Computer Vision Problems in 3D Plant Phenotyping

In recent years, there has been significant progress in Computer Vision based plant phenotyping (quantitative analysis of biological properties of plants) technologies. Traditional methods of plant phenotyping are destructive, manual and error prone. Due to non-invasiveness and non-contact properties as well as increased accuracy, imaging techniques are becoming state-of-the-art in plant phenotyping. Among several parameters of plant phenotyping, growth analysis is very important for biological inference. Automating the growth analysis can result in accelerating the throughput in crop production. This thesis contributes to the automation of plant growth analysis. First, we present a novel system for automated and non-invasive/non-contact plant growth measurement. We exploit the recent advancements of sophisticated robotic technologies and near infrared laser scanners to build a 3D imaging system and use state-of-the-art Computer Vision algorithms to fully automate growth measurement. We have set up a gantry robot system having 7 degrees of freedom hanging from the roof of a growth chamber. The payload is a range scanner, which can measure dense depth maps (raw 3D coordinate points in mm) on the surface of an object (the plant). The scanner can be moved around the plant to scan from different viewpoints by programming the robot with a specific trajectory. The sequence of overlapping images can be aligned to obtain a full 3D structure of the plant in raw point cloud format, which can be triangulated to obtain a smooth surface (triangular mesh), enclosing the original plant. We show the capability of the system to capture the well known diurnal pattern of plant growth computed from the surface area and volume of the plant meshes for a number of plant species. Second, we propose a technique to detect branch junctions in plant point cloud data. We demonstrate that using these junctions as feature points, the correspondence estimation can be formulated as a subgraph matching problem, and better matching results than state-of-the-art can be achieved. Also, this idea removes the requirement of a priori knowledge about rotational angles between adjacent scanning viewpoints imposed by the original registration algorithm for complex plant data. Before, this angle information had to be approximately known. Third, we present an algorithm to classify partially occluded leaves by their contours. In general, partial contour matching is a NP-hard problem. We propose a suboptimal matching solution and show that our method outperforms state-of-the-art on 3 public leaf datasets. We anticipate using this algorithm to track growing segmented leaves in our plant range data, even when a leaf becomes partially occluded by other plant matter over time. Finally, we perform some experiments to demonstrate the capability and limitations of the system and highlight the future research directions for Computer Vision based plant phenotyping

Computer Vision Problems in 3D Plant Phenotyping

In recent years, there has been significant progress in Computer Vision based plant phenotyping (quantitative analysis of biological properties of plants) technologies. Traditional methods of plant phenotyping are destructive, manual and error prone. Due to non-invasiveness and non-contact properties as well as increased accuracy, imaging techniques are becoming state-of-the-art in plant phenotyping. Among several parameters of plant phenotyping, growth analysis is very important for biological inference. Automating the growth analysis can result in accelerating the throughput in crop production. This thesis contributes to the automation of plant growth analysis. First, we present a novel system for automated and non-invasive/non-contact plant growth measurement. We exploit the recent advancements of sophisticated robotic technologies and near infrared laser scanners to build a 3D imaging system and use state-of-the-art Computer Vision algorithms to fully automate growth measurement. We have set up a gantry robot system having 7 degrees of freedom hanging from the roof of a growth chamber. The payload is a range scanner, which can measure dense depth maps (raw 3D coordinate points in mm) on the surface of an object (the plant). The scanner can be moved around the plant to scan from different viewpoints by programming the robot with a specific trajectory. The sequence of overlapping images can be aligned to obtain a full 3D structure of the plant in raw point cloud format, which can be triangulated to obtain a smooth surface (triangular mesh), enclosing the original plant. We show the capability of the system to capture the well known diurnal pattern of plant growth computed from the surface area and volume of the plant meshes for a number of plant species. Second, we propose a technique to detect branch junctions in plant point cloud data. We demonstrate that using these junctions as feature points, the correspondence estimation can be formulated as a subgraph matching problem, and better matching results than state-of-the-art can be achieved. Also, this idea removes the requirement of a priori knowledge about rotational angles between adjacent scanning viewpoints imposed by the original registration algorithm for complex plant data. Before, this angle information had to be approximately known. Third, we present an algorithm to classify partially occluded leaves by their contours. In general, partial contour matching is a NP-hard problem. We propose a suboptimal matching solution and show that our method outperforms state-of-the-art on 3 public leaf datasets. We anticipate using this algorithm to track growing segmented leaves in our plant range data, even when a leaf becomes partially occluded by other plant matter over time. Finally, we perform some experiments to demonstrate the capability and limitations of the system and highlight the future research directions for Computer Vision based plant phenotyping

