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

Automated Transverse Crack Mapping System with Optical Sensors and Big Data Analytics

Transverse cracks on bridge decks provide the path for chloride penetration and are the major reason for deck deterioration. For such reasons, collecting information related to the crack widths and spacing of transverse cracks are important. In this study, we focused on developing a data pipeline for automated crack detection using non-contact optical sensors. We developed a data acquisition system that is able to acquire data in a fast and simple way without obstructing traffic. Understanding that GPS is not always available and odometer sensor data can only provide relative positions along the direction of traffic, we focused on providing an alternative localization strategy only using optical sensors. In addition, to improve existing crack detection methods which mostly rely on the low-intensity and localized line-segment characteristics of cracks, we considered the direction and shape of the cracks to make our machine learning approach smarter. The proposed system may serve as a useful inspection tool for big data analytics because the system is easy to deploy and provides multiple properties of cracks. Progression of crack deterioration, if any, both in spatial and temporal scale, can be checked and compared if the system is deployed multiple times

Compact union of disjoint boxes: An efficient decomposition model for binary volumes

This paper presents in detail the CompactUnion of Disjoint Boxes (CUDB), a decomposition modelfor binary volumes that has been recently but brieflyintroduced. This model is an improved version of aprevious model called Ordered Union of Disjoint Boxes(OUDB). We show here, several desirable features thatthis model has versus OUDB, such as less unitary basicelements (boxes) and thus, a better efficiency in someneighborhood operations. We present algorithms forconversion to and from other models, and for basiccomputations as area (2D) or volume (3D). We alsopresent an efficient algorithm for connected-componentlabeling (CCL) that does not follow the classical two-passstrategy. Finally we present an algorithm for collision (oradjacency) detection in static environments. We test theefficiency of CUDB versus existing models with severaldatasets.Peer ReviewedPostprint (published version

A graph-theory-based C-space path planner for mobile robotic manipulators in close-proximity environments

In this thesis a novel guidance method for a 3-degree-of-freedom robotic manipulator arm in 3 dimensions for Improvised Explosive Device (IED) disposal has been developed. The work carried out in this thesis combines existing methods to develop a technique that delivers advantages taken from several other guidance techniques. These features are necessary for the IED disposal application. The work carried out in this thesis includes kinematic and dynamic modelling of robotic manipulators, T-space to C-space conversion, and path generation using Graph Theory to produce a guidance technique which can plan a safe path through a complex unknown environment. The method improves upon advantages given by other techniques in that it produces a suitable path in 3-dimensions in close-proximity environments in real time with no a priori knowledge of the environment, a necessary precursor to the application of this technique to IED disposal missions. To solve the problem of path planning, the thesis derives the kinematics and dynamics of a robotic arm in order to convert the Euclidean coordinates of measured environment data into C-space. Each dimension in C-space is one control input of the arm. The Euclidean start and end locations of the manipulator end effector are translated into C-space. A three-dimensional path is generated between them using Dijkstra’s Algorithm. The technique allows for a single path to be generated to guide the entire arm through the environment, rather than multiple paths to guide each component through the environment. The robotic arm parameters are modelled as a quasi-linear parameter varying system. As such it requires gain scheduling control, thus allowing compensation of the non-linearities in the system. A Genetic Algorithm is applied to tune a set of PID controllers for the dynamic model of the manipulator arm so that the generated path can then be followed using a conventional path-following algorithm. The technique proposed in this thesis is validated using numerical simulations in order to determine its advantages and limitations

Numerical Linear Algebra applications in Archaeology: the seriation and the photometric stereo problems

The aim of this thesis is to explore the application of Numerical Linear Algebra to Archaeology. An ordering problem called the seriation problem, used for dating findings and/or artifacts deposits, is analysed in terms of graph theory. In particular, a Matlab implementation of an algorithm for spectral seriation, based on the use of the Fiedler vector of the Laplacian matrix associated with the problem, is presented. We consider bipartite graphs for describing the seriation problem, since the interrelationship between the units (i.e. archaeological sites) to be reordered, can be described in terms of these graphs. In our archaeological metaphor of seriation, the two disjoint nodes sets into which the vertices of a bipartite graph can be divided, represent the excavation sites and the artifacts found inside them. Since it is a difficult task to determine the closest bipartite network to a given one, we describe how a starting network can be approximated by a bipartite one by solving a sequence of fairly simple optimization problems. Another numerical problem related to Archaeology is the 3D reconstruction of the shape of an object from a set of digital pictures. In particular, the Photometric Stereo (PS) photographic technique is considered

Geometric representation of neuroanatomical data observed in mouse brain at cellular and gross levels

This dissertation studies two problems related to geometric representation of neuroanatomical data: (i) spatial representation and organization of individual neurons, and (ii) reconstruction of three-dimensional neuroanatomical regions from sparse two-dimensional drawings. This work has been motivated by nearby development of new technology, Knife-Edge Scanning Microscopy (KESM), that images a whole mouse brain at cellular level in less than a month. A method is introduced to represent neuronal data observed in the mammalian brain at the cellular level using geometric primitives and spatial indexing. A data representation scheme is defined that captures the geometry of individual neurons using traditional geometric primitives, points and cross-sectional areas along a trajectory. This representation captures inferred synapses as directed links between primitives and spatially indexes observed neurons based on the locations of their cell bodies. This method provides a set of rules for acquisition, representation, and indexing of KESMgenerated data. Neuroanatomical data observed at the gross level provides the underlying regional framework for neuronal circuits. Accumulated expert knowledge on neuroanatomical organization is usually given as a series of sparse two-dimensional contours. A data structure and an algorithm are described to reconstruct separating surfaces among multiple regions from these sparse cross-sectional contours. A topology graph is defined for each region that describes the topological skeleton of the region’s boundary surface and that shows between which contours the surface patches should be generated. A graph-directed triangulation algorithm is provided to reconstruct surface patches between contours. This graph-directed triangulation algorithm combined together with a piecewise parametric curve fitting technique ensures that abutting or shared surface patches are precisely coincident. This method overcomes limitations in i) traditional surfaces-from-contours algorithms that assume binary, not multiple, regionalization of space, and in ii) few existing separating surfaces algorithms that assume conversion of input into a regular volumetric grid, which is not possible with sparse inter-planar resolution

A Message Passing Algorithm for the Minimum Cost Multicut Problem

We propose a dual decomposition and linear program relaxation of the NP -hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral elaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.Comment: Added acknowledgment