Bioimaging and Biomedical Optics Commons^™

Development And Evaluation Of A Connective Tissue Phantom Model For Subsurface Visualization Of Cancers Requiring Wide Local Excision, Kimberly S. Samkoe, Brent D. Bates, Niki N. Tselepidakis, Alisha V. Dsouza, Jason R. Gunn, Dipak B. Ramkumar, Keith D. Paulsen, Brian W. Pogue, Eric R. Henderson

Dartmouth Scholarship

Wide local excision (WLE) of tumors with negative margins remains a challenge because surgeons cannot directly visualize the mass. Fluorescence-guided surgery (FGS) may improve surgical accuracy; however, conventional methods with direct surface tumor visualization are not immediately applicable, and properties of tissues surrounding the cancer must be considered. We developed a phantom model for sarcoma resection with the near-infrared fluorophore IRDye 800CW and used it to iteratively define the properties of connective tissues that typically surround sarcoma tumors. We then tested the ability of a blinded surgeon to resect fluorescent tumor-simulating inclusions with ∼1-cm margins using predetermined target fluorescence intensities …

Image Reconstruction Of The Speed Of Sound And Initial Pressure Distributions In Ultrasound Computed Tomography And Photoacoustic Computed Tomography, Thomas Paul Matthews

McKelvey School of Engineering Theses & Dissertations

Ultrasound computed tomography (USCT) and photoacoustic computed tomography (PACT) are two emerging imaging modalities that have a wide range of potential applications from pre-clinical small animal imaging to cancer screening in human subjects. USCT is typically employed to measure acoustic contrasts, including the speed of sound (SOS) distribution, while PACT typically measures optical contrasts or some related quantity such as the initial pressure distribution. Their complementary contrasts and similar implementations make USCT and PACT a natural fit for a hybrid imaging system. Still, much work remains to realize this promise. First, USCT image reconstruction methods based on the acoustic wave …

Characterization Of Structural Dynamics Of The Human Head Using Magnetic Resonance Elastography, Andrew Arun Badachhape

McKelvey School of Engineering Theses & Dissertations

In traumatic brain injury (TBI), the skull-brain interface, composed of three meningeal layers: the dura mater, arachnoid mater, and pia mater, along with cerebrospinal fluid (CSF) between the layers, plays a vital role in transmitting motion from the skull to brain tissue. Magnetic resonance elastography (MRE) is a noninvasive imaging modality capable of providing in vivo estimates of tissue motion and material properties. The objective of this work is to augment human and phantom MRE studies to better characterize the mechanical contributions of the skull-brain interface to improve the parameterization and validation of computational models of TBI. Three specific aims …

Reconstruction Algorithms For Novel Joint Imaging Techniques In Pet, Homayoon Ranjbar

McKelvey School of Engineering Theses & Dissertations

Positron emission tomography (PET) is an important functional in vivo imaging modality with many clinical applications. Its enormously wide range of applications has made both research and industry combine it with other imaging modalities such as X-ray computed tomography (CT) or magnetic resonance imaging (MRI). The general purpose of this work is to study two cases in PET where the goal is to perform image reconstruction jointly on two data types.

The first case is the Beta-Gamma image reconstruction. Positron emitting isotopes, such as ¹¹C, ¹³N, and ¹⁸F, can be used to label molecules, and tracers, such …

System Optimization And Iterative Image Reconstruction In Photoacoustic Computed Tomography For Breast Imaging, Yang Lou

McKelvey School of Engineering Theses & Dissertations

Photoacoustic computed tomography(PACT), also known as optoacoustic tomography (OAT), is an emerging imaging technique that has developed rapidly in recent years. The combination of the high optical contrast and the high acoustic resolution of this hybrid imaging technique makes it a promising candidate for human breast imaging, where conventional imaging techniques including X-ray mammography, B-mode ultrasound, and MRI suffer from low contrast, low specificity for certain breast types, and additional risks related to ionizing radiation. Though significant works have been done to push the frontier of PACT breast imaging, it is still challenging to successfully build a PACT breast imaging …

Association Between Left Ventricular Mechanics And Diffuse Myocardial Fibrosis In Patients With Repaired Tetralogy Of Fallot: A Cross-Sectional Study, Christopher M. Haggerty, Jonathan D. Suever, Arichanah Pulenthiran, Abba Mejia-Spiegeler, Gregory J. Wehner, Linyuan Jing, Richard J. Charnigo, Brandon K. Fornwalt, Mark A. Fogel

Biomedical Engineering Faculty Publications

Background: Patients with repaired tetralogy of Fallot (TOF) have progressive, adverse biventricular remodeling, leading to abnormal contractile mechanics. Defining the mechanisms underlying this dysfunction, such as diffuse myocardial fibrosis, may provide insights into poor long-term outcomes. We hypothesized that left ventricular (LV) diffuse fibrosis is related to impaired LV mechanics.

