Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Cyber-Agricultural Systems for Crop Breeding and Sustainable Production

The Cyber-Agricultural System (CAS) Represents an overarching Framework of Agriculture that Leverages Recent Advances in Ubiquitous Sensing, Artificial Intelligence, Smart Actuators, and Scalable Cyberinfrastructure (CI) in Both Breeding and Production Agriculture. We Discuss the Recent Progress and Perspective of the Three Fundamental Components of CAS – Sensing, Modeling, and Actuation – and the Emerging Concept of Agricultural Digital Twins (DTs). We Also Discuss How Scalable CI is Becoming a Key Enabler of Smart Agriculture. in This Review We Shed Light on the Significance of CAS in Revolutionizing Crop Breeding and Production by Enhancing Efficiency, Productivity, Sustainability, and Resilience to Changing Climate. Finally, We Identify Underexplored and Promising Future Directions for CAS Research and Development

On the evaluation of methods for the recovery of plant root systems from X-ray computed tomography images

X-ray micro computed tomography (µCT) allows non-destructive visualisation of plant root systems within their soil environment and thus offers an alternative to commonly used destructive methodologies for the examination of plant roots and their interaction with the surrounding soil. Various methods for the recovery of root system information from X-ray CT image data have been presented in the literature. Detailed, ideally quantitative, evaluation is essential, in order to determine the accuracy and limitations of the proposed methods, and to allow potential users to make informed choices between them. This, however, is a complicated task. Three-dimensional ground truth data is expensive to produce, and the complexity of X-ray CT data means that manually generated ground truth may not be definitive. Similarly, artificially generated data is not entirely representative of real samples. The aims of this work are to raise awareness of the evaluation problem and to propose experimental approaches that allow the performance of root extraction methods to be assessed, ultimately improving the techniques available. To illustrate the issues, tests are conducted using both artificially generated images and real data samples

Automated procedures for quantification of rhizosphere physical properties in micro CT images

The rhizosphere, i.e. the zone of soil immediately surrounding plant roots plays a prominent role in supplying plants with water and nutrients. However, surprisingly little is known about rhizosphere physical properties and how they affect root growth, water and nutrient uptake. The lack of non-invasive and non-destructive imaging techniques necessary to observe living roots growing in undisturbed soil have been a main reason for this shortcoming. Recent advances in synchrotron X-ray micro tomography (CMT) provide the potential to directly observe soil physical properties around living roots in-situ.In this work we develop procedures for assisting scientist to study the soil properties by visualizing and automatically processing micro CT images. Specifically image de-noising in the wavelet domain is performed for convenient profiling and segmentation is applied for automated calculation of soil properties. As new measures we proposed the normalized radial and circular aggregation and water transportability and also have shown ways of generalizing the studies for 3D

Nondestructive measurement of fruit and vegetable quality

We review nondestructive techniques for measuring internal and external quality attributes of fruit and vegetables, such as color, size and shape, flavor, texture, and absence of defects. The different techniques are organized according to their physical measurement principle. We first describe each technique and then list some examples. As many of these techniques rely on mathematical models and particular data processing methods, we discuss these where needed. We pay particular attention to techniques that can be implemented online in grading lines

