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Full-Text Articles in Biomedical Engineering and Bioengineering

Tissue Equivalent Gellan Gum Gel Materials For Clinical Mri And Radiation Dosimetry, Pawel Brzozowski Apr 2019

Tissue Equivalent Gellan Gum Gel Materials For Clinical Mri And Radiation Dosimetry, Pawel Brzozowski

Electronic Thesis and Dissertation Repository

Hydrogels contain high amount of water allowing their use as surrogates to human tissues with specific properties that can be tuned by additives. Gellan gum is a gel-forming material of interest and is a replacement for other common gelling agent with limited use as a tissue phantom. Therefore, this thesis examines the application of gellan gum gels as a novel magnetic resonance imaging (MRI) phantom with a design of experiments model to obtain tunable properties. The analysis was extended to include mechanical and electrical properties with a separate design of experiment. Gels doped with synthesized superparamagnetic iron oxide nanoparticles (SPIONs ...


Automatic Brain Tumor Segmentation By Deep Convolutional Networks And Graph Cuts, Zhenyi Wang Jan 2018

Automatic Brain Tumor Segmentation By Deep Convolutional Networks And Graph Cuts, Zhenyi Wang

Electronic Thesis and Dissertation Repository

Brain tumor segmentation in magnetic resonance imaging (MRI) is helpful for diagnostics, growth rate prediction, tumor volume measurements and treatment planning of brain tumor. The difficulties for brain tumor segmentation are mainly due to high variation of brain tumors in size, shape, regularity, location, and their heterogeneous appearance (e.g., contrast, intensity and texture variation for different tumors). Due to recent advances in deep convolutional neural networks for semantic image segmentation, automatic brain tumor segmentation is a promising research direction.

This thesis investigates automatic brain tumor segmentation by combining deep convolutional neural network with regularization by a graph cut. We ...


Evaluating And Improving Cochlear Length Measurements On Clinical Computed Tomography Images, John E. Iyaniwura Aug 2017

Evaluating And Improving Cochlear Length Measurements On Clinical Computed Tomography Images, John E. Iyaniwura

Electronic Thesis and Dissertation Repository

Cochlear implants provide the sensation of sound to deaf individuals. An accurate estimate of cochlear duct length (CDL) is required for pre-operative implant electrode selection and can be obtained from clinical computed tomography (CT) by measuring the “A-value”.

The objectives of this work were to estimate the accuracy and variability in manual A-value measurements, and to automate measurements.

Four specialists repeatedly measured the A-value on clinical CT images from which the inter- and intra-observer variability were calculated. Accuracy was assessed by comparison to measurements on higher resolution micro-CT images. Motivated by this study, software was developed to automate the A-value ...


Nanostructured Biosensor For Tear Glucose Detection Based On Bioluminescence Resonance Energy Transfer (Bret) Mechanism., Denghuang Zhan Aug 2017

Nanostructured Biosensor For Tear Glucose Detection Based On Bioluminescence Resonance Energy Transfer (Bret) Mechanism., Denghuang Zhan

Electronic Thesis and Dissertation Repository

Bioluminescence Resonance Energy Transfer (BRET), a sensitive, non-destructive and self-illuminated method, has been now commonly used to test protein interactions. Here, we describe a BRET sensor for non-invasively detecting glucose molecules. The sensor is made by the bioconjugation of quantum dots and recombinant protein. The recombinant protein contains the bacterial glucose binding protein (GBP) and a bioluminescent protein, Renilla luciferase (Rluc), used as the donor with the emission peak at 470 nm, which is able to excite the acceptor of BRET sensor made of cadmium tellurium quantum dots ( CdTe QDs) with the emission peak at 570 nm. The distance between ...


