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Bioimaging and Biomedical Optics Commons

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Statistical Machine Learning For Breast Cancer Detection With Terahertz Imaging, Tanny Andrea Chavez Esparza 2021 University of Arkansas, Fayetteville

Statistical Machine Learning For Breast Cancer Detection With Terahertz Imaging, Tanny Andrea Chavez Esparza

Graduate Theses and Dissertations

Breast conserving surgery (BCS) is a common breast cancer treatment option, in which the cancerous tissue is excised while leaving most of the healthy breast tissue intact. The lack of in-situ margin evaluation unfortunately results in a re-excision rate of 20-30% for this type of procedure. This study aims to design statistical and machine learning segmentation algorithms for the detection of breast cancer in BCS by using terahertz (THz) imaging. Given the material characterization properties of the non-ionizing radiation in the THz range, we intend to employ the responses from the THz system to identify healthy and cancerous breast tissue …


Development Of Quantitative Ultrasound-Mediated Molecular Imaging Of The Tumor Microenvironment, Trevor Mitcham 2021 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Development Of Quantitative Ultrasound-Mediated Molecular Imaging Of The Tumor Microenvironment, Trevor Mitcham

Dissertations & Theses (Open Access)

While conventional diagnostic imaging modalities provide anatomical information to clinicians, these techniques are not sensitive to critical physiological processes. In order to properly classify cancer, it is necessary to investigate noninvasive methods which can provide insight into these processes, allowing clinicians to determine personalized therapeutic options. Therefore, molecular imaging is focused on visualization and characterization of biomarkers within the tumor microenvironment (TME), which can then be combined with the anatomical information provided from diagnostic imaging.

Two such biomarkers of interest are blood oxygen saturation (SO2) and cell receptor expression. SO2 is a measure of the fraction of …


Quantifying Mucosal Hemodynamics In A Murine Model Of Ulcerative Colitis With Diffuse Reflectance Spectroscopy, Elizabeth A. Bullard, Ariel I. Mundo, Shelby N. Bess, Kathryn P. Miller 2021 University of Arkansas, Fayetteville

Quantifying Mucosal Hemodynamics In A Murine Model Of Ulcerative Colitis With Diffuse Reflectance Spectroscopy, Elizabeth A. Bullard, Ariel I. Mundo, Shelby N. Bess, Kathryn P. Miller

Biomedical Engineering Undergraduate Honors Theses

Ulcerative colitis (UC) is a gastrointestinal, autoimmune disease that causes ulceration and inflammation of the colon with an incidence 10 out of every 100,000 people in North America and Western Europe. Though the exact etiology is uncertain, a number of studies have shown that inflammatory cells along with environmental factors, genetics, and lifestyle habits can contribute to the sustained inflammatory response. In order to determine the cellular mechanism behind relapse and remission of UC, researchers have frequently employed immunohistochemistry, western blotting and gene sequencing, but these destructive analysis methods require the removal of a sample, necessarily limiting these methods to …


Using Deep Learning To Analyze Materials In Medical Images, Carson Molder 2021 University of Arkansas, Fayetteville

Using Deep Learning To Analyze Materials In Medical Images, Carson Molder

Computer Science and Computer Engineering Undergraduate Honors Theses

Modern deep learning architectures have become increasingly popular in medicine, especially for analyzing medical images. In some medical applications, deep learning image analysis models have been more accurate at predicting medical conditions than experts. Deep learning has also been effective for material analysis on photographs. We aim to leverage deep learning to perform material analysis on medical images. Because material datasets for medicine are scarce, we first introduce a texture dataset generation algorithm that automatically samples desired textures from annotated or unannotated medical images. Second, we use a novel Siamese neural network called D-CNN to predict patch similarity and build …


Rare Earth-Doped Glass-Ceramic Scintillators As X-Ray Flat Panel Detector Substrates, Austin M. Thomas 2021 The University of Tennessee

Rare Earth-Doped Glass-Ceramic Scintillators As X-Ray Flat Panel Detector Substrates, Austin M. Thomas

Masters Theses

Digital radiography (DR) is an important two-dimensional imaging technique in the field of medicine that utilizes x-rays to form a digital image. DR employs a flat panel detector that converts incident x-rays, that have passed through the subject, to an electrical signal, which is used to create a digital image. The conversion from x-rays to electrical signals can be done either directly or indirectly. The direct method involves the x-rays being converted to an electrical signal via an array of semiconductors. The indirect method utilizes scintillators to absorb the x-rays and produce light in the visible spectrum, which is then …


Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard 2021 Liberty University

Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard

Senior Honors Theses

Anthraquinones are aromatic organic compounds that have multiple applications in the biomedical field. Some anthraquinone-based compounds are used as fluorophores to contrast cell nuclei while others act as chemotherapeutic agents. However, there are not many fluorescent anthraquinone cell stains currently available. In this study, commercially available anthraquinone dyes, in addition to other dye families and compounds, were reviewed for their unique properties, advantages, and drawbacks. The development and characterization of three novel anthraquinone fluorophores revealed promising photophysical characteristics, like large Stokes shifts. One of the compounds, RBS3, was chosen for fixed and live cell staining and exhibited desirable biomedical properties. …


A Brief Bibliometric Survey Of Explainable Ai In Medical Field, Nilkanth Mukund Deshpande, Shilpa Shailesh Gite 2021 Department of Electronics and Telecommunication, Symbiosis Institute of Technology, Symbiosis International( Deemed University), Lavale, Pune-412115 and Dr. Vithalrao Vikhe Patil College of Engingeering, Ahmednagar

A Brief Bibliometric Survey Of Explainable Ai In Medical Field, Nilkanth Mukund Deshpande, Shilpa Shailesh Gite

Library Philosophy and Practice (e-journal)

Background: This study aims to analyze the work done in the field of explainability related to artificial intelligence, especially in the medical field from 2004 onwards using the bibliometric methods.

Methods: different articles based on the topic leukemia detection were retrieved using one of the most popular database- Scopus. The articles are considered from 2004 onwards. Scopus analyzer is used for different types of analysis including documents by year, source, county and so on. There are other different analysis tools such as VOSviewer Version 1.6.15. This is used for the analysis of different units such as co-authorship, co-occurrences, citation analysis …


Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber 2021 University of Nebraska - Lincoln

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, …


Nanoanalytical Analysis Of Bisphosphonate-Driven Alterations Of Microcalcifications Using A 3d Hydrogel System And In Vivo Mouse Model, Jessica L. Ruiz, Joshua D. Hutcheson, Luis Cardoso, Amirala Bakhshian Nik, Alexandra Condado de Abreu, Tan Pham, Fabrizio Buffolo, Sara Busatto, Stefania Frederici, Andrea Ridolfi, Masanori Aikawa, Sergio Bertazzo, Paolo Bergese, Sheldon Weinbaum, Elena Aikawa 2021 Harvard Medical School

Nanoanalytical Analysis Of Bisphosphonate-Driven Alterations Of Microcalcifications Using A 3d Hydrogel System And In Vivo Mouse Model, Jessica L. Ruiz, Joshua D. Hutcheson, Luis Cardoso, Amirala Bakhshian Nik, Alexandra Condado De Abreu, Tan Pham, Fabrizio Buffolo, Sara Busatto, Stefania Frederici, Andrea Ridolfi, Masanori Aikawa, Sergio Bertazzo, Paolo Bergese, Sheldon Weinbaum, Elena Aikawa

Publications and Research

Vascular calcification predicts atherosclerotic plaque rupture and cardiovascular events. Retrospective studies of women taking bisphosphonates (BiPs), a proposed therapy for vascular calcification, showed that BiPs paradoxically increased morbidity in patients with prior acute cardiovascular events but decreased mortality in event-free patients. Calcifying extracellular vesicles (EVs), released by cells within atherosclerotic plaques, aggregate and nucleate calcification. We hypothesized that BiPs block EV aggregation and modify existing mineral growth, potentially altering microcalcification morphology and the risk of plaque rupture. Three-dimensional (3D) collagen hydrogels incubated with calcifying EVs were used to mimic fibrous cap calcification in vitro, while an ApoE−/− mouse was used …


Nnemo (Neonatal Neuromonitor) - A Hybrid Optical System To Characterize Perfusion And Metabolism In The Newborn Brain, Ajay Rajaram 2021 The University of Western Ontario

Nnemo (Neonatal Neuromonitor) - A Hybrid Optical System To Characterize Perfusion And Metabolism In The Newborn Brain, Ajay Rajaram