Methods: Patients with TOF were evaluated with cardiac magnetic resonance in which modified Look-Locker (MOLLI) T1-mapping and spiral cine Displacement encoding (DENSE) sequences were acquired at three LV short-axis positions. Linear mixed modeling was used to define the association between regional LV mechanics from DENSE based on regional T1-derived diffuse …

Material Properties Design Using Simulations And Experiments For Powder Injection Molding Of Lead Zirconate Titanate (Pzt)., Bhushan Pramod Bandiwadekar

Electronic Theses and Dissertations

Powder injection molding (PIM) process simulations can be performed to minimize the number of injection molding experiments by estimating material properties necessary for PIM simulations. In current work, lead zirconate titanate (PZT) powder-polymer binder feedstock was compounded for 45 vol. % and 52 vol. % solids loading. PIM experiments on designed micro-pillar array geometry were performed using 52 vol. % PZT. Using PIM experiments results as basis, PIM simulations were performed on designed micro-pillar array geometries to understand the effectiveness of PIM simulations with the use of estimated feedstock properties in predicting molding behavior that have micro-features. Additionally, PIM simulations …

Computer-Aided Diagnoses (Cad) System: An Artificial Neural Network Approach To Mri Analysis And Diagnosis Of Alzheimer's Disease (Ad), Berizohar Padilla Cerezo

Master's Theses

Alzheimer’s disease (AD) is a chronic and progressive, irreversible syndrome that deteriorates the cognitive functions. Official death certificates of 2013 reported 84,767 deaths from Alzheimer’s disease, making it the 6th leading cause of death in the United States. The rate of AD is estimated to double by 2050. The neurodegeneration of AD occurs decades before symptoms of dementia are evident. Therefore, having an efficient methodology for the early and proper diagnosis can lead to more effective treatments.

Neuroimaging techniques such as magnetic resonance imaging (MRI) can detect changes in the brain of living subjects. Moreover, medical imaging techniques are the …

18f-Fdg Pet/Ctct-Based Radiomics For The Prediction Of Radiochemotherapy Treatment Outcomes Of Cervical Cancer, Badereldeen Abdulmajeed Altazi

USF Tampa Graduate Theses and Dissertations

Cervical cancer remains the third most commonly diagnosed gynecological malignancy in the United States and throughout the world despite being potentially preventable. Patients diagnosed with cervical cancer may develop local recurrence in the cervix and surrounding structures (vaginal apex, parametrial, or paracervical), regional recurrence in pelvic lymph nodes, distant metastasis, or a combination of all. The management of such treatment outcomes has not been subject to rigorous investigation. Therefore, there is a need for studies and clinical trials that focus on decision making to support the choice of the best treatment modality that leads to the minimal number of adverse …

Ambulatory Systolic Blood Pressure And Obesity Are Independently Associated With Left Ventricular Hypertrophic Remodeling In Children, Linyuan Jing, Christopher D. Nevius, Cassi M. Friday, Jonathan D. Suever, Arichanah Pulenthiran, Abba Mejia-Spiegeler, H. Lester Kirchner, William J. Cochran, Gregory J. Wehner, Aftab S. Chishti, Christopher M. Haggerty, Brandon K. Fornwalt

Biomedical Engineering Faculty Publications

Background: Children with obesity have hypertrophic cardiac remodeling. Hypertension is common in pediatric obesity, and may independently contribute to hypertrophy. We hypothesized that both the degree of obesity and ambulatory blood pressure (ABP) would independently associate with measures of hypertrophic cardiac remodeling in children.

Methods: Children, aged 8–17 years, prospectively underwent cardiovascular magnetic resonance (CMR) and ABP monitoring. Left ventricular (LV) mass indexed to height^2.7(LVMI), myocardial thickness and end-diastolic volume were quantified from a 3D LV model reconstructed from cine balanced steady state free precession images. Categories of remodeling were determined based on cutoff values for LVMI and …

Optimal Hemoglobin Extinction Coefficient Data Set For Near-Infrared Spectroscopy, Yue Zhao, Lina Qiu, Yunlong Sun, Chong Huang, Ting Li

