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Bioimaging and Biomedical Optics Commons

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Sensitivity Analysis Of Geometry Changes In The Simulation Of Basilar Aneurysms, Paul Eserkaln 2016 University of Wisconsin-Milwaukee

Sensitivity Analysis Of Geometry Changes In The Simulation Of Basilar Aneurysms, Paul Eserkaln

Theses and Dissertations

Computer simulation is a useful tool in the research and treatment of basilar aneurysms. Current technology allows researchers to create 3D models from cerebral vasculature in-vivo, allowing for the investigation of surgical options with minimal risk to the patient. The method used to construct these models overlooks smaller lateral arterial branches which are difficult to discern due to resolution limits of the imaging process. These lateral branches have minimal impact on the overall blood flow through the basilar artery, but they play a significant role in the health of the patient, so it is important to ensure sufficient blood will ...


Development Of Breast Tissue Phantoms For Enhanced Terahertz Imaging Utilizing Microdiamond And Nano-Onion Particles, Alec Walter 2016 University of Arkansas, Fayetteville

Development Of Breast Tissue Phantoms For Enhanced Terahertz Imaging Utilizing Microdiamond And Nano-Onion Particles, Alec Walter

Electrical Engineering Undergraduate Honors Theses

This thesis presents the work performed to develop tissue phantoms and a contrast agent that will be used in future research of terahertz time-domain imaging of breast tumor margins. Since an excised breast tumor can contain healthy fibrous and fatty tissues along with invasive ductal carcinoma (IDC), three phantom materials were developed. Solid phantom materials were made by using TX151 to solidify water in order to tune the refractive index and absorption coefficient of the fibrous tissue phantom and IDC phantom to the properties of freshly excised breast tissue. Various amounts of olive oil were added to the water prior ...


A Multi-Channel 3d-Printed Bioreactor For Evaluation Of Growth And Production In The Microalga Dunaliella Sp, Cristian A. Cox 2016 University of Maine

A Multi-Channel 3d-Printed Bioreactor For Evaluation Of Growth And Production In The Microalga Dunaliella Sp, Cristian A. Cox

Electronic Theses and Dissertations

We explored the capabilities of additive manufacturing using a photo-cured jetted material 3D printer to manufacture a milli-microfluidic device with direct application in microalgae Dunaliella sp growth and intracellular compounds biosynthesis tests. A continuous microbioreactor for microalgae culture was CAD designed and successfully built in 1 hour and 49 minutes using black photopolymer cured by UV and a support material. The microreactor was made up of 2 parts including the bioreactor itself and a microchannel network for culture media fluids and microalgae. Both parts were assembled to form a single unit. Additional optical and auxiliar components were added. An external ...


Optical Coherence Photoacoustic Microscopy (Oc-Pam) For Multimodal Imaging, Xiaojing Liu 2016 Florida International University

Optical Coherence Photoacoustic Microscopy (Oc-Pam) For Multimodal Imaging, Xiaojing Liu

FIU Electronic Theses and Dissertations

Optical coherence tomography (OCT) and Photoacoustic microscopy (PAM) are two noninvasive, high-resolution, three-dimensional, biomedical imaging modalities based on different contrast mechanisms. OCT detects the light backscattered from a biological sample either in the time or spectral domain using an interferometer to form an image. PAM is sensitive to optical absorption by detecting the light-induced acoustic waves to form an image. Due to their complementary contrast mechanisms, OCT and PAM are suitable for being combined to achieve multimodal imaging.

In this dissertation, an optical coherence photoacoustic microscopy (OC-PAM) system was developed for in vivo multimodal retinal imaging with a pulsed broadband ...