Computer-Assisted Characterization Of Prostate Cancer On Magnetic Resonance Imaging, Derek J. Soetemans Mar 2017

Computer-Assisted Characterization Of Prostate Cancer On Magnetic Resonance Imaging, Derek J. Soetemans

Electronic Thesis and Dissertation Repository

Prostate cancer (PCa) is one of the most prevalent cancers among men. Early diagnosis can improve survival and reduce treatment costs. Current inter-radiologist variability for detection of PCa is high. The use of multi-parametric magnetic resonance imaging (mpMRI) with machine learning algorithms has been investigated both for improving PCa detection and for PCa diagnosis. Widespread clinical implementation of computer-assisted PCa lesion characterization remains elusive; critically needed is a model that is validated against a histologic reference standard that is densely sampled in an unbiased fashion. We address this using our technique for highly accurate fusion of mpMRI with whole-mount digitized ...


Signal Processing Methods For Quantitative Power Doppler Microvascular Angiography, Mai H. Elfarnawany Aug 2015

Signal Processing Methods For Quantitative Power Doppler Microvascular Angiography, Mai H. Elfarnawany

Electronic Thesis and Dissertation Repository

Operator-dependent instrument settings and the likelihood of image artifacts are two challenges for reliably using three-dimensional (3-D) power Doppler angiography in flow depiction and quantification applications.

To address the operator-dependent settings challenge, an automated method for wall filter cut-off selection, the wall filter selection curve (WFSC) method, was developed using flow-phantom images. The flow-phantom WFSCs guided the development of a theoretical signal model relating color pixel density (CPD) and wall filter cut-off frequency. Simulations using the theoretical model were used to define criteria for the WFSC method to be applied to unprocessed power Doppler signals from 3-D vasculature. The adapted ...


Evaluating Human Performance For Image-Guided Surgical Tasks, Matthew Kenneth Kramers Aug 2014

Evaluating Human Performance For Image-Guided Surgical Tasks, Matthew Kenneth Kramers

Electronic Thesis and Dissertation Repository

The following work focuses on the objective evaluation of human performance for two different interventional tasks; targeted prostate biopsy tasks using a tracked biopsy device, and external ventricular drain placement tasks using a mobile-based augmented reality device for visualization and guidance. In both tasks, a human performance methodology was utilized which respects the trade-off between speed and accuracy for users conducting a series of targeting tasks using each device. This work outlines the development and application of performance evaluation methods using these devices, as well as details regarding the implementation of the mobile AR application. It was determined that the ...


Potential For Photoacoustic Imaging Of Neonatal Brain, Pantea Tavakolian Jul 2014

Potential For Photoacoustic Imaging Of Neonatal Brain, Pantea Tavakolian

Electronic Thesis and Dissertation Repository

Photoacoustic imaging is a hybrid imaging technique that combines many of the merits of both optical and ultrasound imaging. Photoacoustic imaging (PAI) has been hypothesized as a technique for imaging neonatal brain. However, PAI of the brain is more challenging than traditional methods (e.g. near infrared spectroscopy) due to the presence of the skull layer. To evaluate the potential limits the skull places on 3D PAI of the neonatal brain, we constructed a neonatal skull phantom (~1.52-mm thick) with a mixture of epoxy and titanium dioxide powder that provided acoustic insertion loss (1-5MHz) similar to human infant skull ...


Image-Based Registration Methods For Quantification And Compensation Of Prostate Motion During Trans-Rectal Ultrasound (Trus)-Guided Biopsy, Tharindu De Silva Jun 2014

Image-Based Registration Methods For Quantification And Compensation Of Prostate Motion During Trans-Rectal Ultrasound (Trus)-Guided Biopsy, Tharindu De Silva

Electronic Thesis and Dissertation Repository

Prostate biopsy is the clinical standard for cancer diagnosis and is typically performed under two-dimensional (2D) transrectal ultrasound (TRUS) for needle guidance. Unfortunately, most early stage prostate cancers are not visible on ultrasound and the procedure suffers from high false negative rates due to the lack of visible targets. Fusion of pre-biopsy MRI to 3D TRUS for targeted biopsy could improve cancer detection rates and volume of tumor sampled. In MRI-TRUS fusion biopsy systems, patient or prostate motion during the procedure causes misalignments in the MR targets mapped to the live 2D TRUS images, limiting the targeting accuracy of the ...