Biomedical Engineering Faculty Publications

Extinction coefficient (ε) is a critical parameter for quantification of oxy-, deoxy-, and total-hemoglobin concentrations (Δ[HbO₂], Δ[Hb], Δ[tHb]) from optical measurements of Near-infrared spectroscopy (NIRS). There are several different ε data sets which were frequently used in NIRS quantification. A previous study reported that even a small variation in ε could cause a significant difference in hemodynamic measurements. Apparently the selection of an optimal ε data set is important for NIRS. We conducted oxygen-state-varied and blood-concentration-varied model experiments with 57 human blood samples to mimic tissue hemodynamic variations. Seven reported ε data sets were evaluated by comparisons between …

Effects Of Malformed Or Absent Valves To Lymphatic Fluid Transport And Lymphedema In Vivo In Mice, Akshay S. Pujari

Masters Theses

Lymph is primarily composed of fluid and proteins from the blood circulatory system that drain into the space surrounding cells, interstitial space. From the interstitial space, the fluid enters and circulates in the lymphatic system until it is delivered into the venous system. In contrast to the blood circulatory system, the lymphatic system lacks a central pumping organ dictating the predominant driving pressure and velocity of lymph. Transport of lymph via capillaries, pre-collecting and collecting lymphatic vessels relies on the synergy between pressure gradients, local tissue motion, valves and lymphatic vessel contractility. The direction of lymph transport is regulated by …

Pattern Discovery In Brain Imaging Genetics Via Scca Modeling With A Generic Non-Convex Penalty, Lei Du, Kefei Liu, Xiaohui Yao, Jingwen Yan, Shannon L. Risacher, Junwei Han, Lei Guo, Andrew J. Saykin, Li Shen, Michael W. Weiner, Paul Aisen, Ronald Petersen, Clifford R. Jack, William Jagust, John Q. Trojanowki, Arthur W. Toga, Laurel Beckett, Robert C. Green, John Morris, Leslie M. Shaw, Zaven Khachaturian, Greg Sorensen, Maria Carrillo, Lew Kuller, Marc Raichle, Steven Paul, Peter Davies, Howard Fillit, Franz Hefti, David Holtzman, Charles D. Smith, Gregory Jicha, Peter A. Hardy, Partha Sinha, Elizabeth Oates, Gary Conrad

Neurology Faculty Publications

Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only convex, but also singular at the origin, which is a necessary condition for sparsity. Thus most SCCA methods impose ℓ₁-norm onto the individual feature or the structure level of features to pursuit corresponding sparsity. However, the ℓ₁-norm penalty over-penalizes large coefficients and may incurs estimation bias. A number of non-convex penalties are proposed to reduce …

Hierarchical Fusion Based Deep Learning Framework For Lung Nodule Classification, Kazim Sekeroglu

LSU Doctoral Dissertations

Lung cancer is the leading cancer type that causes the mortality in both men and women. Computer aided detection (CAD) and diagnosis systems can play a very important role for helping the physicians in cancer treatments. This dissertation proposes a CAD framework that utilizes a hierarchical fusion based deep learning model for detection of nodules from the stacks of 2D images. In the proposed hierarchical approach, a decision is made at each level individually employing the decisions from the previous level. Further, individual decisions are computed for several perspectives of a volume of interest (VOI). This study explores three different …

Computational Modeling For Abnormal Brain Tissue Segmentation, Brain Tumor Tracking, And Grading, Syed Mohammad Shamin Reza

Electrical & Computer Engineering Theses & Dissertations

This dissertation proposes novel texture feature-based computational models for quantitative analysis of abnormal tissues in two neurological disorders: brain tumor and stroke. Brain tumors are the cells with uncontrolled growth in the brain tissues and one of the major causes of death due to cancer. On the other hand, brain strokes occur due to the sudden interruption of the blood supply which damages the normal brain tissues and frequently causes death or persistent disability. Clinical management of these brain tumors and stroke lesions critically depends on robust quantitative analysis using different imaging modalities including Magnetic Resonance (MR) and Digital Pathology …

Quantitative Yttrium-90 Bremsstrahlung Spect/Ct And Pet/Ct Study For 3d Dosimetry In Radiomicrosphere Therapy, Senait Aknaw Debebe

FIU Electronic Theses and Dissertations

Liver cancer ranks the third most common cause of cancer related mortality worldwide. Radiomicrosphere therapy (RMT), a form of radiation therapy, involves administration of Yttrium-90 (90Y) microspheres to the liver via the hepatic artery. 90Y microspheres bremsstrahlung SPECT/CT or PET/CT imaging could potentially identify an extrahepatic uptake. An early detection of such an uptake, thus, could initiate preventative measures early on. However, the quantitative accuracy of bremsstrahlung SPECT/CT images is limited by the wide and continuous energy spectrum of 90Y bremsstrahlung photons. 90Y PET/CT imaging is also possible but limited by the extremely small internal pair production decay. These limitation …