Electronic Thesis and Dissertation Repository

Premature birth, defined as a gestational period less than 37 weeks, occurs in 8% of infants born in Canada. These births are associated with a higher risk of developing neurological complications. Infants born with very low birth weights (VLBW, < 1500 g) experience cognitive or behavioural deficits at a rate of 40-50%, while a further 5-10% develop major disorders such as cerebral palsy. The likelihood of injury increases with a shorter gestational period and/or a lower birthweight. Intraventricular hemorrhaging (IVH) occurs in 20-25% of VLBW infants, characterized by bleeding in the germinal matrix and surrounding white matter. This highly vascularized region is particularly susceptible to bleeds due to underdeveloped cerebrovascular structures. Severe IVH causes an inflammatory response and subsequent obstruction of cerebrospinal fluid (CSF) drainage, resulting in enlargement of the brain’s ventricles, referred to as post-hemorrhagic ventricular dilatation (PHVD). PHVD increases intracranial pressure and can result in compression/damage of brain tissue.

Diagnosis of IVH and PHVD is regularly performed using cranial ultrasound. Clinicians can visually assess and grade hemorrhaging/ventricle dilatation. Ultrasound, however, is limited in its ability to continuously monitor and only detects irreversible damage. NNeMo (Neonatal NeuroMonitor) is a hybrid optical device combining diffuse correlation (DCS) and near-infrared spectroscopy (NIRS) to simultaneous monitor cerebral blood flow (CBF) and metabolism at the …


Penta-Modal Imaging Platform With Oct- Guided Dynamic Focusing For Simultaneous Multimodal Imaging, Arash Dadkhah 2021 Florida International University

Penta-Modal Imaging Platform With Oct- Guided Dynamic Focusing For Simultaneous Multimodal Imaging, Arash Dadkhah

FIU Electronic Theses and Dissertations

Complex diseases, such as Alzheimer’s disease, are associated with sequences of changes in multiple disease-specific biomarkers. These biomarkers may show dynamic changes at specific stages of disease progression. Thus, testing/monitoring each biomarker may provide insight into specific disease-related processes, which can result in early diagnosis or even development of preventive measures. Obtaining a comprehensive information of biological tissues requires imaging of multiple optical contrasts, which is not typically offered by a single imaging modality. Thus, combining different contrast mechanisms to achieve simultaneous multimodal imaging is desirable. However, this process is highly challenging due to specific optical and hardware requirements for …


Laparoscopic Image Recovery And Stereo Matching, Wenyao Xia 2021 The University of Western Ontario

Laparoscopic Image Recovery And Stereo Matching, Wenyao Xia

Electronic Thesis and Dissertation Repository

Laparoscopic imaging can play a significant role in the minimally invasive surgical procedure. However, laparoscopic images often suffer from insufficient and irregular light sources, specular highlight surfaces, and a lack of depth information. These problems can negatively influence the surgeons during surgery, and lead to erroneous visual tracking and potential surgical risks. Thus, developing effective image-processing algorithms for laparoscopic vision recovery and stereo matching is of significant importance. Most related algorithms are effective on nature images, but less effective on laparoscopic images.

The first purpose of this thesis is to restore low-light laparoscopic vision, where an effective image enhancement method …


Development Of All-Optical Quantitative Ultrasound Imaging System, Mohamed Abdulrahman Almadi 2021 Florida International University

Development Of All-Optical Quantitative Ultrasound Imaging System, Mohamed Abdulrahman Almadi

FIU Electronic Theses and Dissertations

Ultrasound (US) is a well-established deep-tissue imaging modality in biomedicine. It distinguishes different tissue types based on their echogenicity, but this approach provides limited diagnostic sensitivity and accuracy. The majority of the US transducers nowadays rely on lead zirconate titanate (PZT) ceramic elements to transmit and receive ultrasound. Unfortunately, significant limitations arise from these transducers due to their frequency characteristics and complex fabrication process. A recently introduced technique, Quantitative Ultrasound (QUS) Measurement, shows a great promise to improve US-based tissue diagnosis, but it requires a transducer with a large spectrum bandwidth, which is a feature not available in PZT transducers. …


Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew 2021 Washington University in St. Louis

Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

The following sections are included:

  • Present State of Computational Modelling in Fluorescence Nanoscopy

  • Recent Contributions to Computational Modelling in Fluorescence Nanoscopy

  • Outlook on Computational Modelling in Fluorescence Nanoscopy

  • Acknowledgments

  • References


Focused Ultrasound-Mediated Drug Delivery To The Brainstem, Dezhuang Ye 2021 Washington University in St. Louis

