High-performance geometric vascular modelling

Image-based high-performance geometric vascular modelling and reconstruction is an essential component of computer-assisted surgery on the diagnosis, analysis and treatment of cardiovascular diseases. However, it is an extremely challenging task to efficiently reconstruct the accurate geometric structures of blood vessels out of medical images. For one thing, the shape of an individual section of a blood vessel is highly irregular because of the squeeze of other tissues and the deformation caused by vascular diseases. For another, a vascular system is a very complicated network of blood vessels with different types of branching structures. Although some existing vascular modelling techniques can reconstruct the geometric structure of a vascular system, they are either time-consuming or lacking sufficient accuracy. What is more, these techniques rarely consider the interior tissue of the vascular wall, which consists of complicated layered structures. As a result, it is necessary to develop a better vascular geometric modelling technique, which is not only of high performance and high accuracy in the reconstruction of vascular surfaces, but can also be used to model the interior tissue structures of the vascular walls.This research aims to develop a state-of-the-art patient-specific medical image-based geometric vascular modelling technique to solve the above problems. The main contributions of this research are:- Developed and proposed the Skeleton Marching technique to reconstruct the geometric structures of blood vessels with high performance and high accuracy. With the proposed technique, the highly complicated vascular reconstruction task is reduced to a set of simple localised geometric reconstruction tasks, which can be carried out in a parallel manner. These locally reconstructed vascular geometric segments are then combined together using shape-preserving blending operations to faithfully represent the geometric shape of the whole vascular system.- Developed and proposed the Thin Implicit Patch method to realistically model the interior geometric structures of the vascular tissues. This method allows the multi-layer interior tissue structures to be embedded inside the vascular wall to illustrate the geometric details of the blood vessel in real world

Feasibility studies of terrestrial laser scanning in Coastal Geomorphology, Agronomy, and Geoarchaeology

Terrestrial laser scanning (TLS) is a newer, active method of remote sensing for the automatic detection of 3D coordinate points. This method has been developed particularly during the last 20 years, in addition to airborne and mobile laser scanning methods. All these methods use laser light and additional angle measurements for the detection of distances and directions. Thus, several thousands to hundreds of thousands of polar coordinates per second can be measured directly by an automatic deflection of laser beams. For TLS measurements, the coordinates and orientation of the origin of the laser beam can be determined to register different scan positions in a common coordinate system. These measurements are usually conducted by Global Navigation Satellite Systems or total station surveying, but also identical points can be used and data driven methods are possible. Typically, accuracies and point densities of a few centimetres to a few millimetres are achieved depending on the method. The derived 3D point clouds contain millions of points, which can be evaluated in post-processing stages by symbolic or data-driven methods. Besides the creation of digital surface and terrain models, laser scanning is used in many areas for the determination of 3D objects, distances, dimensions, and volumes. In addition, changes can be determined by multi-temporal surveys. The terrestrial laser scanner Riegl LMS Z-420i was used in this work in combination with the Differential Global Positioning System system Topcon Hiper Pro, based on Real Time Kinematic (RTK-DGPS). In addition to the direct position determination of the laser scanner, the position of a self-developed reflector on a ranging pole was measured by the RTK-DGPS system to accurately derive the orientation of each measured point cloud. Moreover, the scanner is equipped with an additional, mounted camera Nikon D200 to capture oriented pictures. These pictures allow colouring the point cloud in true colours and thus allow a better orientation. Furthermore, the pictures can be used for the extraction of detailed 3D information and for texturing the 3D objects. In one of the post-processing steps, the direct georeferencing by RTK-DGPS data was refined using the Multi Station Adjustment, which employs the Iterative Closest Point algorithm. According to the specific objectives, the point clouds were then filtered, clipped, and processed to establish 3D objects for further usage. In this dissertation, the feasibility of the method has been analysed by investigating the applicability of the system, the accuracy, and the post-processing methods by means of case studies from the research areas of coastal geomorphology, agronomy, and geoarchaeology. In general, the measurement system has been proven to be robust and suitable for field surveys in all cases. The surveys themselves, including the selected georeferencing approach, were conducted quickly and reliably. With the refinement of the Multi Station Adjustment a relative accuracy of about 1 cm has been achieved. The absolute accuracy is about 1.5 m, limited by the RTK-DGPS system, which can be enhanced through advanced techniques. Specific post-processing steps have been conducted to solve the specific goals of each research area. The method was applied for coastal geomorphological research in western Greece. This part of the study deals with 3D reconstructed volumes and corresponding masses of boulders, which have been dislocated by high energy events. The boulder masses and other parameters, such as the height and distance to the current sea level, have been used in wave transport equations for the calculation of minimum wave heights and velocities of storm and tsunami scenarios and were compared to each other. A significant increase in accuracy of 30% on average compared with the conventional method of simply measuring the axes was detected. For comparison, annual measurements at seven locations in western Greece were performed over three years (2009-2011) and changes in the sediment budget were successfully detected. The base points of the RTK-DGPS system were marked and used every year. Difficulties arose in areas with high surface roughness and slight changes in the annual position of the laser scanner led to an uneven point density and generated non-existing changes. For this reason, all results were additionally checked by pictures of the mounted camera and a direct point cloud comparison. Similarly, agricultural plants were surveyed by a multi-temporal approach on a field over two years using the stated method. Plant heights and their variability within a field were successfully determined using Crop Surface Models, which represent the top canopy. The spatial variability of plant development was compared with topographic parameters as well as soil properties and significant correlations were found. Furthermore, the method was carried out with four different types of sugar-beet at a higher resolution, which was achieved by increasing the height of the measurement position. The differences between the crop varieties and their growth behaviour under drought stress were represented by the derived plant heights and a relation to biomass and the Leaf Area Index was successfully established. With regard to geoarchaeological investigations in Jordan, Spain, and Egypt, the method was used in order to document respective sites and specific issues, such as proportions and volumes derived from the generated 3D models were solved. However, a full coverage of complexly structured sites, like caves or early settlements is partially prevented by the oversized scanner, slow measurement rates, and the necessary minimum measurement distance. The 3D data can be combined with other data for further research by the common georeference. The selected method has been found suitable to create accurate 3D point clouds and corresponding 3D models that can be used in accordance with the respective research problem. The feasibility of the TLS method for various issues of the case studies was proven, but limitations of the used system have also been detected and are described in the respective chapters. Further methods or other, newer TLS systems may be better suited for specific cases

Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities. Method development for accurate 16S rRNA gene amplicon sequencing

Nucleic acid sequencing can provide a detailed overview of microbial communities in comparison with standard plate-culture methods. Expansion of high-throughput sequencing (HTS) technologies and reduction in analysis costs has allowed for detailed exploration of various habitats with use of amplicon, metagenomics, and metatranscriptomics approaches. However, due to a capital cost of HTS platforms and requirements for batch analysis, genomics-based studies are still not being used as a standard method for the comprehensive examination of environmental or clinical samples for microbial characterization. This research project investigated the potential of a novel nanopore-based sequencing platform from Oxford Nanopore Technologies (ONT) for rapid and accurate analysis of various environmentally complex samples. ONT is an emerging company that developed the first-ever portable nanopore-based sequencing platform called MinIONTM. Portability and miniaturised size of the device gives an immense opportunity for de-centralised, in-field, and real-time analysis of environmental and clinical samples. Nonetheless, benchmarking of this new technology against the current gold-standard platform (i.e., Illumina sequencers) is necessary to evaluate nanopore data and understand its benefits and limitations. The focus of this study is on the evaluation of nanopore sequencing data: read quality, sequencing errors, alignment quality but also bacterial community structure. For this reason, mock bacterial community samples were generated, sequenced and analysed with use of multiple bioinformatics approaches. Furthermore, this study developed sophisticated library preparation and data analyses methods to enable high-accuracy analysis of amplicon libraries from complex microbial communities for sequencing on the nanopore platform. Besides, the best performing library preparation and data analyses methods were used for analysis of environmental samples and compared to high-quality Illumina metagenomics data. This work opens a new possibility for accurate, in-field amplicon analysis of complex samples with the use of MinIONTM and for the development of autonomous biosensing technology for culture-free detection of pathogenic and non-pathogenic microorganisms in water, soil, food, drinks or blood

Proceedings of the 19th European Roundtable for Sustainable Consumption and Production Circular Europe for Sustainability: Design, Production and Consumption

Postprint (published version

Using Differential Adhesion to Control Self-Assembly and Self-Repair of Collections of Modular Mobile Robots

Institute of Perception, Action and BehaviourThis thesis presents a novel distributed control method which allows a collection of independently mobile robotic units, with two or three dimensional movement, to self-assemble into self-repairing hierarchical structures. The proposed method utilises a simple model of the cellular adhesion mechanisms observed in biological cells, allowing the robotic units to form virtually bonded aggregates which behave as predicted by Steinberg’s differential adhesion hypothesis. Simulated robotic units based on the design of the subaquatic HYDRON module are introduced as a possible platform on which the model can be implemented. The units are used to carry out a detailed investigation of the model behaviour and parameter space focusing on the two main tasks of rounding and sorting in both two and three dimensions. These tasks assess the model’s ability to reach a thermodynamically stable configuration when the aggregates consist of either a single population of units or multiple populations of units with differing adhesive properties. The results are analysed in detail with particular attention given to the role of random movements in determining the overall performance, and demonstrate that this model provides a very robust solution to these complex tasks. Finally, a possible extension of this work is presented in which the original model is combined with a genetic regulatory network controller. The performance of this composite is evaluated, and the benefits of this hybrid approach, in which a powerful control system manipulates a robust self-organising behaviour, are discussed

Age composition and survival of public housing stock in Hong Kong

Emerging notably in more developed regions, building stock ageing which is characterised by shrinking new completions and falling “mortality” has been posing challenges to various stakeholders in built environment. To find way out of this transition, we need to know how long buildings will last these days and the factors leading to their “mortality”. By using data from 1950s till to date, a comprehensive investigation is conducted to analyse the age composition and life expectancy of public housing stock in Hong Kong. What comes after are survival analysis and empirical analysis of those demolished to identify the key factors leading to demolition. Presented in this paper are the preliminary findings as well as the research agenda on the theme to model age composition and survival of both private and public building stocks in Hong Kong and other similar cities in Asia Pacific Rim such as Adelaide and Singapore, together with research activities to formulate policies for sustainable urban management

Evaluation of the new Design Summer Year weather data using parametrical buildings

The Charted Institution of Building Services Engineers (CIBSE) updated the near extreme weather (Design Summer Year – DSY) for all 14 locations in the UK in 2016. This new release attempts to address the underlying shortcomings of the previous definition where the averaged dry bulb temperature was the sole metric to choose DSY among source weather years. The aim of this research is to evaluate whether the new definition of the probabilistic DSYs can consistently represent near extreme condition. London historical weather data and their correspondent DSYs were used in this research. Dynamic thermal modelling using EnergyPlus was carried out on large number single zone offices (parametric study) which represent a large portion of cellular offices in the UK. The predicted indoor warmth from the sample building models show that these new definitions are not always able to represent near extreme conditions. Using multiple years as DSY is able to capture different types of summer warmth but how to use one or all of these DSYs to make informed judgement on overheating is rather challenging. The recommended practice from this research is to use more warm years for the evaluation of overheating and choose the near extreme weather from the predicted indoor warmt