Nasopharyngeal Method For Selective Brain Cooling And Development Of A Time-Resolved Near-Infrared Technique To Monitor Brain Temperature And Oxidation Status During Hypothermia, Mohammad Fazel Bakhsheshi May 2014

Nasopharyngeal Method For Selective Brain Cooling And Development Of A Time-Resolved Near-Infrared Technique To Monitor Brain Temperature And Oxidation Status During Hypothermia, Mohammad Fazel Bakhsheshi

Electronic Thesis and Dissertation Repository

Mild hypothermia at 32-35oC (HT) has been shown to be neuroprotective for neurological emergencies following severe head trauma, cardiac arrest and neonatal asphyxia. However, HT has not been widely deployed in clinical settings because: firstly, cooling the whole body below 33-34°C can induce severe complications; therefore, applying HT selectively to the brain could minimize adverse effects by maintaining core body temperature at normal level. Secondly, development of an effective and easy to implement selective brain cooling (SBC) technique, which can quickly induce brain hypothermia while avoiding complications from whole body cooling, remains a challenge. In this thesis ...


Oriented Collagen And Applications Of Waveguide Evanescent Field Scattering (Wefs) Microscopy, Qamrun Nahar Apr 2014

Oriented Collagen And Applications Of Waveguide Evanescent Field Scattering (Wefs) Microscopy, Qamrun Nahar

Electronic Thesis and Dissertation Repository

In this thesis, Waveguide Evanescent Field Scattering (WEFS) microscopy is developed as a non-invasive, label-free live cell imaging technique. This new high-contrast imaging can be employed to study the first hundred nanometers from the surface as it utilizes the evanescent field of a waveguide as the illumination source. Previously, waveguide evanescent field fluorescence (WEFF) microscopy was developed as a fluorescence imaging technique comparable to the total internal reflection fluorescent (TIRF) microscopy. Both the WEFF and WEFS technique utilizes the same fundamental concepts except in WEFS microscopy imaging is accomplished without the application of any fluorescent labeling. In this work, bacterial ...


Surface Functionalization And Bioconjugation Of Nanoparticles For Biomedical Applications, Longyan Chen Jan 2014

Surface Functionalization And Bioconjugation Of Nanoparticles For Biomedical Applications, Longyan Chen

Electronic Thesis and Dissertation Repository

Colloidal inorganic nanoparticles (NPs) have been attracting considerable interest in biomedicine, from drug and gene delivery to imaging, sensing and diagnostics. It is essential to modify the surface of nanoparticles to have enhanced biocompatibility and functionality for the in vitro and in vivo applications, especially in delivering locally and recognizing biomolecules. Herein, the goal of this research work is to develop advanced NPs with well-tailored surface functionalities and/or bio-functionality for the applications in cell tracking and analytes detection.

In the first project, quantum dots incorporating with gelatin nanoparticles (QDs-GNPs) have been developed for bioimaging applications. Two different approaches have ...


Web-Based Simulation And Training Environment For Laparoscopic Camera Calibration, Kartik Thakore Oct 2013

Web-Based Simulation And Training Environment For Laparoscopic Camera Calibration, Kartik Thakore

Electronic Thesis and Dissertation Repository

Endoscopic cameras are increasingly employed in image-guidance procedures, where the video images must be registered to data from other modalities. However, such cameras are susceptible to distortions, requiring calibration before images can be used for registration, tracking and 3D reconstruction. Camera calibration is learned in a laboratory setting, where configuring and adjusting the physical setup is tedious and not necessarily conducive to learning. A centralized resource that utilizes 3D interactive components needs to be available for training on camera calibration. In this project, a web-based training environment for camera calibration is implemented called SimCAM. SimCAM was developed using the Web ...


