Engineering Science - Theses, Dissertations, and other Required Graduate Degree Essays

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Identification of Pacemaking Region in Zebrafish Heart from Optical Mapping Data

Author: 
Date created: 
2013-04-24
Abstract: 

Junctional Ectopic Tachycardia (JET) is a cardiac arrhythmia which occurs immediately after open heart surgery in young children. In specific populations, JET has extremely high incidence, of up to 50%. There has not been a specific mechanism elucidated by clinical data or basic science. As a widely used vertebrate cardiovascular biological model, zebrafish heart is being studied to reveal the leading reasons of JET. Optical mapping (OM) techniques provide an effective approach to observe cardiac functionality by recording zebrafish heart action potential propagation. However, processing of vast amount of OM data also poses challenges on fast and accurate processing, measurement and interpretation. This thesis presents novel automated pipelines for processing zebrafish heart OM data and identifying pacemaking regions from it through signal analysis. We first introduce a preprocessing pipeline for enhancing very low signal-to-noise ratio original OM data, which involves spatial-temporal smoothing, cycle averaging, drifting correction and scaling. After that, we present a computer assisted OM signal manually labeling pipeline, which reduces the manual workload significantly by clustering spatially adjacent similar signals. Furthermore, we make physiologically relevant measurements on OM data and do statistical analysis comparing different labeled regions. Finally, we propose a two-step signal clustering based method to divide atrium into different functional regions followed by pacemaking region identification. We present the formulation of these methods and discuss their validity and performance in various aspects. The work presented in this thesis could lead to significantly faster and larger scaled experimentation in optical mapping related physiology research.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Mirza Faisal Beg
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Towards real-time sea-floor surface reconstruction and classification using 3-D side-scan sonar

Date created: 
2014-07-29
Abstract: 

This thesis presents a computer algorithm to solve two major hurdles for generating real-time automated sea-floor maps with composition classification using 3-D side-scan sonar data. The algorithm consists of two distinct parts: sea-floor profiling and sea-flooring classification with computation acceleration from a graphics processing unit (GPU). The sea-floor profiling algorithm is an automated method that identifies bathymetry data corresponding to the sea-floor while ignoring bathymetry corresponding to water column objects and multi-path returns. The algorithm improves upon a fuzzy curve tracing method to handle discontinuities in the point-cloud data along the sea-floor and to discriminate between the sea-floor and other data. With an average error of 2.6% and a computation time of 7.40ms, the sea-floor profiling algorithm is extremely accurate and efficient. Classification of the sea-floor regions consists of applying image texture methods and machine learning classifiers to side-scan sonar images. In this thesis, a feature space for each side-scan sonar image pixel is created using image texture analysis algorithms, and classified with an artificial neural network. The accuracy and performance of the algorithm is tested with side-scan sonar images from the Underwater Research Lab's Pam Rocks sonar survey. Real-time classification was achieved by the use of GPU computing. Porting the algorithm onto the GPU using OpenCL reduced the per-ping computation time to an average of 100ms, with an average error of 3.4%, making it a viable real-time solution in a sonar system.

Document type: 
Thesis
File(s): 
Senior supervisor: 
John Bird
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Detection of Cardiac Troponin I in circulation using Raman Spectroscopy; an approach to prediction of myocardial infarction

Date created: 
2012-04-02
Abstract: 

Myocardial infarction (MI) pertains to cardiac tissue death, secondary to prolonged inadequate perfusion to myocardial cells. Despite medical advances, MI remains a global leading cause of mortality and morbidity. Minute and subclinical physiological changes occur hours prior to a symptomatically appreciable ‘attack’. These well-established phenomena involve the release of specific cardiac biomarkers into systemic circulation. Quantitative measurement of systemic cTnI concentrations is widely and routinely implemented in the diagnosis of MI. However, current technology is limited to detection of ‘post-attack’ concentrations, which often indicates irreversible damage. Consequently, we aimed to noninvasively detect concentrations of cTnI through biophotonic technology. For the first time in literature, we characterized and repeatedly verified unique Raman signature of mouse cTnI in water and BSA. Further, we investigated concentration changes, optimized integration durations, and proposed a conceptual design. This project potentially begets preclinical detection of biomarkers, earlier diagnosis, prompt medical intervention, and enhanced overall prognosis.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Andrew Rawicz
Department: 
Applied Science: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Enabling Shallow-Water Sidescan Sonar Surveys: Using Across-Track Beamforming on Receive to Suppress Multipath Interference

Date created: 
2014-06-25
Abstract: 

