Automated inter-plant spacing sensing of corn plant seedlings and quantification of laying hen behaviors using 3D computer vision

Within-row plant spacing plays an important role in uniform distribution of water and nutrients among plants, hence affects the final crop yield. While manual in-field manual measurements of within-row plant spacing is time and labor intensive, little work has been carried out to automate the process. An automated system is developed using a state-of-the-art 3D vision sensor that accurately measures within-row corn plant spacing. The system is capable of processing about 1200 images captured from a 61 m crop row containing approximately 280 corn plants in about three and half minutes. Stocking density of laying hens in egg production remains an area of investigation from the standpoints of ensuring hen\u27s ability to perform natural behaviors and production economic efficiency. It is therefore of socio-economic importance to quantify the effect of stocking density on laying hens behaviors and thus wellbeing. In this study, a novel method for automatic quantification of stocking density effect on some natural laying hen behaviors such as locomotion, perching, feeding, drinking and nesting is explored. Image processing techniques are employed on top view images captured with a state-of-the-art time-of-flight (TOF) of light based 3D vision camera for identification as well as tracking of individual hens housed in a 1.2 m 1.2 m pen. A Radio Frequency Identification (RFID) sensor grid consisting of 20 antennas installed underneath the pen floor is used as a recovery system in situations where the imaging system fails to maintain identities of the hens

Photoelastic force measurements in granular materials

Photoelastic techniques are used to make both qualitative and quantitative measurements of the forces within idealized granular materials. The method is based on placing a birefringent granular material between a pair of polarizing filters, so that each region of the material rotates the polarization of light according to the amount of local of stress. In this review paper, we summarize past work using the technique, describe the optics underlying the technique, and illustrate how it can be used to quantitatively determine the vector contact forces between particles in a 2D granular system. We provide a description of software resources available to perform this task, as well as key techniques and resources for building an experimental apparatus

Prediction of Early Vigor from Overhead Images of Carinata Plants

Breeding more resilient, higher yielding crops is an essential component of ensuring ongoing food security. Early season vigor is signi cantly correlated with yields and is often used as an early indicator of tness in breeding programs. Early vigor can be a useful indicator of the health and strength of plants with bene ts such as improved light interception, reduced surface evaporation, and increased biological yield. However, vigor is challenging to measure analytically and is often rated using subjective visual scoring. This traditional method of breeder scoring becomes cumbersome as the size of breeding programs increase. In this study, we used hand-held cameras tted on gimbals to capture images which were then used as the source for automated vigor scoring. We have employed a novel image metric, the extent of plant growth from the row centerline, as an indicator of vigor. Along with this feature, additional features were used for training a random forest model and a support vector machine, both of which were able to predict expert vigor ratings with an 88:9% and 88% accuracies respectively, providing the potential for more reliable, higher throughput vigor estimates

Low-cost and automated phenotyping system “Phenomenon” for multi-sensor in situ monitoring in plant in vitro culture

Background: The current development of sensor technologies towards ever more cost-effective and powerful systems is steadily increasing the application of low-cost sensors in different horticultural sectors. In plant in vitro culture, as a fundamental technique for plant breeding and plant propagation, the majority of evaluation methods to describe the performance of these cultures are based on destructive approaches, limiting data to unique endpoint measurements. Therefore, a non-destructive phenotyping system capable of automated, continuous and objective quantification of in vitro plant traits is desirable. Results: An automated low-cost multi-sensor system acquiring phenotypic data of plant in vitro cultures was developed and evaluated. Unique hardware and software components were selected to construct a xyz-scanning system with an adequate accuracy for consistent data acquisition. Relevant plant growth predictors, such as projected area of explants and average canopy height were determined employing multi-sensory imaging and various developmental processes could be monitored and documented. The validation of the RGB image segmentation pipeline using a random forest classifier revealed very strong correlation with manual pixel annotation. Depth imaging by a laser distance sensor of plant in vitro cultures enabled the description of the dynamic behavior of the average canopy height, the maximum plant height, but also the culture media height and volume. Projected plant area in depth data by RANSAC (random sample consensus) segmentation approach well matched the projected plant area by RGB image processing pipeline. In addition, a successful proof of concept for in situ spectral fluorescence monitoring was achieved and challenges of thermal imaging were documented. Potential use cases for the digital quantification of key performance parameters in research and commercial application are discussed. Conclusion: The technical realization of “Phenomenon” allows phenotyping of plant in vitro cultures under highly challenging conditions and enables multi-sensory monitoring through closed vessels, ensuring the aseptic status of the cultures. Automated sensor application in plant tissue culture promises great potential for a non-destructive growth analysis enhancing commercial propagation as well as enabling research with novel digital parameters recorded over time

Automatic Retrieval of Skeletal Structures of Trees from Terrestrial Laser Scanner Data

