Bioimaging and Biomedical Optics Commons^™

In Vivo Metabolic And Vascular Response To Hypoxia In Twist Knockdown Murine Breast Cancer, Brandon Sturgill

Graduate Theses and Dissertations

Twist transcription factor is often overexpressed in aggressive tumors. Although needed in early embryonic development for organogenesis, Twist is known to induce an epithelial to mesenchymal transition in cells. In cancer, epithelial to mesenchymal transitions can lead to increased motility and invasiveness. It has also been linked to metabolic reprogramming and increased metastatic risk. Furthermore, metabolic preferences can increase proliferation, enhance metastatic potential, and influence the site of metastasis. We hypothesize that Twist directly affects the metabolism of cancer cells. We expect to see in vivo what we have seen in vitro; Twist overexpression should promote a shift away from …

Quantitative Analysis Techniques For Assessing Organelle Organization And Dynamics In Individual Cells, Isaac Vargas

Graduate Theses and Dissertations

In biomedical optics and microscopy, the organization and morphology of organelles have been widely studied. In spite of novel imaging techniques, there is still a lack of quantitative tools to easily measure cellular characteristics from image data. Previous studies have explored multiple approaches to assess organelle organization and alignment, resulting in complicated and extensive algorithms that are both subject to multiple steps of image processing and influenced by non-cellular artifacts. In this thesis, a technique called the Modified Blanket Method (MBM) is introduced to quantify organelle organization through measurements of fractal dimension (FD) on a pixel-by-pixel basis. With the use …

Optical Spectrsocopy Of Murine Breast Tumor To Distinguish Indolent From Aggressive Disease, Joel Rodriguez Troncoso

Biomedical Engineering Undergraduate Honors Theses

Breast cancer accounts for 30% of all cancer. Metastasis is the primary cause of death among breast cancer patients. Additionally, current molecular profiling methods such as Oncotype DX, which are expensive and not widely available at all clinical facilities, only determine the risk of recurrence after treatment. Therefore, there are no current method capable of identifying metastatic patients in advance.As a result, there is an unmet clinical need to develop a cost-effective prognostic to differentiate between indolent and aggressive breast tumors. In this study, we implemented diffuse reflectance spectroscopy (DRS) system to evaluate functional changes in tumor xenografts originated from …

Label-Free Microrna Optical Biosensors, Meimei Lai, Gymama Slaughter

Bioelectrics Publications

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection …

Measuring Collagen Arrangement And Its Relationship With Preterm Birth Using Mueller Matrix Polarimetry, Joseph James Chue-Sang

FIU Electronic Theses and Dissertations

Preterm birth (PTB) is defined as delivery prior to 37 weeks of gestation. It is the leading cause of infant death worldwide, responsible for infant neurological disorders, long-term cognitive impairment, as well as chronic health issues involving the auditory, visual, digestive, and respiratory systems. In expectant mothers, causes for PTB can include infection, inflammation, vascular disease, short intervals between pregnancies, multiple gestations and genetic factors. In the U.S., PTB occurs in over 11% of births and at an elevated 18.1% in Miami-Dade County, FL; while in the developing world the incidence of PB is over 15%. Early identification of at-risk …

Design, Construction And Application Of A Home-Built, Two-Photon Microscope, William P. Breeding

Electronic Theses and Dissertations

Two-photon microscopy (TPM) is a powerful, versatile imaging modality for the study of biological systems. This thesis overviews the relevant physics involved in TPM, design considerations and process of constructing a home-built, two-photon microscope, and provides a set of procedures to operate the system. Furthermore, this work explores several applications of TPM through the study of single-cell metabolism and imaging the cellular-material interface. Explored in particular depth was the imaging of cellulose nanofiber (CNF) materials, with the goal of understanding the three-dimensional nature of fibroblast cell growth when embedded within the materials. This work uncovered several optical properties of CNF, …

Multi-Dimensional Extension Of The Alternating Minimization Algorithm In X-Ray Computed Tomography, Jingwei Lu

McKelvey School of Engineering Theses & Dissertations

X-ray computed tomography (CT) is an important and effective tool in medical and industrial imaging applications. The state-of-the-art methods to reconstruct CT images have had great development but also face challenges. This dissertation derives novel algorithms to reduce bias and metal artifacts in a wide variety of imaging modalities and increase performance in low-dose scenarios. The most widely available CT systems still use the single-energy CT (SECT), which is good at showing the anatomic structure of the patient body. However, in SECT image reconstruction, energy-related information is lost. In applications like radiation treatment planning and dose prediction, accurate energy-related information …

