An in situ image-based phenotyping system for hydroponic maize seedling roots based on DB-UNet and customized skeleton-based analysis

monitoring capabilities, and existing models have limited accuracy in root segmentation. To address these issues, we developed a crop root phenotyping system integrating crop cultivation and data collection. We also proposed a DB-UNet model for hydroponic maize root segmentation. DB-UNet builds a CNN-ViT dual-branch parallel structure during encoder downsampling level. The lightweight ViT branch uses sequential downsampling to achieve global topological dependency modeling while reducing computational costs. An attention fusion module dynamically calibrate dual-branch features weights, achieving complementary fusion of local root edge details and global context information. we constructed a mixed loss function combining Dice loss, Focal loss, and structural consistency KL loss to solve class imbalance, hard sample segmentation, and semantic divergence of dual-branch features. On our custom hydroponic maize root dataset, DB-UNet achieved an mIoU of 91.02%, an FG IoU of 82.78%, and a Centerline-Dice of 97.72%.Compared to classic UNet, mIoU, FG IoU, and Centerline-Dice increased by 0.92%, 1.84%, and 1.99%, respectively. Plant-level five-fold cross-validation further showed that DB-UNet maintained stable segmentation performance across different plant-level partitions. Based on DB-UNet segmentation results, we propose a custom skeleton-based algorithm for multi-trait root phenotyping, enabling the extraction of total root length and root branch points. Root area is calculated from binary mask pixel statistics. Compared to the traditional Zhang-Suen algorithm, the average relative error of root length measurement is reduced to 3.14%, which is 8.42 percentage points lower than the traditional method. Furthermore, we analyzed relationships between segmentation accuracy metrics and phenotypic relative errors. Higher segmentation quality generally led to lower phenotypic relative errors and more reliable trait measurements. In particular, Centerline-Dice was closely associated with root length estimation, whereas pixel-level segmentation consistency was more closely related to root area measurement. Pearson and Spearman correlation analyses showed a strong positive correlation between maize plant height and total root length, with coefficients of 0.8466 and 0.8634, respectively.