Focused Ultrasound-Mediated Drug Delivery To The Brainstem, Dezhuang Ye

McKelvey School of Engineering Theses & Dissertations

Brainstem gliomas are tumors that occur in the brainstem, the brain region that connects the brain to the spinal cord and controls vital body functions. The critical anatomic location of the brainstem precludes surgical intervention and limits the use of invasive therapeutic techniques. Moreover, the frequently intact blood-brain barrier (BBB) of most brainstem gliomas prevents therapeutic agents from reaching the diseased site. The currently available techniques for brain drug delivery are either invasive (e.g., convection-enhanced delivery) or lack targeting to the diseased site (e.g., intranasal brain drug delivery). Novel techniques that can noninvasively overcome the BBB are critically needed for …


When The Brain Plays A Game: Neural Responses To Visual Dynamics During Naturalistic Visual Tasks, Jason Ki 2021 CUNY City College

When The Brain Plays A Game: Neural Responses To Visual Dynamics During Naturalistic Visual Tasks, Jason Ki

Dissertations and Theses

Many day-to-day tasks involve processing of complex visual information in a continuous stream. While much of our knowledge on visual processing has been established from reductionist approaches in lab-controlled settings, very little is known about the processing of complex dynamic stimuli experienced in everyday scenarios. Traditional investigations employ event-related paradigms that involve presentation of simple stimuli at select locations in visual space and discrete moments in time. In contrast, visual stimuli in real-life are highly dynamic, spatially-heterogeneous, and semantically rich. Moreover, traditional experiments impose unnatural task constraints (e.g., inhibited saccades), thus, it is unclear whether theories developed under the reductionist …


Assessing Midbrain Abnormalities In Parkinson’S Disease Using Magnetic Resonance Imaging, Kiarash Ghassaban 2021 Wayne State University

Assessing Midbrain Abnormalities In Parkinson’S Disease Using Magnetic Resonance Imaging, Kiarash Ghassaban

Wayne State University Dissertations

Diagnosing early-stage Parkinson’s disease (PD) and its manifestations is still a clinical challenge. Previous imaging studies using iron, neuromelanin (NM) and the Nigrosome-1 (N1) measures in the substantia nigra (SN) by themselves have been unable to provide sufficiently high diagnostic performance for these methods to be adopted clinically. In this dissertation, we start by studying idiopathic PD patients at their intermediate stages of the disease to evaluate the role of global and regional iron in the major deep gray matter nuclei. Then, we only focus on the NM complex in the midbrain and how neuronal loss interact with iron overload …


Perceptually Improved Medical Image Translations Using Conditional Generative Adversarial Networks, Anurag Vaidya 2021 Bucknell University

Perceptually Improved Medical Image Translations Using Conditional Generative Adversarial Networks, Anurag Vaidya

Honors Theses

Magnetic resonance imaging (MRI) can help visualize various brain regions. Typical MRI sequences consist of T1-weighted sequence (favorable for observing large brain structures), T2-weighted sequence (useful for pathology), and T2-FLAIR scan (useful for pathology with suppression of signal from water). While these different scans provide complementary information, acquiring them leads to acquisition times of ~1 hour and an average cost of $2,600, presenting significant barriers. To reduce these costs associated with brain MRIs, we present pTransGAN, a generative adversarial network capable of translating both healthy and unhealthy T1 scans into T2 scans. We show that the addition of non-adversarial …


Imaging Potential In Saturation Recovery Methods For Sarcoidosis Patients With Medical Devices, Samantha Zhao 2021 Virginia Commonwealth University

Imaging Potential In Saturation Recovery Methods For Sarcoidosis Patients With Medical Devices, Samantha Zhao

Theses and Dissertations

Cardiovascular magnetic resonance (CMR) imaging is a preferred imaging methodology due to its lack of ionizing radiation and ability to detect myocardial inflammation and fibrosis using quantitative T1 mapping techniques. Cardiac sarcoidosis (CS) is characterized as the formation of granulomas in the myocardium. Current methods for detection include measuring non-cardiac specific C-reactive protein (CRP) levels, or PET imaging, which uses ionizing radiation, therefore CMR would make an ideal imaging option. However, many CS patients have implanted cardiac devices which can cause degradation in image. The modified Look-Locker inversion recovery (MOLLI) method is widely used in quantitative T1 mapping with high …


Characterization & Calibration Of Foresight Ice, Hareem Nisar, Terry M Peters, Elvis C.S. Chen 2021 Western University

Characterization & Calibration Of Foresight Ice, Hareem Nisar, Terry M Peters, Elvis C.S. Chen

Robarts Imaging Publications

No abstract provided.


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