Multi-Dimensional Extension Of The Alternating Minimization Algorithm In X-Ray Computed Tomography, Jingwei Lu

McKelvey School of Engineering Theses & Dissertations

X-ray computed tomography (CT) is an important and effective tool in medical and industrial

imaging applications. The state-of-the-art methods to reconstruct CT images have had

great development but also face challenges. This dissertation derives novel algorithms to

reduce bias and metal artifacts in a wide variety of imaging modalities and increase performance

in low-dose scenarios.

The most widely available CT systems still use the single-energy CT (SECT), which is

good at showing the anatomic structure of the patient body. However, in SECT image

reconstruction, energy-related information is lost. In applications like radiation treatment

planning and dose prediction, accurate energy-related information …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.

Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available. Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …

Investigation Of The Effect Of Age On Regenerative Outcomes Following Treatment Of Volumetric Muscle Loss Injuries, John Taehwan Kim

Graduate Theses and Dissertations

Volumetric muscle loss (VML) is a traumatic injury in skeletal muscle resulting in the bulk loss of more than 20% of the muscle’s volume. Included in the bulk loss of muscle is the skeletal muscle niche comprised of nerve bundles, vasculature, local progenitor cells, basal lamina, and muscle fibers, overwhelming innate repair mechanisms. The hallmark of VML injury is the excessive accumulation of non-contractile, fibrotic tissue and permanent functional deficits. Though predominant in the younger demographic, the elderly population is also captured within VML injuries. There are many factors that change with aging in skeletal muscle that may further hinder …

Automatic Methods To Enhance The Quality Of Colonoscopy Video, Nidhal Kareem Shukur Azawi

Graduate Theses and Dissertations

Colonoscopy is a form of endoscopy because it uses colonoscopy device to help the doctor to understand a colon patient. Enhancing the quality of Colonoscopy images is a challenge because of the wet and dynamic environment inside the colon causes many problems even the colonoscope devise has a good quality. Some of these problems are blurriness, specular highlights shiny areas.

In this work, different kinds of techniques have been investigated in order to improve the quality of colonoscopy images. Also, variety of preprocessing approaches (removing bad images, resizing images, median filtration with and without image resizing) have been conducted to …

Visualizing Ischemic Skin Flap Necrosis Through Phasor Analysis Of Autofluorescence Lifetime Images, Hallie Ramser Toomer

Graduate Theses and Dissertations

Necrotic skin flaps are difficult to predict and treat due to the lack of quantitative biomarkers. Label-free multiphoton microscopy is well suited for non-invasively monitoring skin metabolism through NAD(P)H and other intrinsic fluorophores, and offers immediate future directions for assessing necrosis in the clinic. The objective of this study was to assess whether phasor FLIM could be used to evaluate skin flap status and treatment efficacy in ex vivo skin sections. Phasor maps revealed differences in growth factor treatment and region, but changes in skin flap autofluorescence at 755nm excitation and 460nm emission were not just related to NAD(P)H. A …

Resolving Intravoxel White Matter Structures In The Human Brain Using Regularized Regression And Clustering, Andrea Hart, Brianna Smith, Sean Smith, Elijah Sales, Jacqueline Hernandez-Camargo, Yarlin Mayor Garcia, Felix Zhan, Lori Griswold, Brian Dunkelberger, Michael R. Schwob, Sharang Chaudhry, Justin Zhan, Laxmi Gewali, Paul Oh

Computer Science Faculty Research

The human brain is a complex system of neural tissue that varies significantly between individuals. Although the technology that delineates these neural pathways does not currently exist, medical imaging modalities, such as diffusion magnetic resonance imaging (dMRI), can be leveraged for mathematical identification. The purpose of this work is to develop a novel method employing machine learning techniques to determine intravoxel nerve number and direction from dMRI data. The method was tested on multiple synthetic datasets and showed promising estimation accuracy and robustness for multi-nerve systems under a variety of conditions, including highly noisy data and imprecision in parameter assumptions.