Fabricating Cost-Effective Nanostructures For Biomedical Applications, Erden Ertorer Sep 2013

Fabricating Cost-Effective Nanostructures For Biomedical Applications, Erden Ertorer

Electronic Thesis and Dissertation Repository

In this thesis we described inexpensive alternatives to fabricate nanostructures on planar substrates and provided example applications to discuss the efficiency of fabricated nanostructures.

The first method we described is forming large area systematically changing multi-shape nanoscale structures on a chip by laser interference lithography. We analyzed the fabricated structures at different substrate positions with respect to exposure time, exposure angle and associated light intensity profile. We presented experimental details related to the fabrication of symmetric and biaxial periodic nanostructures on photoresist, silicon surfaces, and ion-milled glass substrates. Behavior of osteoblasts and osteoclasts on the nanostructures was investigated. These results ...


Automated Segmentation Of Left And Right Ventricles In Mri And Classification Of The Myocarfium Abnormalities, Cyrus (Mohammad Saleh) Nambakhsh Sep 2013

Automated Segmentation Of Left And Right Ventricles In Mri And Classification Of The Myocarfium Abnormalities, Cyrus (Mohammad Saleh) Nambakhsh

Electronic Thesis and Dissertation Repository

A fundamental step in diagnosis of cardiovascular diseases, automated left and right ventricle (LV and RV) segmentation in cardiac magnetic resonance images (MRI) is still acknowledged to be a difficult problem. Although algorithms for LV segmentation do exist, they require either extensive training or intensive user inputs. RV segmentation in MRI has yet to be solved and is still acknowledged a completely unsolved problem because its shape is not symmetric and circular, its deformations are complex and varies extensively over the cardiac phases, and it includes papillary muscles. In this thesis, I investigate fast detection of the LV endo- and ...


Vascular Segmentation Algorithms For Generating 3d Atherosclerotic Measurements, Eranga Ukwatta Aug 2013

Vascular Segmentation Algorithms For Generating 3d Atherosclerotic Measurements, Eranga Ukwatta

Electronic Thesis and Dissertation Repository

Atherosclerosis manifests as plaques within large arteries of the body and remains as a leading cause of mortality and morbidity in the world. Major cardiovascular events may occur in patients without known preexisting symptoms, thus it is important to monitor progression and regression of the plaque burden in the arteries for evaluating patient's response to therapy. In this dissertation, our main focus is quantification of plaque burden from the carotid and femoral arteries, which are major sites for plaque formation, and are straight forward to image noninvasively due to their superficial location. Recently, 3D measurements of plaque burden have ...


Numerical Investigation Of The Interdependence Between Humeral Implant Position And Bone Removal Amount For Total Elbow Arthroplasty, Alexander J. Heroux Aug 2013

Numerical Investigation Of The Interdependence Between Humeral Implant Position And Bone Removal Amount For Total Elbow Arthroplasty, Alexander J. Heroux

Electronic Thesis and Dissertation Repository

Total elbow arthroplasty is a surgical procedure used to replace an afflicted articulation with prosthetic joint components. A good alignment between the native and prosthetic flexion-extension axes of the elbow is required to preserve its functionality. However, this is often unobtainable because of the mismatch between humeral canal and implant stem geometries. To correct this, surgeons are often required to intraoperatively make error-prone decisions when determining an appropriate implant posture that minimizes the amount of cortical bone to be removed while maintaining the alignment between the two flexion-extension axes. To address this issue, the present study has developed computational tools ...


