Single Tree Detection from Airborne Laser Scanning Data: A Stochastic Approach

Characterizing and monitoring forests are of great scientific and managerial interests, such as understanding the global carbon circle, biodiversity conservation and management of natural resources. As an alternative or compliment to traditional remote sensing techniques, airborne laser scanning (ALS) has been placed in a very advantageous position in forest studies, for its unique ability to directly measure the distribution of vegetation materials in the vertical direction, as well as the terrain beneath the forest canopy. Serving as basis for tree-wise forest biophysical parameter and species information retrieval, single tree detection is a very motivating research topic in forest inventory. The objective of the study is to develop a method from the perspective of computer vision to detect single trees automatically from ALS data. For this purpose, this study explored different aspects of the problem. It starts from an improved pipeline for canopy height model (CHM) generation, which alleviates the distortion of tree crown shapes presented on CHMs resulted from conventional procedures due to the shadow effects of ALS data and produces pit-free CHM. The single tree detection method consists of a hybrid framework which integrates low-level image processing techniques, i.e. local maxima filtering (LM) and marker-controlled watershed segmentation (MCWS), into a high-level probabilistic model. In the proposed approach, tree crowns in the forest plot are modelled as a configuration of circular objects. The configuration containing the best possible set of detected tree objects is estimated by a global optimization solver in a probabilistic framework. The model features an accelerated optimization process compared with classical stochastic models, e.g. marked point processes. The parameter estimation is another issue: the study investigated both a reference-based supervised and an Expectation-Maximization (EM) based unsupervised method to estimate the parameters in the model. The model was tested in a temperate mature coniferous forest in Ontario, Canada, as well as simulated coniferous forest plots with various degrees of crown overlap. The experimental results showed the effectiveness of our proposed method, which was capable of reducing the commission errors produced by local maxima filtering based methods, thus increasing the overall detection accuracy by approximately 10% on all of the datasets

Blind deconvolution of sparse pulse sequences under a minimum distance constraint: a partially collapsed Gibbs sampler method

For blind deconvolution of an unknown sparse sequence convolved with an unknown pulse, a powerful Bayesian method employs the Gibbs sampler in combination with a Bernoulli–Gaussian prior modeling sparsity. In this paper, we extend this method by introducing a minimum distance constraint for the pulses in the sequence. This is physically relevant in applications including layer detection, medical imaging, seismology, and multipath parameter estimation. We propose a Bayesian method for blind deconvolution that is based on a modified Bernoulli–Gaussian prior including a minimum distance constraint factor. The core of our method is a partially collapsed Gibbs sampler (PCGS) that tolerates and even exploits the strong local dependencies introduced by the minimum distance constraint. Simulation results demonstrate significant performance gains compared to a recently proposed PCGS. The main advantages of the minimum distance constraint are a substantial reduction of computational complexity and of the number of spurious components in the deconvolution result

COMBINING MARKOV RANDOM FIELD AND MARKED POINT PROCESS FOR MICROSCOPY IMAGE MODELING

In many microscopy image analysis applications, it is of critical importance to addres

Activity Analysis; Finding Explanations for Sets of Events

Automatic activity recognition is the computational process of analysing visual input and reasoning about detections to understand the performed events. In all but the simplest scenarios, an activity involves multiple interleaved events, some related and others independent. The activity in a car park or at a playground would typically include many events. This research assumes the possible events and any constraints between the events can be defined for the given scene. Analysing the activity should thus recognise a complete and consistent set of events; this is referred to as a global explanation of the activity. By seeking a global explanation that satisfies the activity’s constraints, infeasible interpretations can be avoided, and ambiguous observations may be resolved. An activity’s events and any natural constraints are defined using a grammar formalism. Attribute Multiset Grammars (AMG) are chosen because they allow defining hierarchies, as well as attribute rules and constraints. When used for recognition, detectors are employed to gather a set of detections. Parsing the set of detections by the AMG provides a global explanation. To find the best parse tree given a set of detections, a Bayesian network models the probability distribution over the space of possible parse trees. Heuristic and exhaustive search techniques are proposed to find the maximum a posteriori global explanation. The framework is tested for two activities: the activity in a bicycle rack, and around a building entrance. The first case study involves people locking bicycles onto a bicycle rack and picking them up later. The best global explanation for all detections gathered during the day resolves local ambiguities from occlusion or clutter. Intensive testing on 5 full days proved global analysis achieves higher recognition rates. The second case study tracks people and any objects they are carrying as they enter and exit a building entrance. A complete sequence of the person entering and exiting multiple times is recovered by the global explanation

