Three-Dimensional Phenotyping Pipeline of Potted Plants Based on Neural Radiation Fields and Path Segmentation

Abstract

Precise acquisition of potted plant traits has great theoretical significance and practical value for variety selection and guiding scientific cultivation practices. Although phenotypic analysis using two dimensional(2D) digital images is simple and efficient, leaf occlusion reduces the available phenotype information. To address the current challenge of acquiring sufficient non-destructive information from living potted plants, we proposed a three dimensional (3D) phenotyping pipeline that combines neural radiation field reconstruction with path analysis. An indoor collection system was constructed to obtain multi-view image sequences of potted plants. The structure from motion and neural radiance fields (SFM-NeRF) algorithm was then utilized to reconstruct 3D point clouds, which were subsequently denoised and calibrated. Geometric-feature-based path analysis was employed to separate stems from leaves, and density clustering methods were applied to segment the canopy leaves. Phenotypic parameters of potted plant organs were extracted, including height, stem thickness, leaf length, leaf width, and leaf area, and they were manually measured to obtain the true values. The results showed that the coefficient of determination (R2) values, indicating the correlation between the model traits and the true traits, ranged from 0.89 to 0.98, indicating a strong correlation. The reconstruction quality was good. Additionally, 22 potted plants were selected for exploratory experiments. The results indicated that the method was capable of reconstructing plants of various varieties, and the experiments identified key conditions essential for successful reconstruction. In summary, this study developed a low-cost and robust 3D phenotyping pipeline for the phenotype analysis of potted plants. This proposed pipeline not only meets daily production requirements but also advances the field of phenotype calculation for potted plants.

Plant phenotyping relevance

植物の3D形状再構成、器官分離・葉分割、形質抽出を一体化したフェノタイピング手法を開発し、手測定との相関で検証しているため、方法が研究の中心である。

Code and data availability

The supplied blocks describe a 3D phenotyping pipeline (SFM-NeRF reconstruction, path/DBSCAN segmentation, trait extraction) but contain no public dataset deposit, no author code repository, and no supplement (pmc-prop-has-supplement no). The only URLs mentioned are generic tool references (Open3D, CloudCompare), which

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