CotSkNet: Semantic segmentation of point clouds and phenotypic trait extraction for fragile organs in densely planted cotton under field conditions

Accurate segmentation of fine-scale organs from 3D point clouds poses a substantial challenge in high-throughput plant phenotyping (HTP), where existing methods are hindered by the loss of topological features and the resulting low accuracy. To address this, we introduce CotSkNet, a semantic segmentation network based on structured representation learning. This approach is the first to define plant architecture as a knowledge-based intermediate representation that integrates geometric, topological, and hierarchical relationships, thereby incorporating topological information into the segmentation process. CotSkNet features an innovative Topological Geometric Feature Fusion Extractor and a Two-Way Reinforcement Module to efficiently extract and enhance salient features. Furthermore, the proposed Topological Attention Aggregator enables dynamic focus on key branch points. On a dataset of 403 field-grown cotton plants, our method achieved mean intersection over union values of 91.55%, 92.37%, and 98.21% for the main stem, fruiting branches, and leaves, respectively, far surpassing those of mainstream methods. Moreover, automatically extracted phenotypic parameters, such as plant height and fruiting branch length showed excellent consistency with manual measurements (R 2 > 0.91, root mean square error (RMSE) < 0.14). This study confirms that structured representation learning excels at capturing fine-organ phenotypes, providing an innovative analytical pathway for HTP in complex field crops.