Research on forest ecosystems receives high attention, especially nowadays with regard to sustainable management of renewable resources and the climate change. In particular, accurate information on the 3D structure of a tree is important for forest science and bioclimatology, but also in the scope of commercial applications. Conventional methods to measure geometric plant features are labor- and time-intensive. For detailed analysis, trees have to be cut down, which is often undesirable. Here, Terrestrial Laser Scanning (TLS) provides a particularly attractive tool because of its contactless measurement technique. The object geometry is reproduced as a 3D point cloud. The objective of this thesis is the automatic retrieval of the spatial structure of trees from TLS data. We focus on forest scenes with comparably high stand density and with many occlusions resulting from it. The varying level of detail of TLS data poses a big challenge. We present two fully automatic methods to obtain skeletal structures from scanned trees that have complementary properties. First, we explain a method that retrieves the entire tree skeleton from 3D data of co-registered scans. The branching structure is obtained from a voxel space representation by searching paths from branch tips to the trunk. The trunk is determined in advance from the 3D points. The skeleton of a tree is generated as a 3D line graph. Besides 3D coordinates and range, a scan provides 2D indices from the intensity image for each measurement. This is exploited in the second method that processes individual scans. Furthermore, we introduce a novel concept to manage TLS data that facilitated the researchwork. Initially, the range image is segmented into connected components. We describe a procedure to retrieve the boundary of a component that is capable of tracing inner depth discontinuities. A 2D skeleton is generated from the boundary information and used to decompose the component into sub components. A Principal Curve is computed from the 3D point set that is associated with a sub component. The skeletal structure of a connected component is summarized as a set of polylines. Objective evaluation of the results remains an open problem because the task itself is ill-defined: There exists no clear definition of what the true skeleton should be w.r.t. a given point set. Consequently, we are not able to assess the correctness of the methods quantitatively, but have to rely on visual assessment of results and provide a thorough discussion of the particularities of both methods. We present experiment results of both methods. The first method efficiently retrieves full skeletons of trees, which approximate the branching structure. The level of detail is mainly governed by the voxel space and therefore, smaller branches are reproduced inadequately. The second method retrieves partial skeletons of a tree with high reproduction accuracy. The method is sensitive to noise in the boundary, but the results are very promising. There are plenty of possibilities to enhance the method’s robustness. The combination of the strengths of both presented methods needs to be investigated further and may lead to a robust way to obtain complete tree skeletons from TLS data automatically.Die Erforschung des ÖkosystemsWald spielt gerade heutzutage im Hinblick auf den nachhaltigen Umgang mit nachwachsenden Rohstoffen und den Klimawandel eine große Rolle. Insbesondere die exakte Beschreibung der dreidimensionalen Struktur eines Baumes ist wichtig für die Forstwissenschaften und Bioklimatologie, aber auch im Rahmen kommerzieller Anwendungen. Die konventionellen Methoden um geometrische Pflanzenmerkmale zu messen sind arbeitsintensiv und zeitaufwändig. Für eine genaue Analyse müssen Bäume gefällt werden, was oft unerwünscht ist. Hierbei bietet sich das Terrestrische Laserscanning (TLS) als besonders attraktives Werkzeug aufgrund seines kontaktlosen Messprinzips an. Die Objektgeometrie wird als 3D-Punktwolke wiedergegeben. Basierend darauf ist das Ziel der Arbeit die automatische Bestimmung der räumlichen Baumstruktur aus TLS-Daten. Der Fokus liegt dabei auf Waldszenen mit vergleichsweise hoher Bestandesdichte und mit zahlreichen daraus resultierenden Verdeckungen. Die Auswertung dieser TLS-Daten, die einen unterschiedlichen Grad an Detailreichtum aufweisen, stellt eine große Herausforderung dar. Zwei vollautomatische Methoden zur Generierung von Skelettstrukturen von gescannten Bäumen, welche komplementäre Eigenschaften besitzen, werden vorgestellt. Bei der ersten Methode wird das Gesamtskelett eines Baumes aus 3D-Daten von registrierten Scans bestimmt. Die Aststruktur wird von einer Voxelraum-Repräsentation abgeleitet indem Pfade von Astspitzen zum Stamm gesucht werden. Der Stamm wird im Voraus aus den 3D-Punkten rekonstruiert. Das Baumskelett wird als 3D-Liniengraph erzeugt. Für jeden gemessenen Punkt stellt ein Scan neben 3D-Koordinaten und Distanzwerten auch 2D-Indizes zur Verfügung, die sich aus dem Intensitätsbild ergeben. Bei der zweiten Methode, die auf Einzelscans arbeitet, wird dies ausgenutzt. Außerdem wird ein neuartiges Konzept zum Management von TLS-Daten beschrieben, welches die Forschungsarbeit erleichtert hat. Zunächst wird das Tiefenbild in Komponenten aufgeteilt. Es wird eine Prozedur zur Bestimmung von Komponentenkonturen vorgestellt, die in der Lage ist innere Tiefendiskontinuitäten zu verfolgen. Von der Konturinformation wird ein 2D-Skelett generiert, welches benutzt wird um die Komponente in Teilkomponenten zu zerlegen. Von der 3D-Punktmenge, die mit einer Teilkomponente assoziiert ist, wird eine Principal Curve berechnet. Die Skelettstruktur einer Komponente im Tiefenbild wird als Menge von Polylinien zusammengefasst. Die objektive Evaluation der Resultate stellt weiterhin ein ungelöstes Problem dar, weil die Aufgabe selbst nicht klar erfassbar ist: Es existiert keine eindeutige Definition davon was das wahre Skelett in Bezug auf eine gegebene Punktmenge sein sollte. Die Korrektheit der Methoden kann daher nicht quantitativ beschrieben werden. Aus diesem Grund, können die Ergebnisse nur visuell beurteiltwerden. Weiterhinwerden die Charakteristiken beider Methoden eingehend diskutiert. Es werden Experimentresultate beider Methoden vorgestellt. Die erste Methode bestimmt effizient das Skelett eines Baumes, welches die Aststruktur approximiert. Der Detaillierungsgrad wird hauptsächlich durch den Voxelraum bestimmt, weshalb kleinere Äste nicht angemessen reproduziert werden. Die zweite Methode rekonstruiert Teilskelette eines Baums mit hoher Detailtreue. Die Methode reagiert sensibel auf Rauschen in der Kontur, dennoch sind die Ergebnisse vielversprechend. Es gibt eine Vielzahl von Möglichkeiten die Robustheit der Methode zu verbessern. Die Kombination der Stärken von beiden präsentierten Methoden sollte weiter untersucht werden und kann zu einem robusteren Ansatz führen um vollständige Baumskelette automatisch aus TLS-Daten zu generieren