Evolution of Strigamia centipedes (Chilopoda): a first molecular assessment of phylogeny and divergence times

We present a first phylogenetic and temporal framework, with biogeographical insights, for the centipedes of the genus Strigamia, which are widespread predators in the forest soils of the Northern Hemisphere and comprise the evo-devo model species Strigamia maritima. The phylogeny was estimated by different methods of maximum likelihood and Bayesian inference from sequences of two mitochondrial (16S, COI) and two nuclear (18S, 28S) genes, obtained from 16 species from all major areas of the global range of the genus and encompassing most of the overall morphological and ecological diversity. Divergence times were estimated after calibration upon the fossil record of centipedes. We found that major lineages of extant species of Strigamia separated most probably around 60 million years (Ma) ago. The two most diverse lineages diversified during the last 30 Ma and are today segregated geographically, one in Europe and another in Eastern Asia. This latter region hosts a hitherto underestimated richness and anatomical diversity of species, including three still unknown, yet morphologically well distinct species, which are here described as new: Strigamia inthanoni sp. n. from Thailand, Strigamia korsosi sp. n. from the Ryukyu Islands and Strigamia nana sp. n. from Taiwan. The northern European model species S. maritima is more strictly related to the Eastern Asian lineage, from which it most probably separated around 35 Ma ago before the major diversification of the latter

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model

Abstract Background Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh throughput genomic sequencing both provide rapid, robust, and comprehensive methods to identify CNVs on a whole-genome scale. Results We developed a Bayesian statistical analysis algorithm for the detection of CNVs from both types of genomic data. The algorithm can analyze such data obtained from PCR-based bacterial artificial chromosome arrays, high-density oligonucleotide arrays, and more recently developed high-throughput DNA sequencing. Treating parameters--e.g., the number of CNVs, the position of each CNV, and the data noise level--that define the underlying data generating process as random variables, our approach derives the posterior distribution of the genomic CNV structure given the observed data. Sampling from the posterior distribution using a Markov chain Monte Carlo method, we get not only best estimates for these unknown parameters but also Bayesian credible intervals for the estimates. We illustrate the characteristics of our algorithm by applying it to both synthetic and experimental data sets in comparison to other segmentation algorithms. Conclusions In particular, the synthetic data comparison shows that our method is more sensitive than other approaches at low false positive rates. Furthermore, given its Bayesian origin, our method can also be seen as a technique to refine CNVs identified by fast point-estimate methods and also as a framework to integrate array-CGH and sequencing data with other CNV-related biological knowledge, all through informative priors.</p