PI‑Plat: a high‑resolution image‑based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits

Background: Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components. Results: The major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches. Conclusions: For harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals

Network trade-offs and homeostasis in Arabidopsis shoot architectures.

Understanding the optimization objectives that shape shoot architectures remains a critical problem in plant biology. Here, we performed 3D scanning of 152 Arabidopsis shoot architectures, including wildtype and 10 mutant strains, and we uncovered a design principle that describes how architectures make trade-offs between competing objectives. First, we used graph-theoretic analysis to show that Arabidopsis shoot architectures strike a Pareto optimal that can be captured as maximizing performance in transporting nutrients and minimizing costs in building the architecture. Second, we identify small sets of genes that can be mutated to shift the weight prioritizing one objective over the other. Third, we show that this prioritization weight feature is significantly less variable across replicates of the same genotype compared to other common plant traits (e.g., number of rosette leaves, total volume occupied). This suggests that this feature is a robust descriptor of a genotype, and that local variability in structure may be compensated for globally in a homeostatic manner. Overall, our work provides a framework to understand optimization trade-offs made by shoot architectures and provides evidence that these trade-offs can be modified genetically, which may aid plant breeding and selection efforts.Gatsby Charitable Foundation Grant number GAT3272

Cassava root crown phenotyping using three-dimension (3D) multi-view stereo reconstruction

Phenotypic analysis of cassava root crowns (CRCs) so far has been limited to visual inspection and very few measurements due to its laborious process in the feld. Here, we developed a platform for acquiring 3D CRC models using close-range photogrammetry for phenotypic analysis. The state of the art is a low cost and easy to set up 3D acquisition requiring only a background sheet, a reference object and a camera, compatible with feld experiments in remote areas. We tested diferent software with CRC samples, and Agisoft and Blender were the most suitable software for generating high-quality 3D models and data analysis, respectively. We optimized the workfow by testing diferent numbers of images for 3D reconstruction and found that a minimum of 25 images per CRC can provide high quality 3D models. Up to ten traits, including 3D crown volumes, 3D crown surface, root density, surface to-volume ratio, root numbers, root angle, crown diameter, cylinder soil volume, CRC compactness and root length can be extracted providing novel parameters for studying cassava storage roots. We applied this platform to partial-inbred cassava populations and demonstrated that our platform provides reliable 3D CRC modelling for phenotypic analysis, analysis of genetic variances and supporting breeding selection

Robotic Technologies for High-Throughput Plant Phenotyping: Contemporary Reviews and Future Perspectives

Phenotyping plants is an essential component of any effort to develop new crop varieties. As plant breeders seek to increase crop productivity and produce more food for the future, the amount of phenotype information they require will also increase. Traditional plant phenotyping relying on manual measurement is laborious, time-consuming, error-prone, and costly. Plant phenotyping robots have emerged as a high-throughput technology to measure morphological, chemical and physiological properties of large number of plants. Several robotic systems have been developed to fulfill different phenotyping missions. In particular, robotic phenotyping has the potential to enable efficient monitoring of changes in plant traits over time in both controlled environments and in the field. The operation of these robots can be challenging as a result of the dynamic nature of plants and the agricultural environments. Here we discuss developments in phenotyping robots, and the challenges which have been overcome and others which remain outstanding. In addition, some perspective applications of the phenotyping robots are also presented. We optimistically anticipate that autonomous and robotic systems will make great leaps forward in the next 10 years to advance the plant phenotyping research into a new era

Smart indoor plantation system using soil moisture sensor and light dependent resistor sensor