Sidescan sonars are used to provide a high resolution 2D image of the seafloor, but when used in shallow water these side-looking systems are vulnerable to multipath interference. In some cases, this interference affects image interpretation and downstream processing such as target recognition or bottom classification. However, it is possible to suppress multipath interference by using a small array featuring a vertical stack of receivers. This thesis investigates the extent to which conventional beamforming techniques, used on receive, can suppress multipath interference. Two novel techniques are proposed, one that suppresses surface interference and one that suppresses bottom-bounce multipath. Experimental data are presented which illustrate the impact that multipath interference has on sidescan images. To establish the effectiveness of the proposed methods, the methods are applied to theoretical models of the experimental data, and are applied to the experimental data as well. This thesis proposes the use of a fixed broad beam to suppress interference arriving from the surface. A sidescan array utilizing a vertical stack of six receive elements was constructed, and is shown to be effective at providing a clear view of the seafloor when surface interference is present. Experimental data collected with the experimental array are presented. A theoretical analysis examines the relative path strengths of the received signals for different across-track beam patterns, and examines how these signals are affected when beamforming is applied on receive. The experimental data are processed using the proposed method and are significantly improved, revealing a shipwreck that was not visible in the original image. Suppressing bottom-bounce multipath signals is more difficult, and this thesis proposes the use of time-varying conventional beamforming techniques as a method to realize this second goal. Two sidescan images, both contaminated with bottom-bounce multipath, are presented and modeled. The experimental data are processed using the proposed methods, and a clear view of the seafloor is provided. It is concluded that a sidescan sonar which employs across-track beamforming on a receive array is a valuable tool for suppressing the multipath and surface interference which arise in shallow water surveys.

Document type: 
Thesis
File(s): 
Senior supervisor: 
John Bird
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) Ph.D.

An experimental study of remote multi-modal interface in robotic systems

Date created: 
2014-06-18
Abstract: 

This thesis investigates the limits of vibrato tactile haptic feedback when interacting with 3D virtual scenes. In this study, the spatial locations of the objects are mapped to the work-volume of the user using a Kinect sensor. In addition, the location of the hand of the user is determined using marker-based visual processing. The depth information is used to build a vibrotactile map on a haptic glove enhanced with vibration motors. The users can perceive the location and dimension of remote objects by moving their hand inside a scanning region. A marker detection camera provides the location and orientation of the user’s hand (glove) to map the corresponding tactile message. A preliminary study was conducted to explore how different users can perceive such haptic experiences. Factors such as total number of objects detected, object separation resolution, dimension-based and shape-based discrimination were evaluated. The preliminary results showed that the localization and counting of objects can be attained with a high degree of success. The users were able to classify groups of objects of different dimensions based on the perceived haptic feedback.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Shahram Payandeh
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Theory of Dipoles, Array Factors, and Multi-Element Antennas with Physics-Based Propagation for Mobile Communications

Date created: 
2014-04-29
Abstract: 

Bandwidth, volume and energy are the basic resources for communications, and current signal processing techniques use these in many different ways. The bandwidth is limited by the antenna size, and maximizing the bandwidth of the elements and the design of multielement antennas (MEAs) require new research. This two-part thesis addresses antenna theoretic bandwidth and MEA evaluation. The limiting bandwidth of the most fundamental antenna element - the dipole - remains elusive despite its long research history. This motivates Part I, in which the bandwidth of the electric dipole is developed from theoretical and numerical methods, and recent measurements. The resulting antenna-theoretic bandwidth of the dipole with a feed gap offers new benchmark results for compact elements. The lossless, thin dipole with finite gap has a much wider bandwidth than was previously known, and the non-radiating feed is identified as the challenge to realize the available bandwidth. Using multiple-input multiple-output (MIMO) and other diversity techniques with large dimensions (many elements) is the key technology for high spectral efficiency. But large dimension MIMO is not yet used commercially, and the design methodology and evaluation of MEAs is undeveloped. There is no standard for evaluating MEAs used for MIMO communications, and currently, the physical evaluation of a MIMO terminal comprises coarse throughput tests in an idealized environment. The real-world performance of the terminal, and especially the antenna performance, remains unclear from such tests. This motivates Part II, which explores MEA evaluation using physical antenna parameters together with site-specific, ray-traced models for the spatial channel. Ray-tracing calculation is well established, but its application with MEAs is in its infancy. Using third-party ray-tracing files, an approach for evaluating MEAs for urban channels is presented. The advantage is that it maintains the full control of being computer-driven, thereby avoiding expensive,hard-to-repeat physical measurements, while incorporating the ground-truth of empirical antenna parameters.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Rodney G. Vaughan
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) Ph.D.

