Bioimaging and Biomedical Optics Commons^™

A Study Of Acoustically Activated Nanodroplets, Songita Choudhury

Theses & Dissertations

Current treatment of acute myocardial infarction (AMI), which is the main pathophysiological event leading to death in the United States, has advanced considerably with the introduction of emergent percutaneous interventions, but there remains an urgent need for novel techniques to rapidly and accurately detect infarcted or ischemic tissue that results from AMI. Ultrasound contrast agents, also known as microbubbles (MB), have become commonplace in echocardiography. However, MBs are purely intravascular tracers and unable to cross endothelial barriers due to size. The limitations of MBs, namely size and short circulation times within the human body, led to the development of phase-change …

Modeling Eeg And Tdcs In Scirun Software Packages, Aiden Keene, Aiden Thomas Keene

Senior Honors Projects

Never before has there been a greater emphasis on improving the shortcomings of treating mental health conditions. Our generation has more knowledge about technological practices with the potential to monitor and treat mental health symptoms than that of any generation before us. A breakthrough in this field made by CREmedical is called Tripolar Concentric Ring Electrodes (TCRE’s), which can measure signals from the brain more accurately than conventional electrodes. At CREmedical, TCREs are being used to study differences in electrical activity in the brain so as to identify abnormalities, and monitor responses to stimulation therapies. This semester I had the …

Extraction And Analysis Of Vector Flow Imaging Data In A Pediatric Population, Bailey Stinnett

Biomedical Engineering Undergraduate Honors Theses

Vector flow imaging (VFI) is a new ultrasound technology that provides real time, angle-independent visualization of flow velocities in the heart and great vessels. Thus far, VFI has been used for superficial applications due to the limited penetration depth of available transducer probes; however, this depth in smaller pediatric patients enables adequate aortic views. In this project, VFI was used to study pediatric aortic stenosis (PAS)—a congenital heart defect that results in the narrowing of the aorta and/or aortic valve. The decision to refer PAS patients for surgical or catheter-based intervention is initially based on Doppler ultrasound. VFI is potentially …

Quantification Of Tumor-Associated Macrophages Following Immunomodulation Therapy In A Murine Allograft Model Of Colorectal Carcinoma, Caroline Spainhour

Biomedical Engineering Undergraduate Honors Theses

Colorectal Carcinoma (CRC) is one of the deadliest cancers in the world, with 150,000 new cases annually in the United States. Traditional treatments include chemotherapy and invasive surgery; however, research has shown that only 25% of patients that undergo traditional treatment have a positive result. Immunotherapy is an emerging form of cancer treatment that utilizes the patients’immune system to fight cancer cells by targeting inflammation, which plays a large role in the proliferation and metastasis of cancer cells.

Tumor-associated macrophages (TAMs) are immune cells that affect the inflammatory microenvironment of tumors. TAMs are M1 in the early stages of tumors, …

Comparison Of Varying Tissue Freezing Methods On Murine Colonic Tissue, James Hughes

Biomedical Engineering Undergraduate Honors Theses

Histology often requires a tissue specimen to be embedded so that it may be sectioned, stained, and mounted on a microscope slide for viewing. One common method of tissue embedding for rapid histology is freezing, since freezing allows tissue to be stored without the need for fixing. Frozen tissue is often embedded in a medium such as Optimal Cutting Temperature (OCT) compound so that it can be sectioned using a cryostat. However, factors such as ice-crystal formation during the freezing process can cause damage to the tissue. As such, the protocol used to freeze the tissue can affect the quality …

Experimental And Model-Based Terahertz Imaging And Spectroscopy For Mice, Human, And Phantom Breast Cancer Tissues, Tyler Bowman

Graduate Theses and Dissertations

The goal of this work is to investigate terahertz technology for assessing the surgical margins of breast tumors through electromagnetic modeling and terahertz experiments. The measurements were conducted using a pulsed terahertz system that provides time and frequency domain signals. Three types of breast tissues were investigated in this work. The first was formalin-fixed, paraffin-embedded tissues from human infiltrating ductal and lobular carcinomas. The second was human tumors excised within 24-hours of lumpectomy or mastectomy surgeries. The third was xenograft and transgenic mice breast cancer tumors grown in a controlled laboratory environment to achieve more data for statistical analysis.

Experimental …

Renal Granulomatosis Post Intravesical Bacillus Calmette-Guerin Therapy For Non-Muscle-Invasive Bladder Cancer, Karen Tran-Harding, Rashmi T. Nair, Halemane S. Ganesh

Radiology Faculty Publications

Intravesical Bacillus Calmette–Guerin (BCG) immunotherapy is a proven, effective treatment for intermediate- and high-risk non-muscle-invasive bladder cancer. Minor side effects are common and expected but systemic effects can occur in < 5% of treated patients. We present a rare case of a 49-year-old male that presented with fever and chills after 3 weeks of intravesical BCG therapy post transurethral resection of bladder tumor. New renal lesions were present on contrast-enhanced computed tomography scan which was histologically proven to be necrotizing renal granulomatosis.

