An end-to-end workflow based on multimodal 3D imaging and machine learning for non-destructive diagnosis of grapevine trunk diseases

Abstract

Quantifying healthy and degraded inner tissues in plants is of great interest in agronomy, for example, to assess plant health and quality and monitor physiological traits or diseases. However, detecting functional and degraded plant tissues in-vivo without harming the plant is extremely challenging. New solutions are needed in ligneous and perennial species, for which the sustainability of plantations is crucial. To tackle this challenge, we developed a novel approach based on multimodal 3D imaging and Artificial Intelligence (AI)-based image processing that allowed a noninvasive diagnosis of inner tissues in living plants. The method was successfully applied to the grapevine (Vitis vinifera L.) in vineyards where sustainability was threatened by trunk diseases, while the sanitary status of vines cannot be ascertained without injuring the plants. By combining MRI and X-ray CT 3D imaging with an automatic voxel classification, we could discriminate intact, degraded, and white rot tissues with a mean global accuracy of over 91%. Each imaging modality contribution to tissue detection was evaluated, and we identified quantitative structural and physiological markers characterizing wood degradation steps. The combined study of inner tissue distribution versus external foliar symptom history demonstrated that white rot and intact tissue contents are key measurements in evaluating vines sanitary status. We finally proposed a model for an accurate trunk disease diagnosis in grapevine. This work opens new routes for precision agriculture and in-situ monitoring of wood quality and plant health across plant species.

Code and data availability

The paper's imaging datasets (MRI, X-ray CT, photographic volumes, annotations) are only available 'upon reasonable request', but the authors' extended Trainable Segmentation plugin used for the machine-learning voxel classification is explicitly open-source on GitHub.