Piv-Based Investigation Of Hemodynamic Factors In Diseased Carotid Artery Bifurcations With Varying Plaque Geometries, Sarah Kefayati Aug 2013

Piv-Based Investigation Of Hemodynamic Factors In Diseased Carotid Artery Bifurcations With Varying Plaque Geometries, Sarah Kefayati

Electronic Thesis and Dissertation Repository

Ischemic stroke is often a consequence of complications due to clot formation (i.e. thrombosis) at the site of an atherosclerotic plaque developed in the internal carotid artery. Hemodynamic factors, such as shear-stress forces and flow disturbances, can facilitate the key mechanisms of thrombosis. Atherosclerotic plaques can differ in the severity of stenosis (narrowing), in eccentricity (symmetry), as well as inclusion of ulceration (wall roughness). Therefore, in terms of clinical significance, it is important to investigate how the local hemodynamics of the carotid artery is mediated by the geometry of plaque. Knowledge of thrombosis-associated hemodynamics may provide a basis to ...


Reproducibility Of Hyperpolarized Xenon-129 Magnetic Resonance Imaging, Nikhil Kanhere Jul 2013

Reproducibility Of Hyperpolarized Xenon-129 Magnetic Resonance Imaging, Nikhil Kanhere

Electronic Thesis and Dissertation Repository

Spirometry and plethysmography provide gold standard measurements of obstructive lung disease, although these are global measurements of lung function made at the mouth, of a highly regionally heterogeneous disease. Hyperpolarized 129Xe magnetic resonance imaging (MRI) is a non-invasive, non-radiation-based imaging tool for visualizing regional lung structure and function. However, the reproducibility of 129Xe MRI measurements has not yet been studied or determined. Hence, in this thesis, we evaluated the reproducibility of 129Xe MRI using quantitative measurements such as ventilation defect percent (VDP). We showed that 129Xe VDP had high intra-observer and inter-observer reproducibility for repeated scans ...


On The Development Of A Dynamic Contrast-Enhanced Near-Infrared Technique To Measure Cerebral Blood Flow In The Neurocritical Care Unit, Jonathan T. Elliott May 2013

On The Development Of A Dynamic Contrast-Enhanced Near-Infrared Technique To Measure Cerebral Blood Flow In The Neurocritical Care Unit, Jonathan T. Elliott

Electronic Thesis and Dissertation Repository

A dynamic contrast-enhanced (DCE) near-infrared (NIR) method to measure cerebral blood flow (CBF) in the neurocritical care unit (NCU) is described. A primary concern in managing patients with acquired brain injury (ABI) is onset of delayed ischemic injury (DII) caused by complications during the days to weeks following the initial insult, resulting in reduced CBF and impaired oxygen delivery.

The development of a safe, portable, and quantitative DCE-NIR method for measuring CBF in NCU patients is addressed by focusing on four main areas: designing a clinically compatible instrument, developing an appropriate analytical framework, creating a relevant ABI animal model, and ...


Geometrical Analysis And Modeling Of Craniosynostosis, Sahar Shahbazi Nov 2012

Geometrical Analysis And Modeling Of Craniosynostosis, Sahar Shahbazi

Electronic Thesis and Dissertation Repository

Craniosynostosis is a developmental abnormality in skull growth, due to the fusion of one or more sutures\cite{patho}. To accommodate the growing brain. the skull needs to grow quickly in the first few months of life, and most of the growth of the skull at that time occurs at the sutures. Craniosynostosis occurs when one or more sutures are fused in utero, resulting in an abnormal skull shape. Surgical intervention is usually required at a young age, and remodeling of the skull is done for cosmetic reasons as well as to avoid raised intracranial pressure. In order to study ...


Metrics For Evaluating Surgical Microscope Usage During Myringotomy, Arefin M. Shamsil Aug 2012

Metrics For Evaluating Surgical Microscope Usage During Myringotomy, Arefin M. Shamsil

Electronic Thesis and Dissertation Repository

Abstract

Although teaching and learning surgical microscope manoeuvring is a fundamental step in middle ear surgical training, currently there is no objective method to teach or assess this skill. This thesis presents an experimental study designed to implement and test sets of metrics capable of numerically evaluating microscope manoeuvrability and qualitatively assessing surgical expertise of a subject during a middle ear surgery called myringotomy. The experiment involved performing a myringotomy on a fixed cadaveric ear. As participants, experienced ear-nose-throat (ENT) surgeons and ENT surgical residents were invited. While performing the procedure, their microscope manoeuvring motions were captured as translational and ...