An Area Based Fan Beam Projection Model, Richard E. Steele, Jiehua Zhu

Honors College Theses

Area based projection models for computed tomography mitigate raw data errors by treating X-Rays as beams, whereas traditional line based projection models treat an X-Ray like a line, thus generating significant error. In an existing area based fan beam projection model, a rotation matrix, Q, simulates the rotation of the emitter detector pair to reduce computational load, but this introduces approximations by using an approximated rotation matrix. We eliminate approximations by deriving an exact formula for the entries of Q. Using a rotation of axes and by considering the neighboring cells' contributions to the area, the result has formulations for …

Characterization Of Computed Tomography Radiomic Features Using Texture Phantoms, Muhammad Shafiq Ul Hassan

USF Tampa Graduate Theses and Dissertations

Radiomics treats images as quantitative data and promises to improve cancer prediction in radiology and therapy response assessment in radiation oncology. However, there are a number of fundamental problems that need to be solved in order to potentially apply radiomic features in clinic. The first basic step in computed tomography (CT) radiomic analysis is the acquisition of images using selectable image acquisition and reconstruction parameters. Radiomic features have shown large variability due to variation of these parameters. Therefore, it is important to develop methods to address these variability issues in radiomic features due to each CT parameter. To this end, …

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin …

Optimization Of Microfluidic Chip Fabrication Via Femtosecond Laser Ablation, Kenneth Aycock

Senior Theses

Microfluidic devices have become staple tools in biomedical research and have a promising future as low cost, point-of-care (POC) diagnostic devices. Despite the advancements in microfluidic device technology, the manipulation and fabrication of these systems can be tedious and expensive. Repeatable techniques in which computer-aided designs are translated into microfluidic systems in a matter of minutes are highly desirable both for researchers and manufacturers. Laser ablation of tape substrates has shown promise in producing cost-effective, rapidly manipulable devices, but the work done thus far has utilized continuous wave lasers that perform suboptimally due to the relatively short wavelengths used and …

Radiotherapy-Induced Cherenkov Luminescence Imaging In A Human Body Phantom, Syed Rakin Ahmed, Mengyu Jia, Petr Bruza, Sergei A. Vinogradov, Shudong Jiang, David J. Gladstone, Lesley A. Jarvis, Brian W. Pogue

Dartmouth Scholarship

Radiation therapy produces Cherenkov optical emission in tissue, and this light can be utilized to activate molecular probes. The feasibility of sensing luminescence from a tissue molecular oxygen sensor from within a human body phantom was examined using the geometry of the axillary lymph node region. Detection of regions down to 30-mm deep was feasible with submillimeter spatial resolution with the total quantity of the phosphorescent sensor PtG4 near 1 nanomole. Radiation sheet scanning in an epi-illumination geometry provided optimal coverage, and maximum intensity projection images provided illustration of the concept. This work provides the preliminary information needed to attempt …

P-42 Using The Raspberry Pi For Ecl Reaction Analysis, Jonathan Swerdlow

Honors Scholars & Undergraduate Research Poster Symposium Programs

Using a Raspberry Pi and its camera module, we developed an affordable and easily available system for photographing and analyzing electrochemiluminescent (ECL) reactions. These reactions can be represented as a function of average light intensity over time, allowing for a future program to determine the concentration of certain reactants. Such ECL reactions will be useful in the diagnosis of medical conditions such as cancer without the need for expensive equipment or laboratories. The proposed system will make certain diagnoses easy and available to people across the globe and will likely require only a small blood sample. It will also be …

Optimal Wavelength Selection For Optical Spectroscopy Of Hemoglobin And Water Within A Simulated Light-Scattering Tissue, Mikael Marois, Stephen L. Jacques, Keith D. Paulsen

Dartmouth Scholarship

An algorithm that selects optimal wavelengths for spectral fitting of diffuse light reflectance spectra using a nonnegative least squares method is presented. Oxyhemoglobin, deoxyhemoglobin, and water are considered representative absorbers, but the approach is not constrained or limited by absorber selection provided native basis spectra are available. The method removes wavelengths iteratively from a scattering-modulated absorption matrix by maximizing the product of its singular values and offers considerable improvements over previously published wavelength selection schemes. Resulting wavelength selections are valid for a broad range of optical properties and yield lower RMS errors than other wavelength combinations. The method is easily …

Biomedical Optics Scientific Community, Brian W. Pogue

Dartmouth Scholarship

The new Editor-in-Chief, Brian Pogue, gives an overview of the biomedical optics community.