The development and evaluation of computer vision algorithms for the control of an autonomous horticultural vehicle

Economic and environmental pressures have led to a demand for reduced chemical use in crop production. In response to this, precision agriculture techniques have been developed that aim to increase the efficiency of farming operations by more targeted application of chemical treatment. The concept of plant scale husbandry (PSH) has emerged as the logical extreme of precision techniques, where crop and weed plants are treated on an individual basis. To investigate the feasibility of PSH, an autonomous horticultural vehicle has been developed at the Silsoe Research Institute. This thesis describes the development of computer vision algorithms for the experimental vehicle which aim to aid navigation in the field and also allow differential treatment of crop and weed. The algorithm, based upon an extended Kalman filter, exploits the semi-structured nature of the field environment in which the vehicle operates, namely the grid pattern formed by the crop planting. By tracking this grid pattern in the images captured by the vehicles camera as it traverses the field, it is possible to extract information to aid vehicle navigation, such as bearing and offset from the grid of plants. The grid structure can also act as a cue for crop/weed discrimination on the basis of plant position on the ground plane. In addition to tracking the grid pattern, the Kalman filter also estimates the mean distances between the rows of lines and plants in the grid, to cater for variations in the planting procedure. Experiments are described which test the localisation accuracy of the algorithms in offline trials with data captured from the vehicle's camera, and on-line in both a simplified testbed environment and the field. It is found that the algorithms allow safe navigation along the rows of crop. Further experiments demonstrate the crop/weed discrimination performance of the algorithm, both off-line and on-line in a crop treatment experiment performed in the field where all of the crop plants are correctly targeted and no weeds are mistakenly treated

Improving water utilization from a catchment perspective

Water management / Water scarcity / Water use efficiency / Catchment areas / Calibrations / Hydrology / Models / River basins / Participatory management / Water balance / Case studies / Asia / Africa / South Africa / Zimbabwe

Terrestrial laser scanning for vegetation analyses with a special focus on savannas

Savannas are heterogeneous ecosystems, composed of varied spatial combinations and proportions of woody and herbaceous vegetation. Most field-based inventory and remote sensing methods fail to account for the lower stratum vegetation (i.e., shrubs and grasses), and are thus underrepresenting the carbon storage potential of savanna ecosystems. For detailed analyses at the local scale, Terrestrial Laser Scanning (TLS) has proven to be a promising remote sensing technology over the past decade. Accordingly, several review articles already exist on the use of TLS for characterizing 3D vegetation structure. However, a gap exists on the spatial concentrations of TLS studies according to biome for accurate vegetation structure estimation. A comprehensive review was conducted through a meta-analysis of 113 relevant research articles using 18 attributes. The review covered a range of aspects, including the global distribution of TLS studies, parameters retrieved from TLS point clouds and retrieval methods. The review also examined the relationship between the TLS retrieval method and the overall accuracy in parameter extraction. To date, TLS has mainly been used to characterize vegetation in temperate, boreal/taiga and tropical forests, with only little emphasis on savannas. TLS studies in the savanna focused on the extraction of very few vegetation parameters (e.g., DBH and height) and did not consider the shrub contribution to the overall Above Ground Biomass (AGB). Future work should therefore focus on developing new and adjusting existing algorithms for vegetation parameter extraction in the savanna biome, improving predictive AGB models through 3D reconstructions of savanna trees and shrubs as well as quantifying AGB change through the application of multi-temporal TLS. The integration of data from various sources and platforms e.g., TLS with airborne LiDAR is recommended for improved vegetation parameter extraction (including AGB) at larger spatial scales. The review highlights the huge potential of TLS for accurate savanna vegetation extraction by discussing TLS opportunities, challenges and potential future research in the savanna biome