Automatic Branch-Leaf Segmentation and Leaf Phenotypic Parameter Estimation of Pear Trees Based on Three-Dimensional Point Clouds.

Abstract

The leaf phenotypic traits of plants have a significant impact on the efficiency of canopy photosynthesis. However, traditional methods such as destructive sampling will hinder the continuous monitoring of plant growth, while manual measurements in the field are both time-consuming and laborious. Nondestructive and accurate measurements of leaf phenotypic parameters can be achieved through the use of 3D canopy models and object segmentation techniques. This paper proposed an automatic branch-leaf segmentation pipeline based on lidar point cloud and conducted the automatic measurement of leaf inclination angle, length, width, and area, using pear canopy as an example. Firstly, a three-dimensional model using a lidar point cloud was established using SCENE software. Next, 305 pear tree branches were manually divided into branch points and leaf points, and 45 branch samples were selected as test data. Leaf points were further marked as 572 leaf instances on these test data. The PointNet++ model was used, with 260 point clouds as training input to carry out semantic segmentation of branches and leaves. Using the leaf point clouds in the test dataset as input, a single leaf instance was extracted by means of a mean shift clustering algorithm. Finally, based on the single leaf point cloud, the leaf inclination angle was calculated by plane fitting, while the leaf length, width, and area were calculated by midrib fitting and triangulation. The semantic segmentation model was tested on 45 branches, with a mean Precision sem , mean Recall sem , mean F 1 -score , and mean Intersection over Union ( IoU ) of branches and leaves of 0.93, 0.94, 0.93, and 0.88, respectively. For single leaf extraction, the Precision ins , Recall ins , and mean coverage ( mCoV ) were 0.89, 0.92, and 0.87, respectively. Using the proposed method, the estimated leaf inclination, length, width, and area of pear leaves showed a high correlation with manual measurements, with correlation coefficients of 0.94 (root mean squared error: 4.44°), 0.94 (root mean squared error: 0.43 cm), 0.91 (root mean squared error: 0.39 cm), and 0.93 (root mean squared error: 5.21 cm 2 ), respectively. These results demonstrate that the method can automatically and accurately measure the phenotypic parameters of pear leaves. This has great significance for monitoring pear tree growth, simulating canopy photosynthesis, and optimizing orchard management.

Plant phenotyping relevance

LiDAR三次元点群とセグメンテーションを用いて、葉の形態形質を自動抽出・推定する手法を開発し、手測定との相関で検証しているため、植物フェノタイピング手法が中心である。

Code and data availability

植物フェノタイピング解析を再現する公開資産であることを、入力本文と直接リンクから確認できなかったため保留しました。

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