Seed 3D Phenotyping Across Multiple Crops Using 3D Gaussian Splatting

Jun Gao, Chao Zhu (), Junguo Hu, Fei Deng, Zhaoxin Xu and Xiaomin Wang
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Jun Gao: School of Mathematics and Computer Science, Zhejiang A&F University, Hangzhou 310058, China
Chao Zhu: School of Mathematics and Computer Science, Zhejiang A&F University, Hangzhou 310058, China
Junguo Hu: School of Mathematics and Computer Science, Zhejiang A&F University, Hangzhou 310058, China
Fei Deng: School of Mathematics and Computer Science, Zhejiang A&F University, Hangzhou 310058, China
Zhaoxin Xu: School of Mathematics and Computer Science, Zhejiang A&F University, Hangzhou 310058, China
Xiaomin Wang: College of Modern Agriculture, Zhejiang A&F University, Hangzhou 310058, China

Agriculture, 2025, vol. 15, issue 22, 1-20

Abstract: This study introduces a versatile seed 3D reconstruction method that is applicable to multiple crops—including maize, wheat, and rice—and designed to overcome the inefficiency and subjectivity of manual measurements and the high costs of laser-based phenotyping. A panoramic video of the seed is captured and processed through frame sampling to extract multi-view images. Structure-from-Motion (SFM) is employed for sparse reconstruction and camera pose estimation, while 3D Gaussian Splatting (3DGS) is utilized for high-fidelity dense reconstruction, generating detailed point cloud models. The subsequent point cloud preprocessing, filtering, and segmentation enable the extraction of key phenotypic parameters, including length, width, height, surface area, and volume. The experimental evaluations demonstrated a high measurement accuracy, with coefficients of determination (R 2 ) for length, width, and height reaching 0.9361, 0.8889, and 0.946, respectively. Moreover, the reconstructed models exhibit superior image quality, with peak signal-to-noise ratio (PSNR) values consistently ranging from 35 to 37 dB, underscoring the robustness of 3DGS in preserving fine structural details. Compared to conventional multi-view stereo (MVS) techniques, the proposed method can achieve significantly improved reconstruction accuracy and visual fidelity. The key outcomes of this study confirm that the 3DGS-based pipeline provides a highly accurate, efficient, and scalable solution for digital phenotyping, establishing a robust foundation for its application across diverse crop species.

Keywords: computer vision; point cloud; 3D phenotype measurement; segmentation; 3D Gaussian Splatting (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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