LBD-PointNet++: a point cloud segmentation network for phenotypic trait extraction of broccoli seedlings

Broccoli is a globally significant vegetable, but climate change and soil salinization increasingly threaten its productivity. Precise seedling phenotyping is essential for selecting salt-tolerant germplasm, yet traditional manual methods are labor-intensive and error-prone. This study develops LBD-PointNet++, an optimized 3D point cloud semantic segmentation model for automated phenotypic parameter extraction of broccoli seedlings at the germination and early developmental phase under salt stress. High-fidelity 3D point clouds were reconstructed from a precision three-view imaging system using Structure from Motion (SfM) algorithms. LBD-PointNet++ introduces three core optimizations: (1) a Large Kernel Attention (LKA) mechanism using 3D sparse decomposition to capture long-range global dependencies; (2) a Dual Uncertainty and Shape-Adaptive Sampling (DUSAS) mechanism to preserve high-frequency features of fragile stems and margins; and (3) a joint Boundary-Aware Nested Contrastive and Adaptive Varifocal Joint Loss (BNCV-Loss) to effectively isolate overlapping leaves. Experimental results demonstrate superior performance, achieving an overall mean Intersection over Union (mIoU) of 88.07% across all three categories (Leaf, Stem, and Pot) and a Mean F1-score of 93.48%. Compared to state-of-the-art Transformer architectures like PTv3, LBD-PointNet++ achieves higher accuracy with less than 6% of the parameter volume and over twofold faster inference speed. Furthermore, dynamic monitoring across NaCl gradients (0-250 mmol/L) revealed a potential non-linear threshold effect, identifying 100 mmol/L as a preliminary phenotypic threshold under these conditions. Beyond this threshold, growth inhibition intensified rapidly; At 250 mmol/L, plant height decreased by 54.43% and the 3D entity volume shrank to approximately one-fifth of the control group. In summary, LBD-PointNet++ provides a high-efficiency solution for phenotypic identification and digital breeding of salt-tolerant Brassicaceae crops.