Using Feature Extraction From Deep Convolutional Neural Networks For Pathological Image Analysis And Its Visual Interpretability, Wei-Wen Hsu

Electrical & Computer Engineering Theses & Dissertations

This dissertation presents a computer-aided diagnosis (CAD) system using deep learning approaches for lesion detection and classification on whole-slide images (WSIs) with breast cancer. The deep features being distinguishing in classification from the convolutional neural networks (CNN) are demonstrated in this study to provide comprehensive interpretability for the proposed CAD system using the domain knowledge in pathology. In the experiment, a total of 186 slides of WSIs were collected and classified into three categories: Non-Carcinoma, Ductal Carcinoma in Situ (DCIS), and Invasive Ductal Carcinoma (IDC). Instead of conducting pixel-wise classification (segmentation) into three classes directly, a hierarchical framework with the …

Spatial Frequency Domain Imaging Of Short-Wave Infrared Fluorescence For Biomedical Applications, Joseph P. Leonor

ENGS 88 Honors Thesis (AB Students)

Fluorescence imaging has become a standard in many clinical applications, such as tumor and vasculature imaging. One application that is becoming more prominent in cancer treatment is fluorescence-guided surgery (FGS). Currently, FGS allows surgeons the ability to visually navigate tumors and tissue structures intraoperatively. As a result, they can remove tumor more efficiently while maintaining critical structures within the patient, creating better outcomes and lower recovery times. However, background fluorescence and inability to localize depth create challenges when determining resection boundaries.

Different techniques, such as spatially modulating the illumination and imaging at longer light wavelengths, have been developed to accurately …

Designing A Low-Cost Ultrasound Pulser, Andrea Huey

Honors Theses

Ultrasound imaging allows for those studying living beings to see inside a subject without causing it harm. This allows for real-time images to be taken, leading to ease of observational research. However, while this technology is beneficial to those who utilize it, the devices used to create and receive ultrasound pulses can be incredibly complex, allowing for precise adjustment of the output signal and various other functions, and therefore expensive. The focus of this senior project is the design of a low-cost pulser for use with an ultrasound transducer. While it does not have all the high-level functions of the …

Evaluation Of Human Umbilical Vein Endothelial Cells In Blood Vessel Mimics Through Changes In Gene Expression And Caspase Activity, Conor Charles Hedigan

Master's Theses

Blood vessel mimics (BVMs) are simple tissue engineered blood vessel constructs intended for preclinical testing of vascular devices. This thesis developed and implemented methods to characterize two of these components. The first aim of this thesis investigated the effect of cell culture duration and flow conditions on endothelial cell gene expression, especially regarding endothelial-to-mesenchymal transition (EndMT). A trend of decreased endothelial marker gene expression and increased mesenchymal marker gene expression would indicate EndMT. qPCR analysis revealed that increased cell culture duration did not result in EndMT, and in fact increased endothelial marker expression as cell culture duration increased. Disturbed flow …

A Multimodal Approach To Investigate Brain Reorganization After Spinal Cord Injury Using Functional Magnetic Resonance Imaging And Functional Near-Infrared Spectroscopy, Keerthana Deepti Karunakaran

Dissertations

Traumatic Spinal Cord Injury (SCI) results in structural and functional neurological changes at both the brain and the level of the spinal cord. Anatomical studies indicate decreased grey matter volume in sensorimotor and non-sensorimotor regions of the cortex following SCI; whereas, neurophysiological findings mostly report altered functional activity in the sensorimotor nodes of the cortex, subcortex, and cerebellum. Therefore, it is currently unknown whether tissue atrophy observed in non-motor related areas has any concomitant functional consequences. Furthermore, the neural underpinnings of adaptive neuroplasticity after SCI is not well-defined in the current literature. Hence, this dissertation is a pioneer study investigating …

Dual Modality Optical Coherence Tomography : Technology Development And Biomedical Applications, Farzana Rahmat Zaki

Dissertations

Optical coherence tomography (OCT) is a cross-sectional imaging modality that is widely used in clinical ophthalmology and interventional cardiology. It is highly promising for in situ characterization of tumor tissues. OCT has high spatial resolution and high imaging speed to assist clinical decision making in real-time.

OCT can be used in both structural imaging and mechanical characterization. Malignant tumor tissue alters morphology. Additionally, structural OCT imaging has limited tissue differentiation capability because of the complex and noisy nature of the OCT signal. Moreover, the contrast of structural OCT signal derived from tissue’s light scattering properties has little chemical specificity. Hence, …