A 3D printed plant model for accurate and reliable 3D plant phenotyping.

BACKGROUND: This study addresses the importance of precise referencing in 3-dimensional (3D) plant phenotyping, which is crucial for advancing plant breeding and improving crop production. Traditionally, reference data in plant phenotyping rely on invasive methods. Recent advancements in 3D sensing technologies offer the possibility to collect parameters that cannot be referenced by manual measurements. This work focuses on evaluating a 3D printed sugar beet plant model as a referencing tool. RESULTS: Fused deposition modeling has turned out to be a suitable 3D printing technique for creating reference objects in 3D plant phenotyping. Production deviations of the created reference model were in a low and acceptable range. We were able to achieve deviations ranging from -10 mm to +5 mm. In parallel, we demonstrated a high-dimensional stability of the reference model, reaching only ±4 mm deformation over the course of 1 year. Detailed print files, assembly descriptions, and benchmark parameters are provided, facilitating replication and benefiting the research community. CONCLUSION: Consumer-grade 3D printing was utilized to create a stable and reproducible 3D reference model of a sugar beet plant, addressing challenges in referencing morphological parameters in 3D plant phenotyping. The reference model is applicable in 3 demonstrated use cases: evaluating and comparing 3D sensor systems, investigating the potential accuracy of parameter extraction algorithms, and continuously monitoring these algorithms in practical experiments in greenhouse and field experiments. Using this approach, it is possible to monitor the extraction of a nonverifiable parameter and create reference data. The process serves as a model for developing reference models for other agricultural crops.

UAV-based individual plant detection and geometric parameter extraction in vineyards.

Accurately characterizing vineyard parameters is crucial for precise vineyard management and breeding purposes. Various macroscopic vineyard parameters are required to make informed management decisions, such as pesticide application, defoliation strategies, and determining optimal sugar content in each berry by assessing biomass. In this paper, we present a novel approach that utilizes point cloud data to detect trunk positions and extract macroscopic vineyard characteristics, including plant height, canopy width, and canopy volume. Our approach relies solely on geometric features and is compatible with different training systems and data collected using various 3D sensors. To evaluate the effectiveness and robustness of our proposed approach, we conducted extensive experiments on multiple grapevine rows trained in two different systems. Our method provides more comprehensive canopy characteristics than traditional manual measurements, which are not representative throughout the row. The experimental results demonstrate the accuracy and efficiency of our method in extracting vital macroscopic vineyard characteristics, providing valuable insights for yield monitoring, grape quality optimization, and strategic interventions to enhance vineyard productivity and sustainability.

Pheno4D: A spatio-temporal dataset of maize and tomato plant point clouds for phenotyping and advanced plant analysis.

Understanding the growth and development of individual plants is of central importance in modern agriculture, crop breeding, and crop science. To this end, using 3D data for plant analysis has gained attention over the last years. High-resolution point clouds offer the potential to derive a variety of plant traits, such as plant height, biomass, as well as the number and size of relevant plant organs. Periodically scanning the plants even allows for performing spatio-temporal growth analysis. However, highly accurate 3D point clouds from plants recorded at different growth stages are rare, and acquiring this kind of data is costly. Besides, advanced plant analysis methods from machine learning require annotated training data and thus generate intense manual labor before being able to perform an analysis. To address these issues, we present with this dataset paper a multi-temporal dataset featuring high-resolution registered point clouds of maize and tomato plants, which we manually labeled for computer vision tasks, such as for instance segmentation and 3D reconstruction, providing approximately 260 million labeled 3D points. To highlight the usability of the data and to provide baselines for other researchers, we show a variety of applications ranging from point cloud segmentation to non-rigid registration and surface reconstruction. We believe that our dataset will help to develop new algorithms to advance the research for plant phenotyping, 3D reconstruction, non-rigid registration, and deep learning on raw point clouds. The dataset is freely accessible at https://www.ipb.uni-bonn.de/data/pheno4d/.

An Integrated Positioning and Attitude Determination System for Immersed Tunnel Elements: A Simulation Study.

Immersed tunnel elements need to be exactly controlled during their immersion process. Position and attitude of the element should be determined quickly and accurately to navigate the element from the holding area to the final location in the tunnel trench. In this paper, a newly-developed positioning and attitude determination system, integrating a 3-antenna Global Navigation Satellite System (GNSS) system, an inclinometer and a range-measurement system, is presented. The system is designed to provide the absolute position of both ends of the element with sufficient accuracy in real time. Special attention in the accuracy analysis is paid to the influence of GNSS multipath error and sound speed profile. Simulations are conducted to illustrate the performance of the system in different scenarios. If both elements are very close, the accuracies of the system are higher than 0.02 m in the directions perpendicular to and along the tunnel axis.

Plant, space and time - linked together in an integrative and scalable data management system for phenomic approaches in agronomic field trials.

