Branch-Pipe: Improving Graph Skeletonization around Branch Points in 3D Point Clouds

Abstract

Modern plant phenotyping requires tools that are robust to noise and missing data, while being able to efficiently process large numbers of plants. Here, we studied the skeletonization of plant architectures from 3D point clouds, which is critical for many downstream tasks, including analyses of plant shape, morphology, and branching angles. Specifically, we developed an algorithm to improve skeletonization at branch points (forks) by leveraging the geometric properties of cylinders around branch points. We tested this algorithm on a diverse set of high-resolution 3D point clouds of tomato and tobacco plants, grown in five environments and across multiple developmental timepoints. Compared to existing methods for 3D skeletonization, our method efficiently and more accurately estimated branching angles even in areas with noisy, missing, or non-uniformly sampled data. Our method is also applicable to inorganic datasets, such as scans of industrial pipes or urban scenes containing networks of complex cylindrical shapes.

Plant phenotyping relevance

植物の3D点群から分枝構造を骨格化し、分枝角度を推定するアルゴリズムを開発・比較評価しており、植物表現型の抽出手法が研究の中心です。

Code and data availability

The paper's Data Availability Statement explicitly states that data and code executable are publicly available at the authors' GitHub repository iziamtso/P3D, which is an allowed URL. This covers the paper-specific plant point cloud data and skeletonization analysis code.