Research Article | Open Access

Volume 2025 |Article ID 100065 | https://doi.org/10.1016/j.plaphe.2025.100065

Automatic 3D Plant Organ Instance Segmentation Method Based on PointNeXt and Quickshift++

Sifan Dong,^1,5 Xueyan Fan,^1,5 Xiuhua Li ,^1,2 Yuming Liang,¹ Muqing Zhang,^2,3 Wei Yao,^2,3 Xiping Yang,³ and Zeping Wang⁴

¹State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, School of Electrical Engineering, Guangxi University, Nanning 530004, China
²Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning 530004, China
³State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
⁴Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
⁵Sifan Dong and Xueyan Fan contributed equally to this work.

Abstract

Organ instance segmentation of 3D plant point clouds is a crucial prerequisite for organ-level phenotype estimation. However, most current cloud segmentation methods are usually designed for specific crop, hardly fit for both monocotyledonous and dicotyledonous crops which have significant structural differences. This study therefore proposed a two-stage method with higher generalization ability for single-plant organ instance segmentation based on PointNeXt and Quickshift++. The effectiveness of this method was tested on different types of crops. The dataset includes point clouds of 122 self-acquired sugarcanes, 49 open-accessed maizes, and 77 open-accessed tomatoes. The improved PointNeXt model was trained to implement the semantic segmentation of stems and leaves. The average mOA and mIoU on the test set reaches 96.96 % and 87.15 %, respectively. The Quickshift++ algorithm was then applied to encode the global spatial structure and local connections of plants for rapid localization and segmentation of leaf instance. Our approach outperformed four SOTA methods, ASIS, JSNet, DFSP, and PSegNet in terms of both quantitative and qualitative segmentation results, achieving average values for mPrec, mRec, mF1, and mIoU of 93.32 %, 85.60 %, 87.94 %, and 81.46 %, respectively. The proposed method also yields excellent results for several other plants in their early stages, indicating its generalization ability and applicability for organ instance segmentation for different plants, thus providing a powerful tool for plant phenotypic research.