Human Motion Behaviour Aware Planner (HMBAP) for path planning in dynamic human environments

Author: 
Date created: 
2014-04-23
Abstract: 

For a robot navigating in a human inhabited dynamic environment, the knowledge of how the robot’s movement can influence the trajectory of people around it can be very valuable. In this work we present a Human Motion Behaviour Aware Planner (HMBAP) which incorporates a Human Motion Behaviour Model (HMBM) in its planning stage to take advantage of this. HMBM is a potential field based obstacle avoidance model for people and the proposed planner uses it to give the robot a prediction of how people would react to its planned path. This information is useful for the robot to avoid imminent collisions with people in constricted spaces and the planner finds solutions in situations - called freezing robot problem - where past methods fail to find a solution. The resulting robot behaviour is also similar to how a human would move (in terms of avoidance behaviour) in a similar situation. We believe that this is a desirable feature for a robot navigating in a human inhabited environment. We have implemented HMBAP in simulation and also on the real robot in the RAMP Lab. Both simulations and experiments show the effectiveness of HMBAP.

Document type: 
Thesis
File(s): 
Simulation 1: Robot navigating a T junction in a narrow corridor while avoiding collision with human subjects.
Simulation 2: Robot passing a human subject in a narrow hallway
Simulation 3: Robot navigating a crowd of humans in wide open space
Experiment 1: Robot passing a human subject in a narrow hallway
Experiment 2: Robot navigating a cross-way in a narrow corridor while avoiding collision with human subjects.
Senior supervisor: 
Dr. Kamal Gupta
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Prevention of myocardial infarctions, using non-invasive biophotonics measurement of biomarker cardiac troponin I.

Author: 
Date created: 
2010-12-20
Abstract: 

Coronary Heart Disease is the leading cause of death worldwide. Myocardial Infarctions are one of the most frequent cardiovascular diseases. This research aims to design a non-invasive heart attack detection system based on biphotonic measurements. Several methods such as ECG monitoring, Florescence and Raman Spectroscopy are evaluated and Raman Spectroscopy is chosen due to advantages in sensitivity and efficiency. Since cTnI test is the current gold standard in diagnosing MI, the initial part of this research is based on comprehensive study of this protein. In this research Raman spectra of cTnI is measured and after assessment of possible adjustments to noise level, SERS method is used to obtain the enhanced spectra and consequently a unique cTnI Raman signature. Due to low biological concentrations and low SNR, the spectra are measured in higher concentrations. Finally, a conceptual Raman design is proposed as a part of the instrumentation study of the system.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Andrew Rawicz
Department: 
Applied Science: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Adhesion enhancement of a biomimetic dry adhesive by means of an increase to the Hamaker constant via nanocomposite formation

Date created: 
2013-01-21
Abstract: 

A novel method to increase the van der Waals adhesion of a gecko-inspired polymeric fibrillar dry adhesive through an increase of the polymer’s Hamaker constant is presented. Different metal nanoparticles (NPs) were embedded in the polydimethyl siloxane (PDMS) dry adhesive to create a nanocomposite. The successful process involved the in-situ synthesis of Au nanoparticles within the mushroom caps of the PDMS microfibrils to enhance adhesion. Successful synthesis of the Au NPs was analyzed using Ultraviolet-Visible Spectrophotometry. To quantify the adhesion enhancement, a pull-off force test was employed to compare the adhesive samples before and after the Au nanoparticles were synthesized. The experiments performed indicate an adhesion improvement of up to 2.2x as a result of the increase in the Hamaker constant of the dry adhesive mushroom caps. A model based on the Hamaker approximation to van der Waals forces is evaluated which is in good agreement with the experimental measurements.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Carlo Menon
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

Development of Optical Coherence Tomography for Quantitative Analysis of Cardiac Morphology

Date created: 
2014-04-24
Abstract: 

Transgenic mouse models have been instrumental in the elucidation of the molecular mechanism behind many cardiac diseases such as Marfan syndrome. However, the small size of the murine heart has hampered the characterization of its cardiac morphology. In this project, we describe the development of a murine cardiac imaging modality using optical coherence tomography (OCT). After fixation and optical clearing, the hearts were imaged from multiple perspectives. These data sets were then corrected for refraction and registered together to yield a single volume of the whole heart. From this OCT volume, we then applied techniques from computational anatomy to quantify morphological parameters such as wall thickness, luminal volume, and wall masses. Using this pipeline, we performed a preliminary study comparing the cardiac morphology of a mice model of Marfan syndrome with their wild-type counterparts.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Marinko Sarunic
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.