High-Level Facade Image Interpretation using Marked Point Processes

In this thesis, we address facade image interpretation as one essential ingredient for the generation of high-detailed, semantic meaningful, three-dimensional city-models. Given a single rectified facade image, we detect relevant facade objects such as windows, entrances, and balconies, which yield a description of the image in terms of accurate position and size of these objects. Urban digital three-dimensional reconstruction and documentation is an active area of research with several potential applications, e.g., in the area of digital mapping for navigation, urban planning, emergency management, disaster control or the entertainment industry. A detailed building model which is not just a geometric object enriched with texture, allows for semantic requests as the number of floors or the location of balconies and entrances. Facade image interpretation is one essential step in order to yield such models. In this thesis, we propose the interpretation of facade images by combining evidence for the occurrence of individual object classes which we derive from data, and prior knowledge which guides the image interpretation in its entirety. We present a three-step procedure which generates features that are suited to describe relevant objects, learns a representation that is suited for object detection, and that enables the image interpretation using the results of object detection while incorporating prior knowledge about typical configurations of facade objects, which we learn from training data. According to these three sub-tasks, our major achievements are: We propose a novel method for facade image interpretation based on a marked point process. Therefor, we develop a model for the description of typical configurations of facade objects and propose an image interpretation system which combines evidence derived from data and prior knowledge about typical configurations of facade objects. In order to generate evidence from data, we propose a feature type which we call shapelets. They are scale invariant and provide large distinctiveness for facade objects. Segments of lines, arcs, and ellipses serve as basic features for the generation of shapelets. Therefor, we propose a novel line simplification approach which approximates given pixel-chains by a sequence of lines, circular, and elliptical arcs. Among others, it is based on an adaption to Douglas-Peucker's algorithm, which is based on circles as basic geometric elements We evaluate each step separately. We show the effects of polyline segmentation and simplification on several images with comparable good or even better results, referring to a state-of-the-art algorithm, which proves their large distinctiveness for facade objects. Using shapelets we provide a reasonable classification performance on a challenging dataset, including intra-class variations, clutter, and scale changes. Finally, we show promising results for the facade interpretation system on several datasets and provide a qualitative evaluation which demonstrates the capability of complete and accurate detection of facade objectsHigh-Level Interpretation von Fassaden-Bildern unter Benutzung von Markierten PunktprozessenDas Thema dieser Arbeit ist die Interpretation von Fassadenbildern als wesentlicher Beitrag zur Erstellung hoch detaillierter, semantisch reichhaltiger dreidimensionaler Stadtmodelle. In rektifizierten Einzelaufnahmen von Fassaden detektieren wir relevante Objekte wie Fenster, Türen und Balkone, um daraus eine Bildinterpretation in Form von präzisen Positionen und Größen dieser Objekte abzuleiten. Die digitale dreidimensionale Rekonstruktion urbaner Regionen ist ein aktives Forschungsfeld mit zahlreichen Anwendungen, beispielsweise der Herstellung digitaler Kartenwerke für Navigation, Stadtplanung, Notfallmanagement, Katastrophenschutz oder die Unterhaltungsindustrie. Detaillierte Gebäudemodelle, die nicht nur als geometrische Objekte repräsentiert und durch eine geeignete Textur visuell ansprechend dargestellt werden, erlauben semantische Anfragen, wie beispielsweise nach der Anzahl der Geschosse oder der Position der Balkone oder Eingänge. Die semantische Interpretation von Fassadenbildern ist ein wesentlicher Schritt für die Erzeugung solcher Modelle. In der vorliegenden Arbeit lösen wir diese Aufgabe, indem wir aus Daten abgeleitete Evidenz für das Vorkommen einzelner Objekte mit Vorwissen kombinieren, das die Analyse der gesamten Bildinterpretation steuert. Wir präsentieren dafür ein dreistufiges Verfahren: Wir erzeugen Bildmerkmale, die für die Beschreibung der relevanten Objekte geeignet sind. Wir lernen, auf Basis abgeleiteter Merkmale, eine Repräsentation dieser Objekte. Schließlich realisieren wir die Bildinterpretation basierend auf der zuvor gelernten Repräsentation und dem Vorwissen über typische Konfigurationen von Fassadenobjekten, welches wir aus Trainingsdaten ableiten. Wir leisten dazu die folgenden wissenschaftlichen Beiträge: Wir schlagen eine neuartige Me-thode zur Interpretation von Fassadenbildern vor, die einen sogenannten markierten Punktprozess verwendet. Dafür entwickeln wir ein Modell zur Beschreibung typischer Konfigurationen von Fassadenobjekten und entwickeln ein Bildinterpretationssystem, welches aus Daten abgeleitete Evidenz und a priori Wissen über typische Fassadenkonfigurationen kombiniert. Für die Erzeugung der Evidenz stellen wir Merkmale vor, die wir Shapelets nennen und die skaleninvariant und durch eine ausgesprochene Distinktivität im Bezug auf Fassadenobjekte gekennzeichnet sind. Als Basismerkmale für die Erzeugung der Shapelets dienen Linien-, Kreis- und Ellipsensegmente. Dafür stellen wir eine neuartige Methode zur Vereinfachung von Liniensegmenten vor, die eine Pixelkette durch eine Sequenz von geraden Linienstücken und elliptischen Bogensegmenten approximiert. Diese basiert unter anderem auf einer Adaption des Douglas-Peucker Algorithmus, die anstelle gerader Linienstücke, Bogensegmente als geometrische Basiselemente verwendet. Wir evaluieren jeden dieser drei Teilschritte separat. Wir zeigen Ergebnisse der Liniensegmen-tierung anhand verschiedener Bilder und weisen dabei vergleichbare und teilweise verbesserte Ergebnisse im Vergleich zu bestehende Verfahren nach. Für die vorgeschlagenen Shapelets weisen wir in der Evaluation ihre diskriminativen Eigenschaften im Bezug auf Fassadenobjekte nach. Wir erzeugen auf einem anspruchsvollen Datensatz von skalenvariablen Fassadenobjekten, mit starker Variabilität der Erscheinung innerhalb der Klassen, vielversprechende Klassifikationsergebnisse, die die Verwendbarkeit der gelernten Shapelets für die weitere Interpretation belegen. Schließlich zeigen wir Ergebnisse der Interpretation der Fassadenstruktur anhand verschiedener Datensätze. Die qualitative Evaluation demonstriert die Fähigkeit des vorgeschlagenen Lösungsansatzes zur vollständigen und präzisen Detektion der genannten Fassadenobjekte