Raman Spectroscopy Detects Distant Invasive Brain Cancer Cells Centimeters Beyond Mri Capability In Humans, Michael Jermyn, Joannie Desroches, Jeanne Mercier, Karl St-Arnaud 2016 Dartmouth College

Raman Spectroscopy Detects Distant Invasive Brain Cancer Cells Centimeters Beyond Mri Capability In Humans, Michael Jermyn, Joannie Desroches, Jeanne Mercier, Karl St-Arnaud

Open Dartmouth: Faculty Open Access Articles

Surgical treatment of brain cancer is limited by the inability of current imaging capabilities such as magnetic resonance imaging (MRI) to detect the entirety of this locally invasive cancer. This results in residual cancer cells remaining following surgery, leading to recurrence and death. We demonstrate that intraoperative Raman spectroscopy can detect invasive cancer cells centimeters beyond pathological T1-contrast-enhanced and T2-weighted MRI signals. This intraoperative optical guide can be used to detect invasive cancer cells and minimize post-surgical cancer burden. The detection of distant invasive cancer cells beyond MRI signal has the potential to increase the effectiveness of surgery and directly ...


Video-To-Video Pose And Expression Invariant Face Recognition Using Volumetric Directional Pattern, Vijayan K. Asari, Almabrok Essa 2016 University of Dayton

Video-To-Video Pose And Expression Invariant Face Recognition Using Volumetric Directional Pattern, Vijayan K. Asari, Almabrok Essa

Vijayan K. Asari

Face recognition in video has attracted attention as a cryptic method of human identification in surveillance systems. In this paper, we propose an end-to-end video face recognition system, addressing a difficult problem of identifying human faces in video due to the presence of large variations in facial pose and expression, and poor video resolution. The proposed descriptor, named Volumetric Directional Pattern (VDP), is an oriented and multi-scale volumetric descriptor that is able to extract and fuse the information of multi frames, temporal (dynamic) information, and multiple poses and expressions of faces in input video to produce feature vectors, which are ...


Shape Complexes: The Intersection Of Label Orderings And Star Convexity Constraints In Continuous Max-Flow Medical Image Segmentation., John S H Baxter, Jiro Inoue, Maria Drangova, Terry M Peters 2016 Western University

Shape Complexes: The Intersection Of Label Orderings And Star Convexity Constraints In Continuous Max-Flow Medical Image Segmentation., John S H Baxter, Jiro Inoue, Maria Drangova, Terry M Peters

Robarts Imaging Publications

Optimization-based segmentation approaches deriving from discrete graph-cuts and continuous max-flow have become increasingly nuanced, allowing for topological and geometric constraints on the resulting segmentation while retaining global optimality. However, these two considerations, topological and geometric, have yet to be combined in a unified manner. The concept of "shape complexes," which combine geodesic star convexity with extendable continuous max-flow solvers, is presented. These shape complexes allow more complicated shapes to be created through the use of multiple labels and super-labels, with geodesic star convexity governed by a topological ordering. These problems can be optimized using extendable continuous max-flow solvers. Previous approaches ...


A Fourier Description Of Covariance, And Separation Of Simultaneously Encoded Slices With In-Plane Acceleration In Fmri, Mary C. Kociuba 2016 Marquette University

A Fourier Description Of Covariance, And Separation Of Simultaneously Encoded Slices With In-Plane Acceleration In Fmri, Mary C. Kociuba

Dissertations (2009 -)

Functional magnetic resonance imaging (fMRI) studies aim to identify localized neural regions associated with a cognitive task performed by the subject. An indirect measure of the brain activity is the blood oxygenation level dependent (BOLD) signal fluctuations observed within the complex-valued spatial frequencies measured over time. The standard practice in fMRI is to discard the phase information after image reconstruction, even with evidence of biological task-related change in the phase time-series. In the first aim of this dissertation, a complex-valued time-series covariance is derived as a linear combination of second order temporal Fourier frequency coefficients. As opposed to magnitude-only analysis ...


