Root-TransUNet enables high-throughput phenotyping of

Introduction: Plant parasitism by sedentary plant-parasitic nematodes is a dynamic and continuously evolving process, accompanied by profound remodelling of host root system architecture across distinct infection stages. However, the physiology and anisotropic growth of Arabidopsis thaliana roots under Heterodera schachtii infection, together with complex lateral root proliferation and increasingly dense, overlapping morphology, pose substantial challenges for accurate image segmentation. Methods: Here, we introduce Root-TransUNet, an optimised segmentation architecture that extends TransUNet by incorporating a composite loss function to improve boundary precision and structural continuity, as well as dual-stage strip-pooling (SP) modules to enhance elongated and directional root features. These adaptations address the unique morphological complexity of the infected root system. Additionally, we integrated Root-TransUNet into a high-throughput phenotyping pipeline and applied it to an existing dataset of ~120,000 images of 362 A. thaliana MAGIC recombinant inbred lines collected over several months of infection. By extracting root system architecture traits, including root surface area and estimated root volume across infection stages, we enabled stage-specific association analyses between host root growth and nematode performance across these genotypes. Results: Root-TransUNet achieved strong segmentation performance, demonstrating improved structural continuity and boundary precision compared with widely used CNN- and Transformer-based baselines, including UNet++. Stage-specific analyses revealed that the relationship between host root traits and nematode performance changed as infection progressed. During establishment, nematode number was largely independent of initial root size and varied strongly among genotypes, whereas during the reproductive phase (10-30 dpi), greater root expansion coincided with reduced estimated nematode volume accumulation. Notably, nematode burden was largely independent of host root size before infection, indicating that root quantity was generally not a limiting factor for infection in this experiment. Discussion: These results demonstrate that Root-TransUNet can robustly segment infected root systems across a wide range of nematode infection densities, providing a scalable image-analysis framework for studying plant-parasitic nematode parasitism in combination with host root phenotyping.