High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms

Towards automated phenotyping in plant tissue culture

Plant in vitro culture techniques comprise important fundamental methods of modern plant research, propagation and breeding. Innovative scientific approaches to further develop the cultivation process, therefore, have the potential of far-reaching impact on many different areas. In particular, automation can increase efficiency of in vitro propagation, a domain currently con-strained by intensive manual labor. Automated phenotyping of plant in vitro culture bears the potential to extend the evaluation of in vitro plants from manual destructive endpoint measurements to continuous and objective digital quantification of plant traits. Consequently, this can lead to a better understanding of crucial developmental processes and will help to clarify the emergence of physiological disorders of plant in vitro cultures. The aim of this dissertation was to investigate and exemplify the potential of optical sensing methods and machine learning in plant in vitro culture from an interdisciplinary point of view. A novel robotic phenotyping system for automated, non-destructive, multi-dimensional in situ detection of plant traits based on low-cost sensor technology was con-ceptualized, developed and tested. Various sensor technologies, including an RGB camera, a laser distance sensor, a micro spectrometer, and a thermal camera, were applied partly for the first time under these challenging conditions and evaluated with respect to the resulting data quality and feasibility. In addition to the development of new dynamic, semi-automated data processing pipelines, the automatic acquisition of multisensory data across an entire subculture passage of plant in vitro cultures was demonstrated. This allowed novel time series images of different developmental processes of plant in vitro cultures and the emergence of physiological disorders to be captured in situ for the first time. The digital determination of relevant parameters such as projected plant area, average canopy height, and maximum plant height, was demonstrated, which can be used as critical descriptors of plant growth performance in vitro. In addition, a novel method of non-destructive quantification of media volume by depth data was developed which may allow monitoring of water uptake by plants and evaporation from the culture medium. The phenotyping system was used to investigate the etiology of the physiological growth anomaly hyperhydricity. Therefore, digital monitoring of the morphology and along with spectro-scopic studies of reflectance behavior over time were conducted. The new optical characteristics identified by classical spectral analysis, such as reduced reflectance and major absorption peaks of hyperhydricity in the SWIR region could be validated to be the main discriminating features by a trained support vector machine with a balanced accuracy of 84% on test set, demonstrating the feasibility of a spectral detection of hyperhydricity. In addition, an RGB image dataset was used for automated detection of hyperhydricity using deep neural networks. The high-performance metrics with precision of 83.8% and recall of 95.7% on test images underscore the presence of for detection sufficient number of discriminating features within the spatial RGB data, thus a second approach is proposed for automatic detection of hyperhydricity based on RGB images. The resulting multimodal sensor data sets of the robotic phenotyping system were tested as a supporting tool of an e-learning module in higher education to increase the digital skills in the field of sensing, data processing and data analysis, and evaluated by means of a student survey. This proof-of-concept study revealed an overall high level of acceptance and advocacy by students with 70% good to very good rating. However, with increased complexity of the learning task, stu-dents experienced excessive demands and rated the respective session lower. In summary, this study is expected to pave the way for increased use of automated sensor-based phenotyping in conjunction with machine learning in plant research and commercial mi-cropropagation in the future.Die pflanzliche In-vitro-Kultur umfasst wichtige grundlegende Methoden der modernen Pflanzenforschung, -vermehrung und -züchtung. Innovative wissenschaftliche Ansätze zur Wei-terentwicklung des Kultivierungsprozess können daher weitreichenden Einfluss auf viele unter-schiedliche Bereiche haben. Insbesondere die Automatisierung kann die Effizienz der In-vitro-Vermehrung steigern, die derzeit durch die intensive manuelle Arbeit beschränkt wird. Automa-tisierte Phänotypisierung von In-vitro-Kulturen ermöglicht es, die Erfassung von manuellen de-struktiven Endpunktmessungen auf eine kontinuierliche, objektive und digitale Quantifizierung der Pflanzenmerkmale auszuweiten. Dies kann zu einem besseren Verständnis entscheidender Entwicklungsprozesse führen und die Entstehung physiologischer Störungen zu klären. Ziel