High Resolution Imaging Of The Mitral Valve In The Natural State With 7 Tesla Mri, Sam E. Stephens, Serguei Liachenko, Neil B. Ingels, Jonathan F. Wenk, Morten O. Jensen

Mechanical Engineering Faculty Publications

Imaging techniques of the mitral valve have improved tremendously during the last decade, but challenges persist. The delicate changes in annulus shape and papillary muscle position throughout the cardiac cycle have significant impact on the stress distribution in the leaflets and chords, thus preservation of anatomically accurate positioning is critical. The aim of this study was to develop an in vitro method and apparatus for obtaining high-resolution 3D MRI images of porcine mitral valves in both the diastolic and systolic configurations with physiologically appropriate annular shape, papillary muscle positions and orientations, specific to the heart from which the valve was …

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 …

Use Of Imaging Biomarkers To Assess Perfusion And Glucose Metabolism In The Skeletal Muscle Of Dystrophic Mice, Nabeel Ahmad, Ian Welch, Robert Grange, Jennifer Hadway, Savita Dhanvantari, David Hill, Ting-Yim Lee, Lisa M Hoffman

Lisa Hoffman

BACKGROUND: Duchenne muscular dystrophy (DMD) is a severe neuromuscular disease that affects 1 in 3500 boys. The disease is characterized by progressive muscle degeneration that results from mutations in or loss of the cytoskeletal protein, dystrophin, from the glycoprotein membrane complex, thus increasing the susceptibility of contractile muscle to injury. To date, disease progression is typically assessed using invasive techniques such as muscle biopsies, and while there are recent reports of the use of magnetic resonance, ultrasound and optical imaging technologies to address the issue of disease progression and monitoring therapeutic intervention in dystrophic mice, our study aims to validate …

Performance Assessment Of Diffuse Optical Spectroscopic Imaging Instruments In A 2-Year Multicenter Breast Cancer Trial, Anais Leproux, Thomas D.O. Sullivan, Albert E. Cerussi, Amanda Durkin, Brian Hill, Nola M. Hylton, Arjun G. Yodh, Stefan A. Carp, David A. Boas, Shudong Jiang, Keith D. Paulsen, Brian W. Pogue, Darren M. Roblyr, Wei T. Yang, Bruce J. Tromberg

Dartmouth Scholarship

We present a framework for characterizing the performance of an experimental imaging technology, diffuse optical spectroscopic imaging (DOSI), in a 2-year multicenter American College of Radiology Imaging Network (ACRIN) breast cancer study (ACRIN-6691). DOSI instruments combine broadband frequency-domain photon migration with time-independent near-infrared (650 to 1000 nm) spectroscopy to measure tissue absorption and reduced scattering spectra and tissue hemoglobin, water, and lipid composition. The goal of ACRIN-6691 was to test the effectiveness of optically derived imaging endpoints in predicting the final pathologic response of neoadjuvant chemotherapy (NAC). Sixty patients were enrolled over a 2-year period at participating sites and received …

Photodynamic Therapy: Agents And Mechanisms, Rebecca Claire Gilson

McKelvey School of Engineering Theses & Dissertations

Despite enormous efforts, cancer remains a leading cause of morbidity and mortality world-wide. The main challenges currently facing cancer therapy include lack of adequate tumor targeting, failure to treat hypoxic tumor cells, and induction therapy resistant tumors. A solution to these limitations can be found in photodynamic therapy (PDT) which combines light and light activatable compounds, photosensitizers (PSs), to produce cytotoxic reactive oxygen species (ROS) to damage tumor tissue. This creates a spatiotemporal therapeutic effect, where cell damage only occurs at the intersection of the PS and light. PDT can treat tumors through unique mechanisms which reduce induction of tumor …

Dual-Tuned Removable Common-Mode Current Trap For Mri, Angel G. Enriquez, Joseph V. Rispoli

The Summer Undergraduate Research Fellowship (SURF) Symposium

Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) are preferred methods of gathering information from the body due to their non-invasive approach of obtaining a diagnosis. MRI can obtain spatial mappings from a region of interest, while MRS can obtain metabolic information from different elements. Dual-tuned radiofrequency (RF) coils are able to capture signals produced by both hydrogen atoms and a second atom of interest. Unwanted shield currents occur in these scans, which can cause image distortion, while the high energy dissipated can create harmful heat, which can injure the patient. These shield currents, also known as common-mode currents, …

