A method for calculating and simulating phenotype of soybean based on 3D reconstruction

Abstract

In plant phenotypic research, accurate organ segmentation and crop simulation are crucial for optimizing crop planting and increasing yield. In this study, an efficient method for soybean organ segmentation and phenotypic growth simulation was explored based on 3D reconstruction technology. Taking Dongnong252 soybean as the research object, the soybean phenotype acquisition system based on Kinect sensor was used to achieve high-precision and non-destructive acquisition of soybean canopy images during the whole growth period. First, conditional filtering and statistical filtering were used to remove noise. Then, combined with the Intrinsic Shape Signatures-Coherent Point Drift (ISS-CPD) and the Iterative Closest Point (ICP) algorithms, the multi-view three-dimensional (3D) canopy structure of soybean was reconstructed, which provided a reliable basis for plant stem and leaf segmentation. On this basis, the average accuracy of plant stem and leaf segmentation was 79.99% by using the Distance-field-based segmentation pipeline (DFSP) algorithm. Furthermore, the accurate information was provided for extracting and calculating 3D phenotypic parameters such as plant height, crown width, stem thickness, leaf length and leaf width from three scales of whole plant, stem and leaf. The calculated values were highly consistent with the measured values, with an average coefficient of determination of 0.9654 and an average percentage error of 3.4862%. Meanwhile, by analyzing the quantitative relationship between phenotypic parameters and physiological development time, the data-driven Richards growth simulation model was introduced to accurately predict the growth process of soybean plants. The coefficient of determination R2 values of each phenotypic simulation model reached above 0.9357, which improved the goodness of fit of the model by 0.03 compared with the Logistic model, and its root mean square error (RMSE) ranged from 0.0020 to 0.1112. The research results indicated that this method had high accuracy and reliability in 3D reconstruction of soybean canopy, phenotype calculation, and growth simulation. It could provide quantitative indicators for soybean variety selection, planting, and management, and provide technical support and reference for high-throughput phenotype acquisition and analysis of field crops.