Bioimaging and Biomedical Optics Commons^™

Image Registration Of Ex-Vivo Mri To Sparsely Sectioned Histology Of Hippocampal And Neocortical Temporal Lobe Specimens., Maged Goubran, Cathie Crukley, Sandrine De Ribaupierre, Terence M Peters, Ali R Khan

Robarts Imaging Publications

Intractable or drug-resistant epilepsy occurs in up to 30% of epilepsy patients, with many of these patients undergoing surgical excision of the affected brain region to achieve seizure control. Recent magnetic resonance imaging (MRI) sequences and analysis techniques have the potential to detect abnormalities not identified with diagnostic MRI protocols. Prospective studies involving pre-operative imaging and collection of surgically-resected tissue provide a unique opportunity for verification and tuning of these image analysis techniques, since direct comparison can be made against histopathology, and can lead to better prediction of surgical outcomes and potentially less invasive procedures. To carry out MRI and …

Dopaminergic Modulation Of Memory And Affective Processing In Parkinson Depression, Lee X. Blonder, John T. Slevin, Richard J. Kryscio, Catherine A. Martin, Anders H. Andersen, Charles D Smith, Frederick A. Schmitt

Magnetic Resonance Imaging and Spectroscopy Center Faculty Publications

Depression is common in Parkinson's disease and is associated with cognitive impairment. Dopaminergic medications are effective in treating the motor symptoms of Parkinson's disease; however, little is known regarding the effects of dopaminergic pharmacotherapy on cognitive function in depressed Parkinson patients. This study examines the neuropsychological effects of dopaminergic pharmacotherapy in Parkinsonian depression. We compared cognitive function in depressed and non-depressed Parkinson patients at two time-points: following overnight withdrawal and after the usual morning regimen of dopaminergic medications. A total of 28 non-demented, right-handed patients with mild to moderate idiopathic Parkinson's disease participated. Ten of these patients were depressed according …

In Vivo Flow Measurements Of Murine Renal Arteries And Veins With High Frequency Ultrasound, Amy E. Bogucki, Hilary D. Schroeder, Alexa A. Yrineo, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

The number of glomeruli in the kidneys has been shown to have an effect on the decline in renal function over time (Brenner, Garcia, Anderson 1988). Furthermore, flow in the renal arteries and veins may depend on the number of glomeruli in the kidney. Consistent in vivo measurements of volumetric flow in the renal arteries and veins are difficult to obtain. Thus, the purpose of this study was to develop non-invasive imaging techniques capable of estimating arterial and venous flow to kidneys. A high-frequency small animal ultrasound system was chosen based upon its excellent spatial and temporal resolution when imaging …

In Vivo Method For Labeling And Tracking Cells In The Mammalian Limb Bud, James T. Mccarthy, Andrew Schilb, Sarah Calve

The Summer Undergraduate Research Fellowship (SURF) Symposium

The extracellular matrix (ECM) is composed of many different proteins excreted by cells and is believed to play a very important role in development as well as regeneration and wound healing. In this research, a method to determine the ECM’s effect on the migration of muscle progenitor cells into the mammalian limb bud was investigated. It has traditionally been difficult to obtain in vivo images of the limb bud, due to the difficulty of maintaining embryos in culture and limitations of imaging techniques. In this study, we have worked on optimizing the culture conditions to allow growth of mouse embryos …

Visualization Of Complex Flow Patterns In Angiotensin Ii-Induced Dissecting Murine Abdominal Aortic Aneurysms With High Frequency Ultrasound, Hilary D. Schroeder, Alexa A. Yrineo, Amy E. Bogucki, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysm (AAA) rupture is a common cause of mortality in the United States. Current treatments are only employed once the risk of rupture outweighs the risks associated with surgery. Murine models have been developed to characterize AAA pathogenesis in the hope that new treatments will be developed. For this study, angiotensin II (AngII) was infused subcutaneously into apolipoprotein E-deficient (ApoE^-/-) mice using an osmotic mini-pump over 28 days. ApoE^-/- mice (16-week-old, 3 females, 2 males) were imaged using a VisualSonics Vevo 2100 high frequency ultrasound before pump implantation and 3, 7, 14, 21, and 27 …

Development Of Non-Invasive In Vivo Ultrasound Imaging Techniques For Elastase-Induced Experimental Abdominal Aortic Aneurysms, Alexa A. Yrineo, Elizabeth A. Nunamaker, Hilary D. Schroeder, Amy E. Bogucki, Craig J. Goergen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Abdominal aortic aneurysms (AAAs) are pathological dilations of the aorta which are associated with significant morbidity and mortality. The underlying mechanisms that cause this inflammatory disease are not fully understood and thus, are currently under investigation. In the hopes of preventing disease progression, rodent models that mimic the human condition have been developed to provide insight into the pathogenesis of AAAs. In this study, porcine pancreatic elastase (0.44 U; Sigma-Aldrich) was infused into the infrarenal aortas of male, Sprague Dawley rats to induce aneurysms. To perform the surgery, temporary ligatures were placed around proximal and distal sections of the abdominal …

Characterization Of Two-Dimensional Oculomotor Control During Goal-Directed Eye Movements In Humans, Vincent Dang

Master's Theses (2009 -)