Plantation methods, including hydroponics, have been extensively used in agriculture. They also employed a time-based irrigation system for the plant. The goal of this project was to create a self-sustaining indoor plantation system that uses soil moisture sensor data to control the flow of water when the sensor detects that the soil is almost dry. Soil conditions are monitored, and crops are irrigated more efficiently with the help of this new technology. Water is conserved by just watering the plants when they absolutely need it, rather than watering them continually all the time as the traditional method would require. Light-dependent resistors are used to measure the brightness of the surroundings in this project. As a result, the grow light will be activated when the ambient light level drops. With the help of a soil moisture sensor and a light-dependent resistor (LDR), one can create a system that automatically waters and lights plants. Finally, the soil moisture sensor collects data for the sprinkler system and displays it on the LCD screen, and then the appropriate measures are taken. When the soil's humidity level is high, the water that flows will be stopped

In Vivo Human-Like Robotic Phenotyping of Leaf and Stem Traits in Maize and Sorghum in Greenhouse

In plant phenotyping, the measurement of morphological, physiological and chemical traits of leaves and stems is needed to investigate and monitor the condition of plants. The manual measurement of these properties is time consuming, tedious, error prone, and laborious. The use of robots is a new approach to accomplish such endeavors, which enables automatic monitoring with minimal human intervention. In this study, two plant phenotyping robotic systems were developed to realize automated measurement of plant leaf properties and stem diameter which could reduce the tediousness of data collection compare to manual measurements. The robotic systems comprised of a four degree of freedom (DOF) robotic manipulator and a Time-of-Flight (TOF) camera. Robotic grippers were developed to integrate an optical fiber cable (coupled to a portable spectrometer) for leaf spectral reflectance measurement, a thermistor for leaf temperature measurement, and a linear potentiometer for stem diameter measurement. An Image processing technique and deep learning method were used to identify grasping points on leaves and stems, respectively. The systems were tested in a greenhouse using maize and sorghum plants. The results from the leaf phenotyping robot experiment showed that leaf temperature measurements by the phenotyping robot were correlated with those measured manually by a human researcher (R2 = 0.58 for maize and 0.63 for sorghum). The leaf spectral measurements by the phenotyping robot predicted leaf chlorophyll, water content and potassium with moderate success (R2 ranged from 0.52 to 0.61), whereas the prediction for leaf nitrogen and phosphorus were poor. The total execution time to grasp and take measurements from one leaf was 35.5±4.4 s for maize and 38.5±5.7 s for sorghum. Furthermore, the test showed that the grasping success rate was 78% for maize and 48% for sorghum. The experimental results from the stem phenotyping robot demonstrated a high correlation between the manual and automated stem diameter measurements (R2 \u3e 0.98). The execution time for stem diameter measurement was 45.3 s. The system could successfully detect and localize, and also grasp the stem for all plants during the experiment. Both robots could decrease the tediousness of collecting phenotypes compare to manual measurements. The phenotyping robots can be useful to complement the traditional image-based high-throughput plant phenotyping in greenhouses by collecting in vivo morphological, physiological, and biochemical trait measurements for plant leaves and stems. Advisors: Yufeng Ge, Santosh Pitl

Height Measurement of Basil Crops for Smart Irrigation Applications in Greenhouses using Commercial Sensors

Plant height is a key phenotypic attribute that directly represents how well a plant grows. It can also be a useful parameter in computing other important features such as yield and biomass. As the number of greenhouses increase, the traditional method of measuring plant height requires more time and labor, which increases demand for developing a reliable and affordable method to perform automated height measurements of plants. This research is aimed to develop a solution to automatically measure plant height in greenhouses using low cost sensors and computer vision techniques. For this purpose, the performance of various depth sensing technologies was compared by considering the following: camera price, measurement resolution, the field of view and compatibility with the application requirements. After analyzing the alternatives, the decision was to use the Intel RealSense D435 3D Active IR Stereo Depth Camera. The algorithms developed were used to monitor plant growth of basil. Results demonstrated a promising performance of the developed system in practice