Microdose Fluorescence Imaging Of Aby-029 On An Operating Microscope Adapted By Custom Illumination And Imaging Modules, Jonathan T. Elliott, Alisha V. Dsouza, Kayla Marra, Brian W. Pogue, David Roberts, Keith Paulsen 2016 Dartmouth College

Microdose Fluorescence Imaging Of Aby-029 On An Operating Microscope Adapted By Custom Illumination And Imaging Modules, Jonathan T. Elliott, Alisha V. Dsouza, Kayla Marra, Brian W. Pogue, David Roberts, Keith Paulsen

Open Dartmouth: Faculty Open Access Articles

Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials.


Diffuse Optical Measurements Of Head And Neck Tumor Hemodynamics For Early Prediction Of Chemoradiation Therapy Outcomes, Lixin Dong, Mahesh Kudrimoti, Daniel Irwin, Li Chen, Sameera Kumar, Yu Shang, Chong Huang, Ellis L. Johnson, Scott D. Stevens, Brent J. Shelton, Guoqiang Yu 2016 University of Kentucky

Diffuse Optical Measurements Of Head And Neck Tumor Hemodynamics For Early Prediction Of Chemoradiation Therapy Outcomes, Lixin Dong, Mahesh Kudrimoti, Daniel Irwin, Li Chen, Sameera Kumar, Yu Shang, Chong Huang, Ellis L. Johnson, Scott D. Stevens, Brent J. Shelton, Guoqiang Yu

Biomedical Engineering Faculty Publications

This study used a hybrid near-infrared diffuse optical instrument to monitor tumor hemodynamic responses to chemoradiation therapy for early prediction of treatment outcomes in patients with head and neck cancer. Forty-seven patients were measured once per week to evaluate the hemodynamic status of clinically involved cervical lymph nodes as surrogates for the primary tumor response. Patients were classified into two groups: complete response (CR) (n = 29) and incomplete response (IR) (n = 18). Tumor hemodynamic responses were found to be associated with clinical outcomes (CR/IR), wherein the associations differed depending on human papillomavirus (HPV-16) status. In HPV-16 positive patients, significantly ...


Low-Cost Compact Diffuse Speckle Contrast Flowmeter Using Small Laser Diode And Bare Charge-Coupled-Device, Chong Huang, Myeongsu Seong, Joshua Paul Morgan, Siavash Mazdeyasna, Jae Gwan Kim, Jeffrey Todd Hastings, Guoqiang Yu 2016 University of Kentucky

Low-Cost Compact Diffuse Speckle Contrast Flowmeter Using Small Laser Diode And Bare Charge-Coupled-Device, Chong Huang, Myeongsu Seong, Joshua Paul Morgan, Siavash Mazdeyasna, Jae Gwan Kim, Jeffrey Todd Hastings, Guoqiang Yu

Biomedical Engineering Faculty Publications

We report a low-cost compact diffuse speckle contrast flowmeter (DSCF) consisting of a small laser diode and a bare charge-coupled-device (CCD) chip, which can be used for contact measurements of blood flow variations in relatively deep tissues (up to ∼8  mm). Measurements of large flow variations by the contact DSCF probe are compared to a noncontact CCD-based diffuse speckle contrast spectroscopy and a standard contact diffuse correlation spectroscopy in tissue phantoms and a human forearm. Bland–Altman analysis shows no significant bias with good limits of agreement among these measurements: 96.5% ± 2.2% (94.4% to 100.0%) in ...


Lipid Detection In Pig Arteries Using Intravascular Photoacoustic Imaging, Jieying Mai, Yingchun Cao, Ayeeshik Kole, Michael Sturek, Ji-Xin Cheng 2016 Purdue University

Lipid Detection In Pig Arteries Using Intravascular Photoacoustic Imaging, Jieying Mai, Yingchun Cao, Ayeeshik Kole, Michael Sturek, Ji-Xin Cheng

The Summer Undergraduate Research Fellowship (SURF) Symposium

Heart disease is the leading cause of death in the United States and worldwide. Each year over 370,000 people died from coronary artery disease in America. As the primary form of coronary artery disease, atherosclerosis behaves as lipid-rich plaque development inside an artery wall. Vulnerable plaques are those prone to rupture, which may result in thrombus or even death. Typical hallmarks of a vulnerable plaque include thin fibrous cap, a large lipid-rich necrotic core and inflammatory infiltrate. The identification and accurate detection of these lipid depositions in the arterial wall is crucial in the diagnosis of atherosclerosis. However, none ...


