Deep Learning for Soybean Cyst Nematode Detection: A Comparison of Vision Transformer and CNN with Multispectral Imaging

Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean in North America. Even at low to moderate infestation levels, SCN can cause 20–30% yield loss without producing any visible aboveground symptoms. In severely infested fields, yield reductions can reach 60–70% and, in extreme cases, exceed 80%. Prior research on identifying SCN infestations has primarily relied on traditional machine-learning methods applied to Unmanned Aerial System (UAS)-based multispectral imagery, with limited success. This study hypothesizes that deep-learning (DL) methods can more effectively capture the subtle spectral and spatial signatures in multispectral images of SCN stress. To address this gap, we evaluate the performance of advanced DL architectures, including Vision Transformer (ViT) and a customized Convolutional Neural Network (CNN), for detecting SCN infestation in soybean fields using multispectral UAS imagery. Spectral analysis of the multispectral imagery revealed that the near-infrared (NIR) band is a strong discriminator between non-detected and SCN-infested areas. The DL models trained and tested across multiple growth stages showed promising results. The four-timestamp ViT model (3 June, 29 July, 19 August, and 2 September) achieved an F1-score of 0.74, while the five-timestamp SCN–CNN model (3 June, 22 July, 29 July, 19 August, and 2 September) achieved an F1-score of 0.75. Although overall performance was comparable, ViT demonstrated more stable performance across varying training and test data distributions. These findings highlight the effectiveness of DL architectures to automatically extract subtle, complex plant features from multispectral imagery throughout the growing season. Compared with manual, time-consuming soil-sampling techniques, the proposed framework enables more precise spatial and temporal monitoring of SCN infestations across fields.