A method for detecting tomato canopies’ phenotypic traits based on improved skeleton extraction algorithm

Abstract

Automatic acquisition of tomato canopies’ phenotypic traits is essential for tomato varieties’ selection and scientific cultivation. Due to the infinite growth characteristics of tomato, its organ development is stochastic and the canopies' internal structure of is also complex. These make it challenging to obtain organs’ detailed phenotypic traits. Thus, this work proposed a method for detecting tomato canopies’ phenotypic traits based on improved skeleton extraction algorithm (ISEA). Firstly, after collecting tomato canopies' point cloud data from multiple perspectives, this work reconstructed its three-dimensional (3D) model accurately. Secondly, the least squares method was used to simplify the spatial contraction model of the Laplace Skeleton Extraction algorithm to obtain the tomatoes’ skeleton point set. On this basic, Greedy algorithm was used to optimise the Edge Collapse algorithm to extract more accurate and reliable skeleton structure. Then, in conjunction with the canopy growth characteristics of the crop and the Intrinsic Shape Signatures (ISS) principle, the simplified skeleton structure was subjected to local principal component analysis (PCA), which achieved the separation of tomatoes’ main stem and leaves. Finally, a modelling algorithm based on Delaunay triangulation was applied to construct the separated organs’ model to calculate phenotypic traits such as stem diameter, leaf area index and average leaf inclination. The calculated results were also compared with the measured values at different growth stages for performance evaluation. The average precision, average recall, average accuracy and micro F1 score of ISEA were 0.9144, 0.7751, 0.7243 and 0.8306, respectively. The overall R2 between calculated values and measured values for stem diameter, leaf area index and average leaf inclination were 0.9638, 0.9067, and 0.9428, and the root mean square errors (RMSE) were 0.3922, 0.0029, and 0.0186, respectively. As a result, the proposed method can extract a simple skeleton from the complex tomato canopy and calculate phenotypic traits accurately. It also provided solid technical support for studying the interaction about “genotype-phenotype-envirotype” in tomato.