3d Modeling Of Murine Abdominal Aortic Aneurysms: Quantification Of Segmentation And Volumetric Reconstruction, Paula A. Sarmiento, Amelia R. Adelsperger, Craig J. Goergen Ph.D. 2016 Universidad de Los Andes - Colombia

3d Modeling Of Murine Abdominal Aortic Aneurysms: Quantification Of Segmentation And Volumetric Reconstruction, Paula A. Sarmiento, Amelia R. Adelsperger, Craig J. Goergen Ph.D.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal Aortic Aneurysms (AAA) cause 5,900 deaths in the United States each year. Surgical intervention is clinically studied by non-invasive techniques such as computed tomography and magnetic resonance imaging. However, three-dimensional (3D) ultrasound imaging has become an inexpensive alternative and useful tool to characterize aneurysms, allowing for reconstruction of the vessel, quantification of hemodynamics through computational fluid dynamics (CFD) simulation, and possible prediction of aortic expansion and rupture. However, current analysis techniques for these images require the use of multiple software platforms for either modeling or simulation, prompting the need for alternatives to improve data processing. This study monitors ...


Diagnostic Quality Assessment Of Compressed Sensing Accelerated Magnetic Resonance Neuroimaging., Mohammad Kayvanrad, Amy Lin, Rohit Joshi, Jack Chiu, Terry Peters 2016 Western University

Diagnostic Quality Assessment Of Compressed Sensing Accelerated Magnetic Resonance Neuroimaging., Mohammad Kayvanrad, Amy Lin, Rohit Joshi, Jack Chiu, Terry Peters

Robarts Imaging Publications

PURPOSE: To determine the efficacy of compressed sensing (CS) reconstructions for specific clinical magnetic resonance neuroimaging applications beyond more conventional acceleration techniques such as parallel imaging (PI) and low-resolution acquisitions.

MATERIALS AND METHODS: Raw k-space data were acquired from five healthy volunteers on a 3T scanner using a 32-channel head coil using T2 -FLAIR, FIESTA-C, time of flight (TOF), and spoiled gradient echo (SPGR) sequences. In a series of blinded studies, three radiologists independently evaluated CS, PI (GRAPPA), and low-resolution images at up to 5× accelerations. Synthetic T2 -FLAIR images with artificial lesions were used to assess diagnostic accuracy for ...


Fluorochlorozirconate Glass Ceramics For Computed Radiography, Adam Wesley Evans 2016 University of Tennessee, Knoxville

Fluorochlorozirconate Glass Ceramics For Computed Radiography, Adam Wesley Evans

Masters Theses

Heat treating fluorochlorozirconate (FCZ) glasses nucleates nanocrystals in the glass matrix, resulting in a glass ceramic that has optical properties suitable for use as a medical imaging plate. As the temperature of heat treatment rises, the resulting FCZ glass-ceramic becomes increasingly more opaque as the size of the orthorhombic phase BaCl­2[barium chloride] nanocrystals grow within the glass matrix. This opaqueness negatively affects imaging. The effect of adding Fe3+[iron] on the valence state of zirconium and overall glass quality was investigated.

Samples were synthesized and characterized with differential scanning calorimetry to determine the temperature of the orthorhombic ...