dieser Dissertation war es, das Potential optischer Erfassungsmethoden und des maschinellen Lernens für die pflanzliche In-vitro-Kultur unter interdisziplinären Gesichtspunk-ten zu untersuchen und exemplarisch aufzuzeigen. Ein neuartiger Phänotypisierungsroboter zur automatisierten, zerstörungsfreien, mehrdimensionalen In-situ-Erfassung von Pflanzenmerkmalen wurde auf Basis kostengünstiger Sensortechnik entwickelt. Unterschiedliche Sensortechnologien, darunter eine RGB-Kamera, ein Laser-Distanzsensor, ein Mikrospektrometer und eine Wärmebildkamera, wurden teils zum ersten Mal unter diesen schwierigen Bedingungen eingesetzt und im Hinblick auf die resultierende Datenqualität und Realisierbarkeit bewertet. Neben der Entwicklung dynamischer, halbautomatischer Datenverarbeitungspipelines, wurde die automatische Erfassung multisensorischer Daten über eine gesamte Subkulturpassage der In-vitro-Kulturen demonstriert. Dadurch konnte erstmals Zeitrafferaufnahmen verschiedener Ent-wicklungsprozesse von pflanzlichen In-vitro-Kulturen und das Auftreten von physiologischen Störungen in situ erfasst werden. Die digitale Bestimmung relevanter Kenngrößen wie der proji-zierten Pflanzenfläche, der durchschnittlichen Bestandshöhe und der maximalen Pflanzenhöhe wurde demonstriert, die als wichtige Deskriptoren für das pflanzliche Wachstum dienen können. Darüber hinaus konnte eine neue Methode für die Pflanzenwissenschaften entwickelt werden, um die Wasseraufnahme von Pflanzen und die Verdunstung von Kulturmedien auf der Grundlage einer zerstörungsfreien Quantifizierung des Medienvolumens zu überwachen. Der Phänotypisierungsroboter wurde zur Untersuchung der Entstehung der Wachs-tumsanomalie Hyperhydrizität eingesetzt. Hierfür wurden ein digitales Monitoring der Morpho-logie der Explantate mit begleitenden spektroskopischen Untersuchungen des Reflexionsverhal-tens im Zeitverlauf durchgeführt. Die durch Spektralanalyse identifizierten optischen Merkmale, wie den reduzierter Reflexionsgrad und die Hauptabsorptionspeaks der Hyperhydrizität in der SWIR-Region, konnten als die wichtigsten Unterscheidungsmerkmale durch ein Support-Vektor-Maschine-Model mit einer Genauigkeit von 84% auf dem Testsatz validiert werden und damit Machbarkeit der spektrale Identifizierung von Hyperhydrizität aufzeigen. Darüber wurde für die automatische Detektion der Hyperhydrizität auf Basis von RGB-Bildern ein neuronales Netz trainiert. Die hohen Kennzahlen im Testdatensatz wie die Präzision von 83,8 % und einem Recall von 95,7 % unterstreichen das Vorhandensein einer für die Erkennung ausreichenden Anzahl von Unterscheidungsmerkmalen innerhalb der räumlichen RGB-Daten. Somit konnte ein zweiter An-satz der automatischen Detektion von Hyperhydrizität durch RGB-Bilder präsentiert werden. Die resultierenden Sensordatensätze des Phänotypisierungsroboters wurden als unter-stützendes Werkzeug eines E-Learning Moduls zur Steigerung digitaler Kompetenzen im Bereich Sensortechnik, Datenverarbeitung und -auswertung in der Hochschulausbildung erprobt und an-hand der Befragung von Studierenden evaluiert. Diese Machbarkeitsstudie ergab eine insgesamt hohe Akzeptanz durch die Studierenden mit 70% guten bis sehr guten Bewertungen. Mit zuneh-mender Komplexität der Lernaufgabe fühlten sich die Studierenden jedoch überfordert und bewerteten die jeweilige Session schlechter. Zusammenfassend zielt diese Arbeit darauf ab den Weg für einen verstärkten Einsatz der automatisierten, sensorbasierten Phänotypisierung in Kombination mit den Techniken des ma-schinellen Lernens der Forschung und der kommerziellen Mikrovermehrung zukünftig zu ebnen.Bundesministerium für Ernährung und Landwirtschaft (BMEL)/Digitale Experimentierfelder/28DE103F18/E

Approaches to three-dimensional reconstruction of plant shoot topology and geometry

There are currently 805 million people classified as chronically undernourished, and yet the World’s population is still increasing. At the same time, global warming is causing more frequent and severe flooding and drought, thus destroying crops and reducing the amount of land available for agriculture. Recent studies show that without crop climate adaption, crop productivity will deteriorate. With access to 3D models of real plants it is possible to acquire detailed morphological and gross developmental data that can be used to study their ecophysiology, leading to an increase in crop yield and stability across hostile and changing environments. Here we review approaches to the reconstruction of 3D models of plant shoots from image data, consider current applications in plant and crop science, and identify remaining challenges. We conclude that although phenotyping is receiving an increasing amount of attention – particularly from computer vision researchers – and numerous vision approaches have been proposed, it still remains a highly interactive process. An automated system capable of producing 3D models of plants would significantly aid phenotyping practice, increasing accuracy and repeatability of measurements