Objectively Measuring Effects Of Electro-Acupuncture In Parkinsonian Rhesus Monkeys, Rui Zhang, Anders H. Andersen, Peter A. Hardy, Eric Forman, April Evans, Yi Ai, Jin Yue, Guihua Yue, Don M. Gash, Richard Grondin, Zhiming Zhang

Magnetic Resonance Imaging and Spectroscopy Center Faculty Publications

Acupuncture has increasingly been used as an alternative therapy for treatment of Parkinson’s disease (PD). However, the efficacy of acupunture for PD still remains unclear. The present study was designed to objectively and safely monitor anti-parkinsonian effects of electroacupuncture (EA) and brain activity in nonhuman primates modeling human PD. Six middle-aged rhesus monkeys were extensively studied by a computerized behavioral testing battery and by pharmacological MRI (phMRI) scans with specific dopaminergic drug stimulations. All animals were evaluated for behavior and phMRI responses under normal, parkinsonian, parkinsonian with EA treatment and parkinsonian after EA treatment conditions. Stable parkinsonian features were observed …

Early Emerging Pathogen Detection, Mackenzie Wangenstein

Undergraduate Research & Mentoring Program

A supervised learning technique was employed to identify emerging pathogen species. Portland State University has partnered with the University of New Mexico to take encodings of unknown pathogen molecular structures to determine emerging species.

Study Of Mri Signal In The Presence Of Discrete Spherical Magnetic Particles, Paul Kokeny

Wayne State University Dissertations

Simulating signal behavior in Magnetic Resonance imaging (MRI) is often a necessary step in being able to understand how signal relates to certain physiological parameters. One such parameter of interest in the body is magnetic susceptibility since it is related to iron content. The bulk magnetic susceptibility of an object is a property that describes how magnetized it becomes when placed in an external magnetic field. When the bulk susceptibility of an object arises from the presence of discrete magnetic inclusions, the MRI phase signal inside the object can no longer be determined analytically by assuming it has a continuous …

Optical Coherence Tomography Application To Alopecia In The Scalp, Elizabeth Melcher

Research Opportunities for Engineering Undergraduates (ROEU) Program 2017-18

Alopecia is the loss of hair, whether it be from the scalp or other regions of the body. Current techniques used to best diagnose and track alopecia are often invasive, requiring a biopsy for results. The use of the OCT, or optical coherence tomography, could drastically improve a patient’s experience in undergoing a diagnosis while proving accurate results. The objective of this study is to develop diagnostic algorithms for the rapid, non-invasive diagnosis of alopecia with OCT. The first step is collecting OCT images of a healthy scalp to understand the anatomical structures with the imaging technique.

Design And Development Of A Compact X-Ray Tube For Stationary Ct Architecture, Ashish Vighnahar Avachat

Doctoral Dissertations

"Multisource architectures enable sweeping one or more x-ray beams across the imaging field-of-view faster than physically moving a single x-ray source and/or a detector. Hence, these architectures are attractive for the applications in which temporal resolution plays an important role, for example, cardiac computed tomography (CT) or real-time CT. One of the recent developments in multisource architectures for CT imaging is stationary CT architecture, whereby two separate stationary arrays -- one for x-ray sources and one for detectors -- are utilized to sweep one or more x-ray beams along the gantry and acquire 360 degree projections. To have a stationary …

Multimodal Noncontact Diffuse Optical Reflectance Imaging Of Blood Flow And Fluorescence Contrasts, Daniel Irwin

Theses and Dissertations--Biomedical Engineering

In this study we design a succession of three increasingly adept diffuse optical devices towards the simultaneous 3D imaging of blood flow and fluorescence contrasts in relatively deep tissues. These metrics together can provide future insights into the relationship between blood flow distributions and fluorescent or fluorescently tagged agents. A noncontact diffuse correlation tomography (ncDCT) device was firstly developed to recover flow by mechanically scanning a lens-based apparatus across the sample. The novel flow reconstruction technique and measuring boundary curvature were advanced in tandem. The establishment of CCD camera detection with a high sampling density and flow recovery by speckle …

The Effects Of Emerging Technology On Healthcare And The Difficulties Of Integration, Skyler J. Pavlish-Carpenter

Honors Undergraduate Theses

Background: Disruptive technology describes technology that is significantly more advanced than previous iterations, such as: 3D printing, genetic manipulation, stem cell research, innovative surgical procedures, and computer-based charting software. These technologies often require extensive overhauls to implement into older systems and must overcome many difficult financial and societal complications before they can be widely used. In a field like healthcare that makes frequent advancements, these difficulties can mean that the technology will not be utilized to its full potential or implemented at all.

Objective: To determine the inhibiting factors that prevent disruptive technology from being implemented in conventional healthcare.

Methods: …