Blinking Phase-Change Nanocapsules Enable Background-Free Ultrasound Imaging, Alexander S. Hannah, Geoffrey P. Luke, Stanislav Y. Emelianov 2016 Georgia Institute of Technology

Blinking Phase-Change Nanocapsules Enable Background-Free Ultrasound Imaging, Alexander S. Hannah, Geoffrey P. Luke, Stanislav Y. Emelianov

Open Dartmouth: Faculty Open Access Articles

Microbubbles are widely used as contrast agents to improve the diagnostic capability of conventional, highly speckled, low-contrast ultrasound imaging. However, while microbubbles can be used for molecular imaging, these agents are limited to the vascular space due to their large size (> 1 μm). Smaller microbubbles are desired but their ultrasound visualization is limited due to lower echogenicity or higher resonant frequencies. Here we present nanometer scale, phase changing, blinking nanocapsules (BLInCs), which can be repeatedly optically triggered to provide transient contrast and enable background-free ultrasound imaging. In response to irradiation by near-infrared laser pulses, the BLInCs undergo cycles of rapid ...


Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li 2016 Old Dominion University

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries ...


Portable, Parallel 9-Wavelength Near-Infrared Spectral Tomography (Nirst) System For Efficient Characterization Of Breast Cancer Within The Clinical Oncology Infusion Suite, Yan Zhao, Brian W. Pogue, Steffen J. Haider, Jiang Gui, Roberta diFlorio-Alexander, Keith Paulsen, Shudong Jiang 2016 Dartmouth College

Portable, Parallel 9-Wavelength Near-Infrared Spectral Tomography (Nirst) System For Efficient Characterization Of Breast Cancer Within The Clinical Oncology Infusion Suite, Yan Zhao, Brian W. Pogue, Steffen J. Haider, Jiang Gui, Roberta Diflorio-Alexander, Keith Paulsen, Shudong Jiang

Open Dartmouth: Faculty Open Access Articles

A portable near-infrared spectral tomography (NIRST) system was developed with simultaneous frequency domain (FD) and continuous-wave (CW) optical measurements for efficient characterization of breast cancer in a clinical oncology setting. Simultaneous FD and CW recordings were implemented to speed up acquisition to 3 minutes for all 9 wavelengths, spanning a range from 661nm to 1064nm. An adjustable interface was designed to fit various breast sizes and shapes. Spatial images of oxy- and deoxy-hemoglobin, water, lipid, and scattering components were reconstructed using a 2D FEM approach. The system was tested on a group of 10 normal subjects, who were examined bilaterally ...


Pilot Study To Assess Breathing During Sight-Read Stringed Instrument Performance, Collin T. Erickson, Clark Potter MM, MFA, Gregory Bashford Ph.D 2016 University of Nebraska-Lincoln

Pilot Study To Assess Breathing During Sight-Read Stringed Instrument Performance, Collin T. Erickson, Clark Potter Mm, Mfa, Gregory Bashford Ph.D

UCARE Research Products

For many musicians, one common occurrence during a performance is the presence of stage fright. Stage fright, though not always expressed can influence the confidence and self-esteem of a performer, and thus can affect the quality of the performance. Every day musicians are affected by stage fright, and there has been no exact solution as to how to lessen the feeling of anxiety musicians feel before performing. No data has been collected to find the correlation between the regularity of breathing and the level of stage fright that a person feels during their performance. A way to quantify regularity of ...


The Effectiveness, Efficiency, And Appeal Of Pediatric Echocardiography Protocol Training For First Year Pediatric Cardiology Fellows, Lynne M. Brown 2016 University of Wisconsin-Milwaukee

The Effectiveness, Efficiency, And Appeal Of Pediatric Echocardiography Protocol Training For First Year Pediatric Cardiology Fellows, Lynne M. Brown

Theses and Dissertations

Echocardiography training for pediatric cardiology fellows is complex and academic hospitals strive to provide high-quality training using limited resources. The purpose of this embedded single case study design was to evaluate the effectiveness, efficiency, and appeal of a newly developed 10-day echocardiography protocol learning module for first year pediatric cardiology fellows. Using blended learning methods that included didactic lectures, online learning activities, and interactive games, the learning module was the first step in the process of training pediatric cardiology fellows to perform echocardiograms independently with limited supervision during their first year of fellowship. At the end of the 10-day module ...


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