The study of plant phenotypes based on 3D models has become an important research direction for automatic plant phenotype acquisition. Building a labeled three-dimensional dataset of the whole growth period can help the development of 3D crop plant models in point cloud segmentation. Therefore, the demand for 3D whole plant growth period model datasets with organ-level markers is growing rapidly. In this study, five different soybean varieties were selected, and three-dimensional reconstruction was carried out for the whole growth period (13 stages) of soybean using multiple-view stereo technology (MVS). Leaves, main stems, and stems of the obtained three-dimensional model were manually labeled. Finally, two-point cloud semantic segmentation models, RandLA-Net and BAAF-Net, were used for training. In this paper, 102 soybean stereoscopic plant models were obtained. A dataset with original point clouds was constructed and the subsequent analysis confirmed that the number of plant point clouds was consistent with corresponding real plant development. At the same time, a 3D dataset named Soybean-MVS with labels for the whole soybean growth period was constructed. The test result of mAccs at 88.52% and 87.45% verified the availability of this dataset. In order to further promote the study of point cloud segmentation and phenotype acquisition of soybean plants, this paper proposed an annotated three-dimensional model dataset for the whole growth period of soybean for 3D plant organ segmentation. The release of the dataset can provide an important basis for proposing an updated, highly accurate, and efficient 3D crop model segmentation algorithm. In the future, this dataset will provide important and usable basic data support for the development of three-dimensional point cloud segmentation and phenotype automatic acquisition technology of soybeans.

Soybeans are an essential source of food, protein, and oil worldwide, and the nodules on their root systems play a critical role in nitrogen fixation and plant growth. In this study, we tackled the challenge of limited high-resolution image quantities and the constraints on model learning by innovatively employing image segmentation technology for an in-depth analysis of soybean nodule phenomics. Through a meticulously designed segmentation algorithm, we broke down large-resolution images into numerous smaller ones, effectively improving the model’s learning efficiency and significantly increasing the available data volume, thus laying a solid foundation for subsequent analysis. In terms of model selection and optimization, after several rounds of comparison and testing, YOLOX was identified as the optimal model, achieving an accuracy of 91.38% on the test set with an R² of up to 86%, fully demonstrating its efficiency and reliability in nodule counting tasks. Subsequently, we utilized YOLOV5 for instance segmentation, achieving a precision of 93.8% in quickly and accurately extracting key phenotypic indicators such as the area, circumference, length, and width of the nodules, and calculated the statistical properties of these indicators. This provided a wealth of quantitative data for the morphological study of soybean nodules. The research not only enhanced the efficiency and accuracy of obtaining nodule phenotypic data and reduced costs but also provided important scientific evidence for the selection and breeding of soybean materials, highlighting its potential application value in agricultural research and practical production.