Manual phenotyping of tomato plants is time consuming and labor intensive. Due to the lack of low-cost and open-access 3D phenotyping tools, the dynamic 3D growth of tomato plants during all growth stages has not been fully explored. In this study, based on the 3D structural data points generated by employing structures from motion algorithms on multiple-view images, we proposed a 3D phenotyping pipeline, 3DPhenoMVS, to calculate 17 phenotypic traits of tomato plants covering the whole life cycle. Among all the phenotypic traits, six of them were used for accuracy evaluation because the true values can be generated by manual measurements, and the results showed that the R² values between the phenotypic traits and the manual ones ranged from 0.72 to 0.97. In addition, to investigate the environmental influence on tomato plant growth and yield in the greenhouse, eight tomato plants were chosen and phenotyped during seven growth stages according to different light intensities, temperatures, and humidities. The results showed that stronger light intensity and moderate temperature and humidity contribute to a higher biomass and higher yield. In conclusion, we developed a low-cost and open-access 3D phenotyping pipeline for tomato and other plants, and the generalization test was also complemented on other six species, which demonstrated that the proposed pipeline will benefit plant breeding, cultivation research, and functional genomics in the future.

Point cloud analysis is a crucial task in computer vision. Despite significant advances over the past decade, the developments in agricultural domain have faced challenges due to a scarcity of datasets. To facilitate 3D point cloud research in agriculture community, we introduce Crops3D, the diverse real-world dataset derived from authentic agricultural scenarios. Crops3D distinguishes itself through its unique properties: diversity, authenticity, and complexity. The dataset incorporates data from diverse point cloud acquisition methods, encompassing eight distinct crop types with 1,230 samples, authentically representing crops in the real-world. It stands as the pioneering dataset that comprehensively supports the three critical tasks in 3D crop phenotyping: instance segmentation of individual plants in agricultural settings, plant type perception, and plant organ segmentation. Additionally, the intricate crop structures in Crops3D exhibit higher complexity than available 3D public datasets, showcasing substantial self-occlusion and increased complexity as crops mature. We analyse diverse crop point cloud acquisition methods and evaluate multiple models’ performance with the Crops3D dataset.

Although plant disease recognition is highly important in agricultural production, traditional methods face challenges due to the high costs associated with data collection and the scarcity of samples. Few-shot plant disease identification tasks, which are based on transfer learning, can learn feature representations from a small amount of data; however, most of these methods require pretraining within the relevant domain. Recently, foundation models have demonstrated excellent performance in zero-shot and few-shot learning scenarios. In this study, we explore the potential of foundation models in plant disease recognition by proposing an efficient few-shot plant disease recognition model (PlantCaFo) based on foundation models. This model operates on an end-to-end network structure, integrating prior knowledge from multiple pretraining models. Specifically, we design a lightweight dilated contextual adapter (DCon-Adapter) to learn new knowledge from training data and use a weight decomposition matrix (WDM) to update the text weights. We test the proposed model on a public dataset, PlantVillage, and show that the model achieves an accuracy of 93.53 ​% in a “38-way 16-shot” setting. In addition, we conduct experiments on images collected from natural environments (Cassava dataset), achieving an accuracy improvement of 6.80 ​% over the baseline. To validate the model's generalization performance, we prepare an out-of-distribution dataset with 21 categories, and our model notably increases the accuracy of this dataset. Extensive experiments demonstrate that our model exhibits superior performance over other models in few-shot plant disease identification.

Introduction: Nondestructive detection of crop phenotypic traits in the field is very important for crop breeding. Ground-based mobile platforms equipped with sensors can efficiently and accurately obtain crop phenotypic traits. In this study, we propose a dynamic 3D data acquisition method in the field suitable for various crops by using a consumer-grade RGB-D camera installed on a ground-based movable platform, which can collect RGB images as well as depth images of crop canopy sequences dynamically.Methods: A scale-invariant feature transform (SIFT) operator was used to detect adjacent date frames acquired by the RGB-D camera to calculate the point cloud alignment coarse matching matrix and the displacement distance of adjacent images. The data frames used for point cloud matching were selected according to the calculated displacement distance. Then, the colored ICP (iterative closest point) algorithm was used to determine the fine matching matrix and generate point clouds of the crop row. The clustering method was applied to segment the point cloud of each plant from the crop row point cloud, and 3D phenotypic traits, including plant height, leaf area and projected area of individual plants, were measured.Results and Discussion: We compared the effects of LIDAR and image-based 3D reconstruction methods, and experiments were carried out on corn, tobacco, cottons and Bletilla striata in the seedling stage. The results show that the measurements of the plant height (R²= 0.9~0.96, RSME = 0.015~0.023 m), leaf area (R²= 0.8~0.86, RSME = 0.0011~0.0041 m² ) and projected area (R² = 0.96~0.99) have strong correlations with the manual measurement results. Additionally, 3D reconstruction results with different moving speeds and times throughout the day and in different scenes were also verified. The results show that the method can be applied to dynamic detection with a moving speed up to 0.6 m/s and can achieve acceptable detection results in the daytime, as well as at night. Thus, the proposed method can improve the efficiency of individual crop 3D point cloud data extraction with acceptable accuracy, which is a feasible solution for crop seedling 3D phenotyping outdoors.

Three-dimensional (3D) laser point cloud technology is an important research method in the field of agricultural remote sensing research. The collection and processing technology of terrestrial light detection and ranging (LiDAR) point cloud of crops has greatly promoted the integration of agricultural informatization and intelligence. In a smart farmland based on 3D modern agriculture, the manager can efficiently and conveniently achieve the growth status of crops through the point cloud collection system and processing model integrated in the smart agricultural system. To this end, we took field maize as the research object in this study and processed four sets of field maize point clouds, named Maize-01, Maize-02, Maize-03, and Maize-04, respectively. In this research, we established a field individual maize segmentation model with the density-based clustering algorithm (DBSCAN) as the core, and four groups of field maize were used as research objects. Among them, the value of the overall accuracy (OA) index, which was used to evaluate the comprehensive performance of the model, were 0.98, 0.97, 0.95, and 0.94. Secondly, the multi-condition identification method was used to separate different maize organ point clouds from the individual maize point cloud. In addition, the organ stratification model of field maize was established. In this organ stratification study, we take Maize-04 as the research object and obtained the recognition accuracy rates of four maize organs: tassel, stalk, ear, and leaf at 96.55%, 100%, 100%, and 99.12%, respectively. We also finely segmented the leaf organ obtained from the above-mentioned maize organ stratification model into each leaf individual again. We verified the accuracy of the leaf segmentation method with the leaf length as the representative. In the linear analysis of predicted values of leaf length, $R^2$ was 0.73, $RMSE$ was 0.12 m, and $MAE$ was 0.07 m. In this study, we examined the segmentation of individual crop fields and established 3D information interpretations for crops in the field as well as for crop organs. Results visualized the real scene of the field, which is conducive to analyzing the response mechanism of crop growth and development to various complex environmental factors.