BACKGROUND: To ensure further genetic gain, genomic approaches in plant breeding rely on precise phenotypic data, describing plant structure, function and performance. A more precise characterization of the environment will allow a better dealing with genotype-by-environment-by-management interactions. Therefore, space and time dependencies of the crop production processes have to be considered. The use of novel sensor technologies has drastically increased the amount and diversity of phenotypic data from agronomic field trials. Existing data management systems either do not consider space and time, are not customizable to individual needs such as field trial handling, or have restricted availability. Hence, we propose an integrative data management and information system (DMIS) for handling of traditional and novel sensor-based phenotypic, environmental and management data. The DMIS must be customizable, applicable and scalable from individual users to organizations. RESULTS: Key element of the system is a dynamic PostgreSQL database with GIS-extension, capable of importing, storing and managing all types of data including images. The database references every structural database object and measurement in a threefold approach with semantic, spatial and temporal reference. Timestamps and geo-coordinates allow automated linking of all data. Traits can be precisely defined individually or uploaded as predefined lists. Filtering and selection routines allow compilation of all data for visualization via tables, charts or maps and for export and external statistical analysis. New possibilities of environmental information-based planning of field trials, weather-guided phenotyping and data analysis for outlier or hot-spot detection are demonstrated. CONCLUSIONS: The DMIS supports users in handling experimental field trials with crop plants and modern phenotyping methods. It focuses on linking all space and time dependent processes of plant production. Weather, soil and management, as well as growth and yield formation of the plants can be depicted, thus allowing a more precise interpretation of the results in relation to environment and management. Breeders, extension specialists, official testing agencies and agricultural scientists are assisted in all steps of a typical workflow with planning, designing, conducting, controlling and analyzing field trials to generate new information for decision support in the crop improvement process.

GPS Multipath Analysis Using Fresnel Zones.

GNSS (Global Navigation Satellite Systems) multipath has been subject to scientific research for decades and although numerous methods and techniques have already been developed to mitigate this effect, it is still one of the accuracy-limiting factors in many GNSS applications. Since multipath is highly dependent on the individual antenna environment, there is still a need for new methods and further investigations to increase the understanding of this systematic effect. In this paper, the concept of Fresnel zones is applied to two different aspects of multipath. First, Fresnel zones are determined for the line-of-sight transmission between satellite and receiver. By comparing the boundary of the Fresnel zones to an obstruction adaptive elevation mask, potentially diffracted signals can be identified and excluded from the position estimation process. Both the percentage of epochs with fixed ambiguities and the positioning accuracy can be increased by the proposed method. Second, Fresnel zones are used to analyze the multipath induced by a horizontal and spatially-limited reflector. The comparison of simulated and real signal-to-noise (SNR) observations reveals a relationship between the percentage of the overlap of the Fresnel zone and reflector and the occurrence of multipath. It is found that an overlap of 50% is sufficient to induce multipath effects. This is of special interest, since this does not confirm theoretical assumptions of the multipath theory.

Phenoliner: A New Field Phenotyping Platform for Grapevine Research.

In grapevine research the acquisition of phenotypic data is largely restricted to the field due to its perennial nature and size. The methodologies used to assess morphological traits and phenology are mainly limited to visual scoring. Some measurements for biotic and abiotic stress, as well as for quality assessments, are done by invasive measures. The new evolving sensor technologies provide the opportunity to perform non-destructive evaluations of phenotypic traits using different field phenotyping platforms. One of the biggest technical challenges for field phenotyping of grapevines are the varying light conditions and the background. In the present study the Phenoliner is presented, which represents a novel type of a robust field phenotyping platform. The vehicle is based on a grape harvester following the concept of a moveable tunnel. The tunnel it is equipped with different sensor systems (RGB and NIR camera system, hyperspectral camera, RTK-GPS, orientation sensor) and an artificial broadband light source. It is independent from external light conditions and in combination with artificial background, the Phenoliner enables standardised acquisition of high-quality, geo-referenced sensor data.

Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions.

In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter.

Real-time single-frequency GPS/MEMS-IMU attitude determination of lightweight UAVs.

In this paper, a newly-developed direct georeferencing system for the guidance, navigation and control of lightweight unmanned aerial vehicles (UAVs), having a weight limit of 5 kg and a size limit of 1.5 m, and for UAV-based surveying and remote sensing applications is presented. The system is intended to provide highly accurate positions and attitudes (better than 5 cm and 0.5°) in real time, using lightweight components. The main focus of this paper is on the attitude determination with the system. This attitude determination is based on an onboard single-frequency GPS baseline, MEMS (micro-electro-mechanical systems) inertial sensor readings, magnetic field observations and a 3D position measurement. All of this information is integrated in a sixteen-state error space Kalman filter. Special attention in the algorithm development is paid to the carrier phase ambiguity resolution of the single-frequency GPS baseline observations. We aim at a reliable and instantaneous ambiguity resolution, since the system is used in urban areas, where frequent losses of the GPS signal lock occur and the GPS measurement conditions are challenging. Flight tests and a comparison to a navigation-grade inertial navigation system illustrate the performance of the developed system in dynamic situations. Evaluations show that the accuracies of the system are 0.05° for the roll and the pitch angle and 0.2° for the yaw angle. The ambiguities of the single-frequency GPS baseline can be resolved instantaneously in more than 90% of the cases.

Wavelet based approach for posture transition estimation using a waist worn accelerometer.

The ability to rise from a chair is considered to be important to achieve functional independence and quality of life. This sit-to-stand task is also a good indicator to assess condition of patients with chronic diseases. We developed a wavelet based algorithm for detecting and calculating the durations of sit-to-stand and stand-to-sit transitions from the signal vector magnitude of the measured acceleration signal. The algorithm was tested on waist worn accelerometer data collected from young subjects as well as geriatric patients. The test demonstrates that both transitions can be detected by using wavelet transformation applied to signal magnitude vector. Wavelet analysis produces an estimate of the transition pattern that can be used to calculate the transition duration that further gives clinically significant information on the patients condition. The method can be applied in a real life ambulatory monitoring system for assessing the condition of a patient living at home.