Multi-Color Ultra-High Resolution Imaging, David A. Miller, Michael Mlodzianoski, Sheng Liu, Fang Huang

The Summer Undergraduate Research Fellowship (SURF) Symposium

Fluorescence microscopy, which allows multiple-color imaging, plays an important role in observing structures inside cells with high specificity. The advent of super-resolution fluorescence microscopy, or nanoscopy techniques such as single-molecule switching nanoscopy (SMSN), has extended the application range of fluorescence microscopy beyond the diffraction limit, achieving up to 10-fold improvement in spatial resolution. At the same time, the recent development of expansion microscopy (ExM) allows samples to be physically expanded by 4-fold in the lateral dimensions providing another independent method to resolve structures beyond the diffraction limit. When combined, ExM-SMSN makes it possible to achieve another significant leap in resolution …

Gui For Mri-Compatible Neural Stimulator And Recorder, Soo Han Soon, Nishant Babaria, Ranajay Mandal, Zhongming Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) are useful tools to analyze brain activities given active stimulation. However, the electromagnetic noise from the MRI distorts the brain signal recording and damages the subject with excessive heat generated on the electrodes attached to the skin. MRI-compatible recording and stimulation systems previously developed at LIBI lab were capable of removing the electromagnetic noise during the imaging process. Previously, the hardware systems had required the integrative software that could control both circuits simultaneously and enable users to easily change recording and stimulation parameters. Graphical user interface (GUI) programmed with computer language informed …

Endothelial Function Is Associated With White Matter Microstructure And Executive Function In Older Adults, Nathan F. Johnson, Brian T. Gold, Christopher A. Brown, Emily F. Anggelis, Alison L. Bailey, Jody L. Clasey, David K. Powell

Physical Therapy Faculty Publications

Age-related declines in endothelial function can lead to cognitive decline. However, little is known about the relationships between endothelial function and specific neurocognitive functions. This study explored the relationship between measures of endothelial function (reactive hyperemia index; RHI), white matter (WM) health (fractional anisotropy, FA, and WM hyperintensity volume, WMH), and executive function (Trail Making Test (TMT); Trail B - Trail A). Participants were 36 older adults between the ages of 59 and 69 (mean age = 63.89 years, SD = 2.94). WMH volume showed no relationship with RHI or executive function. However, there was a positive relationship between RHI …

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 …

Chelator-Free Radiolabeling Of Serrs Nanoparticles For Whole-Body Pet And Intraoperative Raman Imaging, Matthew A. Wall, Travis Shaffer, Stefan Harmsen, Darjus-Felix Tschaharganeh, Chun-Hao Huang, Scott W. Lowe, Charles Michael Drain, Moritz F. Kircher

Publications and Research

A single contrast agent that offers whole-body non-invasive imaging along with the superior sensitivity and spatial resolution of surface-enhanced resonance Raman scattering (SERRS) imaging would allow both pre-operative mapping and intraoperative imaging and thus be highly desirable. We hypothesized that labeling our recently reported ultrabright SERRS nanoparticles with a suitable radiotracer would enable pre-operative identification of regions of interest with whole body imaging that can be rapidly corroborated with a Raman imaging device or handheld Raman scanner in order to provide high precision guidance during surgical procedures. Here we present a straightforward new method that produces radiolabeled SERRS nanoparticles for …

Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid

Computational Modeling & Simulation Engineering Theses & Dissertations

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to …

Skin Tone Tracking Device (Chromaband), Ziyang Bian

Computer Engineering

It’s long been said that your skin is a window into your health and with many illnesses the first signs of trouble actually show up in your skin. So if we have this natural warning system, then why isn’t anyone able to effectively use it to predict changes in our health? The problem is that currently there is no reliable way to accurately measure the change in skin tone and how these changes may or may not change with variations in health. This project’s aim is to design and develop a device that will record the changes in a user’s …

Optimizing A Standard Fasting Time For 2-Nbdg Uptake Studies In Murine Breast Cancers, Andrew C. Briley

Biomedical Engineering Undergraduate Honors Theses

Recently, there has been a larger use of 2-NBDG, a fluorescent glucose analog, to study glucose uptake in different cell types. These cell types have ranged anywhere from bacteria to human cancer cells. However, there has yet to be a standard procedure and practice for using 2-NBDG. In this study, our goal is to create a standard fasting time for the cells before introducing 2-NBDG to them. This study uses 4T07 cells, a murine breast cancer cell line, to help optimize this fasting time. These cells were fasted at different time points in order to find the ideal fasting time. …