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This study advances agricultural computer vision by replacing a CNN backbone with a self-supervised Vision Transformer (DINOv3) to automate root trait estimation from minirhizotron imagery. By utilizing parameter-efficient fine-tuning on frozen weights, the model achieves high regression accuracy ($R^2$ > 0.93) while leveraging existing numeric archives without requiring manual masks. This approach directly addresses data scarcity in phenotyping by enabling high-throughput analysis of below-ground crop processes through advanced machine learning architectures.
RootQuantV2: Adapting a Vision Foundation Model for Root-Trait Regression from Minirhizotron Imagery
arXiv:2609.25567v1 Announce Type: cross Abstract: A lack of high-throughput phenotyping solutions for root traits in field-grown crops has severely constrained understanding and improvement of below-ground traits and processes. Minirhizotrons are the standard non-destructive root-phenotyping method in field environments. Computer vision solutions are needed to allow automated trait estimation at scale, but training data is scarce and human annotations are often inaccessible because they reside in proprietary software that only exports per-image scalar totals of root length and surface area. Nevertheless, large numeric archives of these root traits already exist. RootQuant showed that the traits can be predicted directly from the whole image by regression, thus removing manually traced masks from the pipeline; RootQuantV2 takes that idea further by replacing RootQuant's CNN backbone with a self-supervised ViT. We adapt a frozen DINOv3 ViT-L/16 with a hybrid parameter-efficient scheme. Training only 11.9M parameters (3.78% of the model), RootQuantV2 achieves length and area $R^2$ of 0.950 and 0.930, respectively, while lowering length/area RMSE by 24.3%/20.7% over RootQuant. RootQuantV2 thus repurposes legacy numeric archives for high-throughput, automated root trait estimation.
Abstract:A lack of high-throughput phenotyping solutions for root traits in field-grown crops has severely constrained understanding and improvement of below-ground traits and processes. Minirhizotrons are the standard non-destructive root-phenotyping method in field environments. Computer vision solutions are needed to allow automated trait estimation at scale, but training data is scarce and human annotations are often inaccessible because they reside in proprietary software that only exports per-image scalar totals of root length and surface area. Nevertheless, large numeric archives of these root traits already exist. RootQuant showed that the traits can be predicted directly from the whole image by regression, thus removing manually traced masks from the pipeline; RootQuantV2 takes that idea further by replacing RootQuant's CNN backbone with a self-supervised ViT. We adapt a frozen DINOv3 ViT-L/16 with a hybrid parameter-efficient scheme. Training only 11.9M parameters (3.78% of the model), RootQuantV2 achieves length and area $R^2$ of 0.950 and 0.930, respectively, while lowering length/area RMSE by 24.3%/20.7% over RootQuant. RootQuantV2 thus repurposes legacy numeric archives for high-throughput, automated root trait estimation.
20 pages (15 main + 5 references), 4 figures, 5 tables. Accepted to the Computer Vision in Plant Phenotyping and Agriculture (CVPPA) Workshop at ECCV 2026. Code and weights: this https URL
Computer Vision and Pattern Recognition (cs.CV); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Quantitative Methods (q-bio.QM)
I.4.8; I.2.10; J.3
arXiv:2609.25567 [cs.CV]
(or arXiv:2609.25567v1 [cs.CV] for this version)
https://doi.org/10.48550/arXiv.2609.25567 arXiv-issued DOI via DataCite (pending registration)
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