. A total of 700 spectra and 70 images were acquired using the Vis-NIR spectrometer and hyperspectral camera, respectively, under controlled conditions and spectral preprocessing was applied to enhance signal quality. For spectrometer data, classification models were developed using soft independent modelling of class analogy (SIMCA), artificial neural networks (ANN), and histogram-based gradient boosting (HisGB). For hyperspectral data, pixel-level spectra were used to train ANN, HisGB, and deep convolutional neural networks (1D and 2D CNNs). Among the spectrometer models, the combination of second derivative preprocessing with HisGB achieved the highest performance (F1-score: 98.52%). For HSI, HisGB yielded the highest pixel-level classification accuracy (F1-score: 97.83%; error: 2.49%), followed by 1D CNN (F1-score: 96.85%). Spatial analysis revealed that HisGB and 1D CNN produced consistent classification maps across genotypes, whereas ANN and 2D CNN exhibited higher misclassification rates, particularly for morphologically similar classes such as shallot and bon-sorkh. At image level, the hyperspectral camera outperformed the Vis-NIR spectrometer, achieving perfect classification across all models. These results demonstrate the potential of hyperspectral imaging, especially when combined with ensemble and deep learning approaches, for high-throughput, non-destructive seed sorting and genotype purity assessment. The study also emphasizes the trade-off between the lower cost but reduced precision of the Vis-NIR spectrometer and the superior accuracy offered by the hyperspectral camera.