Augmented Image-Guidance For Transcatheter Aortic Valve Implantation, Pencilla Lang Jul 2012

Augmented Image-Guidance For Transcatheter Aortic Valve Implantation, Pencilla Lang

Electronic Thesis and Dissertation Repository

The introduction of transcatheter aortic valve implantation (TAVI), an innovative stent-based technique for delivery of a bioprosthetic valve, has resulted in a paradigm shift in treatment options for elderly patients with aortic stenosis. While there have been major advancements in valve design and access routes, TAVI still relies largely on single-plane fluoroscopy for intraoperative navigation and guidance, which provides only gross imaging of anatomical structures. Inadequate imaging leading to suboptimal valve positioning contributes to many of the early complications experienced by TAVI patients, including valve embolism, coronary ostia obstruction, paravalvular leak, heart block, and secondary nephrotoxicity from contrast use.

A ...


Real-Time Prostate Motion Tracking For Robot-Assisted Laparoscopic Radical Prostatectomy, Mehdi Esteghamatian May 2012

Real-Time Prostate Motion Tracking For Robot-Assisted Laparoscopic Radical Prostatectomy, Mehdi Esteghamatian

Electronic Thesis and Dissertation Repository

Radical prostatectomy surgery (RP) is the gold standard for treatment of localized prostate cancer (PCa). Recently, emergence of minimally invasive techniques such as Laparoscopic Radical Prostatectomy (LRP) and Robot-Assisted Laparoscopic Radical Prostatectomy (RARP) has improved the outcomes for prostatectomy. However, it remains difficult for surgeons to make informed decisions regarding resection margins and nerve sparing since the location of the tumour within the organ is not usually visible in a laparoscopic view. While MRI enables visualization of the salient structures and cancer foci, its efficacy in LRP is reduced unless it is fused into a stereoscopic view such that homologous ...


Modeling Lung Tissue Motions And Deformations: Applications In Tumor Ablative Procedures, Ali Sadeghi Naini May 2011

Modeling Lung Tissue Motions And Deformations: Applications In Tumor Ablative Procedures, Ali Sadeghi Naini

Electronic Thesis and Dissertation Repository

Various types of motion and deformation that the lung undergoes during minimally invasive tumor ablative procedures have been investigated and modeled in this dissertation. The lung frequently undergoes continuous large respiratory deformation, which can greatly affect the pre-planned outcome of the operation, hence deformation compensation becomes necessary. The first type of major deformation involved in a target lung throughout a tumor ablative procedure is the one encountered in procedures where the lung is totally deflated before starting the operation. A consequence of this deflation is that pre-operative images (acquired while the lung was partially inflated) become inaccurate for targeting the ...


Virtual And Augmented Reality Techniques For Minimally Invasive Cardiac Interventions: Concept, Design, Evaluation And Pre-Clinical Implementation, Cristian A. Linte Aug 2010

Virtual And Augmented Reality Techniques For Minimally Invasive Cardiac Interventions: Concept, Design, Evaluation And Pre-Clinical Implementation, Cristian A. Linte

Electronic Thesis and Dissertation Repository

While less invasive techniques have been employed for some procedures, most intracardiac interventions are still performed under cardiopulmonary bypass, on the drained, arrested heart. The progress toward off-pump intracardiac interventions has been hampered by the lack of adequate visualization inside the beating heart.

This thesis describes the development, assessment, and pre-clinical implementation of a mixed reality environment that integrates pre-operative imaging and modeling with surgical tracking technologies and real-time ultrasound imaging. The intra-operative echo images are augmented with pre-operative representations of the cardiac anatomy and virtual models of the delivery instruments tracked in real time using magnetic tracking technologies. As ...