A Deep Learning Approach for High-Throughput Multi-Tissue Cell Segmentation and Phenotypic Analysis in Chinese Cabbage Leaf Cross-Sections

Quantitative analysis of leaf cell microstructure is crucial for deciphering agronomic traits in Chinese cabbage, including photosynthetic efficiency, stress tolerance, and yield potential. Traditional manual observation methods are inefficient and highly subjective, failing to meet the demands of large-scale breeding for high-throughput, reproducible microscopic phenotyping. To transition breeding practices from experience-driven to data-driven, there is an urgent need to establish automated, standardized systems for acquiring cell-scale phenotypes. Therefore, this study proposes an automated instance segmentation and phenotyping analysis framework for multi-tissue cells in Chinese cabbage leaf cross-sections. This framework systematically optimizes Mask R-CNN by introducing an attention mechanism to enhance cellular feature responses in complex backgrounds. It employs weighted multi-scale feature fusion to process densely distributed small-scale cells and integrates a refined boundary optimization module to improve recognition accuracy in adherent and blurred regions. On a microscopic image dataset spanning multiple varieties, this method achieves high-precision predictions in instance segmentation tasks. Based on the predicted cell masks, an interactive phenotyping analysis tool was further developed to automatically extract standardized single-cell morphological parameters, including area, perimeter, and Feret’s diameter. The measured parameters exhibit high consistency with manual annotations (correlation coefficients (r) all exceed 0.97). This framework enables high-throughput, standardized phenotypic analysis at the cellular level of leaf cross-sections, providing a reliable method for the digital and automated interpretation of crop microscopic traits. This technical solution not only supports the systematic integration of microscopic phenotypes in Chinese cabbage breeding but also offers a scalable solution for cellular-scale phenotypic research in other crops.