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Bioimaging and Biomedical Optics Commons

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Cdse Quantum Dots Synthesis Laboratory Course For High School Students, Danlin Zuo, Gyuseok Kim, David Jones 2019 Singh Center for Nanotechnology

Cdse Quantum Dots Synthesis Laboratory Course For High School Students, Danlin Zuo, Gyuseok Kim, David Jones

Protocols and Reports

Cadmium selenide quantum dot is a fascinating subject for leading high school students to the quantum world. An 8-hour laboratory course for up to 12 high school students is proposed. The 8-hour course consist of two 4-hours sections. This laboratory course includes the quantum dot syntheses, absorption and emission characterization, and data analysis. The proposes process runs at relatively lower temperature which means safe and easy, and shows apparent experimental results.


Design, Construction And Application Of A Home-Built, Two-Photon Microscope, William P. Breeding 2019 University of Maine

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 2019 Washington University in St. Louis

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

Engineering and Applied Science 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 2019 Washington University in St. Louis

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

Engineering and Applied Science 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 ...


Investigation Of The Effect Of Age On Regenerative Outcomes Following Treatment Of Volumetric Muscle Loss Injuries, John Taehwan Kim 2019 University of Arkansas, Fayetteville

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

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 ...


Multimodal Quantitative Imaging Of Brain Cancer In Cultured Cells, Xin Feng, Alona Muzikansky, Alonzo H. Ross, Michael R. Hamblin, Peter R. Jermain, Anna N. Yaroslavsky 2019 University of Massachusetts Lowell

Multimodal Quantitative Imaging Of Brain Cancer In Cultured Cells, Xin Feng, Alona Muzikansky, Alonzo H. Ross, Michael R. Hamblin, Peter R. Jermain, Anna N. Yaroslavsky

Open Access Articles

Fluorescence emission, polarization and subcellular localization of methylene blue (MB) were studied in four cancerous and two normal human brain cell lines. Fluorescence emission and polarization images were acquired and analyzed. The co-localization of MB with mitochondria, lysosomes and nuclei of the cells was evaluated. Glioblastoma cells exhibited significantly higher MB fluorescence polarization compared to normal astrocytes. Preferential accumulation of MB in mitochondria of glioblastoma cells may explain higher fluorescence polarization values in cancer cells as compared to normal. These findings may lead to the development of a quantitative method for the detection of brain cancer in single cells.


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 2019 Army Education Outreach Program UNITE

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 Publications

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.


Spatial Frequency Domain Imaging Of Short-Wave Infrared Fluorescence For Biomedical Applications, Joseph P. Leonor 2019 Dartmouth College

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 2019 Union College - Schenectady, NY

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 2019 California Polytechnic State University, San Luis Obispo

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 and Project Reports

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 2019 New Jersey Institute of Technology

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 2019 New Jersey Institute of Technology

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 ...


Quantifying Iron Overload Using Mri, Active Contours, And Convolutional Neural Networks, Andrea Sajewski, Stacey Levine 2019 Duquesne University

Quantifying Iron Overload Using Mri, Active Contours, And Convolutional Neural Networks, Andrea Sajewski, Stacey Levine

Undergraduate Research and Scholarship Symposium

Iron overload, a complication of repeated blood transfusions, can cause tissue damage and organ failure. The body has no regulatory mechanism to excrete excess iron, so iron overload must be closely monitored to guide therapy and measure treatment response. The concentration of iron in the liver is a reliable marker for total body iron content and is now measured noninvasively with magnetic resonance imaging (MRI). MRI produces a diagnostic image by measuring the signals emitted from the body in the presence of a constant magnetic field and radiofrequency pulses. At each pixel, the signal decay constant, T2*, can be calculated ...


A Simplified Crossing Fiber Model In Diffusion Weighted Imaging, Sheng Yang, Kaushik Ghosh, Ken Sakaie, Satya S. Sahoo, Sarah J. Ann Carr, Curtis Tatsuoka 2019 Case Western Reserve University

A Simplified Crossing Fiber Model In Diffusion Weighted Imaging, Sheng Yang, Kaushik Ghosh, Ken Sakaie, Satya S. Sahoo, Sarah J. Ann Carr, Curtis Tatsuoka

Math Faculty Publications

Diffusion MRI (dMRI) is a vital source of imaging data for identifying anatomical connections in the living human brain that form the substrate for information transfer between brain regions. dMRI can thus play a central role toward our understanding of brain function. The quantitative modeling and analysis of dMRI data deduces the features of neural fibers at the voxel level, such as direction and density. The modeling methods that have been developed range from deterministic to probabilistic approaches. Currently, the Ball-and-Stick model serves as a widely implemented probabilistic approach in the tractography toolbox of the popular FSL software package and ...


Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre 2019 University of Connecticut

Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre

Honors Scholar Theses

Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis ...


Investigation Of Acute Radiation-Induced Changes In Oxygenation In A Murine Breast Tumor Model, Alaa Abdelgawad 2019 University of Arkansas, Fayetteville

Investigation Of Acute Radiation-Induced Changes In Oxygenation In A Murine Breast Tumor Model, Alaa Abdelgawad

Biomedical Engineering Undergraduate Honors Theses

Around 50-60% of all cancer patients undergo radiation therapy. Although some patients show complete response with no recurrence, a significant proportion of the population still develop radiation resistance. It is important to identify tumor resistance at early stages of therapy in order to adjust treatment protocol and avoid extra exposure to radiation. Current methods to assess treatment response are only limited to anatomical measurements of tumor volume after therapy. Novel approaches that shed the light on any functional information during the course of radiotherapy could significantly improve our ability to identify patients who do not respond to radiation therapy. Diffuse ...


Diffuse Reflectance Spectroscopy To Quantify In Vivo Tissue Optical Properties: Applications In Human Epithelium And Subcutaneous Murine Colon Cancer, Gage Joseph Greening 2019 University of Arkansas, Fayetteville

Diffuse Reflectance Spectroscopy To Quantify In Vivo Tissue Optical Properties: Applications In Human Epithelium And Subcutaneous Murine Colon Cancer, Gage Joseph Greening

Theses and Dissertations

Colorectal cancer is the 4th most common and 2nd deadliest cancer. Problems exist with predicting which patients will respond best to certain therapy regimens. Diffuse reflectance spectroscopy has been suggested as a candidate to optically monitor a patient’s early response to therapy and has been received favorably in experimentally managing other cancers such as breast and skin. In this dissertation, two diffuse reflectance spectroscopy probes were designed: one with a combined high-resolution microendoscopy modality, and one that was optimized for acquiring data from subcutaneous murine tumors. For both probes, percent errors for estimating tissue optical properties (reduced scattering coefficient ...


Biomedical Engineering Or Biomedical Optics: Will The Real Discipline Please Stand Up?, Brian W. Pogue 2019 Dartmouth College

Biomedical Engineering Or Biomedical Optics: Will The Real Discipline Please Stand Up?, Brian W. Pogue

Open Dartmouth: Faculty Open Access Scholarship

This editorial reflects on the shape of biomedical engineering as a discipline, and its relation to biomedical optics.


Tissue Equivalent Gellan Gum Gel Materials For Clinical Mri And Radiation Dosimetry, Pawel Brzozowski 2019 The University of Western Ontario

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 ...


Characterizing Short-Wave Infrared Fluorescence Of Conventional Near-Infrared Fluorophores, Brook K. Byrd, Margaret R. Folaron, Joseph P. Leonor, Rendall R. Strawbridge, Xu Cao, Petr Bruza, Scott C. Davis 2019 Dartmouth College

Characterizing Short-Wave Infrared Fluorescence Of Conventional Near-Infrared Fluorophores, Brook K. Byrd, Margaret R. Folaron, Joseph P. Leonor, Rendall R. Strawbridge, Xu Cao, Petr Bruza, Scott C. Davis

Open Dartmouth: Faculty Open Access Scholarship

The observed behavior of short-wave infrared (SWIR) light in tissue, characterized by relatively low scatter and subdiffuse photon transport, has generated considerable interest for the potential of SWIR imaging to produce high-resolution, subsurface images of fluorescence activity in vivo. These properties have important implications for fluorescence-guided surgery and preclinical biomedical research. Until recently, translational efforts have been impeded by the conventional understanding that fluorescence molecular imaging in the SWIR regime requires custom molecular probes that do not yet have proven safety profiles in humans. However, recent studies have shown that two readily available near-infrared (NIR-I) fluorophores produce measurable SWIR fluorescence ...


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