@article{Phukon2026, 
author = {Gargee Phukon and Maïda Cardoso and Christophe Goze-Bac and Loïc Le Cunff and Jean-Luc Verdeil and Cédric Moisy and Romain Fernandez},
title = {Atlas-based spatiotemporal MRI phenotyping of 3D fungal spread in grapevine wood},
year = {2026},
journal = {Plant Phenomics},
volume = {8},
number = {2},
pages = {100185},
keywords = {Grapevine trunk diseases (GTDs), Anatomical phenotyping, Time-lapse tracking, Magnetic resonance imaging (MRI), Probabilistic atlas},
url = {https://www.sciopen.com/article/10.1016/j.plaphe.2026.100185},
doi = {10.1016/j.plaphe.2026.100185},
abstract = {In perennial crops, inner wood degradation by pathogens often escapes detection until irreversible damage has occurred. Grapevine trunk diseases (GTDs) are a well-known example in viticulture that alter plants from within, years before foliar symptoms arise, making early assessment difficult. To overcome this limitation, we present a novel non-destructive 3D + t pipeline for high-resolution Magnetic Resonance Imaging (MRI) spatial quantification and monitoring of early internal host tissue degradation resulting from fungal pathogen colonization. The pipeline integrates spatiotemporal anatomical alignment and rigid registration; a generalized cylindrical-coordinate transformation; supervised segmentation of water-depleted regions; and population-level statistical analyses, including population mean images, probabilistic atlases, and 3D lesion descriptors. Applied to multiple Vitis vinifera cultivars inoculated with a fungal wood pathogen, our approach enables in vivo time-lapse comparisons between cultivars and treatments. The results reveal reproducible early degradation signals across individuals and cultivar-dependent differences in lesion progression. Overall, this methodological innovation provides a new paradigm for internal plant phenotyping, enabling non-invasive quantification of disease development and comparative spatiotemporal assessment of host responses in woody plants, with strong potential to advance early diagnosis and management of GTDs and internal diseases.}
}