Oculomotor control is a subset of sensorimotor control that allows humans to make extremely accurate eye movements for ADL. Impairments to oculomotor control can increase the impact of sensorimotor control deficits, especially in neurodegenerative diseases such as MS. Here, a two-dimensional computational control system of saccades and smooth-pursuit eye movements was compiled from literature to systematically characterize oculomotor control in eight visually-healthy humans as a precursor to studying the relationship between oculomotor and sensorimotor control in patient populations. Subjects visually tracked a single dot on a 41 x 30.5 cm monitor in a dark room while eye positions were recorded …

Spectral Discrimination Of Breast Pathologies In Situ Using Spatial Frequency Domain Imaging, Ashley M. Laughney, Venkataramanan Krishnaswamy, Elizabeth J. Rizzo, Mary C. Schwab, Richard J. Barth, David J. Cuccia, Bruce J. Tromberg, Keith D. Paulsen, Brian W. Pogue, Wendy A. Wells

Dartmouth Scholarship

Introduction: Nationally, 25% to 50% of patients undergoing lumpectomy for local management of breast cancer require a secondary excision because of the persistence of residual tumor. Intraoperative assessment of specimen margins by frozen-section analysis is not widely adopted in breast-conserving surgery. Here, a new approach to wide-field optical imaging of breast pathology in situ was tested to determine whether the system could accurately discriminate cancer from benign tissues before routine pathological processing.

Protein Loop Length Estimation From Medium Resolution Cryoem Images, Andrew R. Mcknight

Computer Science Theses & Dissertations

In the post-genomic era, proteomics research presents a new frontier in life science. Proteins play roles in virtually every biological process, and understanding their atomic structures is the key to unraveling how they carry out their work. Compared to the over half million protein sequences in UniProt, only around 25,000 unique sequences have been atomically modeled and deposited to PDB (Protein Databank). Cryoelectron Microscopy (cryoEM) is an important biophysical technique that produces 3D subnanometer resolution images of molecules not amenable to past approaches like x-ray crystallography or nuclear magnetic resonance. De novo modeling is becoming a promising approach to derive …

An Fmri Study On Supra-Spinal Contributions To Upper And Lower Limb Motor Control, Shancheng Bao

Master's Theses (2009 -)

The differences in the neural mechanisms contributing to upper and lower extremity movement have not been fully elucidated, and this might be a factor that leads to the ineffectiveness of rehabilitation techniques for most stroke survivors. It is unclear whether therapies designed for upper extremities should also be used for the lower extremities, and vice versa. In this study, fMRI was used to examine the supraspinal control of UE and LE movement in both neurologically intact individuals and people with post-stroke hemiparesis. We compared the location, volume, and intensity of brain activity associated with upper and lower extremity pedaling and …

Fluorescence Characterization Of Quantum Dots For Use As Biomarkers, Logan M. Grimes

Materials Engineering

Fluorescence profiles of quantum dots (QDs) were characterized to select the ideal QDs for encapsulation in phospholipids for use as biomarkers to selectively adhere to cancer cells. QDs were synthesized and extracted 0, 30, 60, and 90 seconds after precursor compounds were mixed. These extractions were isolated by extraction time. Portions from each vial were coated in a zinc sulfide shelling procedure, leaving at least half of the QD solution unshelled. These samples were characterized over four days to monitor fluctuations in fluorescence. This was done utilizing an Ocean Optics spectrometer in conjunction with Spectra Suite software. The central wavelength, …

Microcapsule Containing Lactic Acid Bacteria For Treatment Of Peptic Ulcers, Brandon Jerome Hinkel

Master's Theses

Probiotics are marketed throughout the world to promote the health of the consumer by improving the microorganisms that normally occur in the intestinal tract (Tannock, 1997). It has also been suggested that probiotics can prevent pathogen infections by adhering to the intestinal mucosa (Lee, Lim, Teng, Ouwehand, Tuomola, & Salminen, 2000). While probiotics can be delivered to the infected areas in multiple fashions, microencapsulation is a newer form of delivering probiotics straight to the infected area. A whey protein microcapsule is thought to protect the probiotics from stomach acid and delivers the treatment to the affected area. To ensure this …

Tracking Points On A Pacing Lead In A Beating Heart, Avinash Ramesh Varma

Master's Theses

Heart failure is a common condition during which the pumping action of the heart is affected because the heart does not contract or relax properly. Heart failure affects about 5 million Americans, with 550,000 new cases diagnosed each year. Cardiac resynchronization therapy (CRT) is used to treat symptoms and other complications associated with a heart failure. While performing CRT, Implantation of a pacing lead in the left ventricle of the heart is a very challenging surgical procedure performed with fluoroscopy. The target location is often difficult to reach through the tortuous coronary venous anatomy, which varies greatly among individuals. Placement …

Biomedical Photoacoustic Imaging Using Gas-Coupled Laser Acoustic Detection, Jami L. Johnson

Student Research Initiative

Several detection methods have been explored for photoacoustic and ultrasound imaging of biological tissues. Piezoelectric transducers are commonly used, which require contact with the sample and have limiting bandwidth characteristics. Interferometry detection exhibits improved bandwidth characteristics and resolution, yet generally require complicated optics and the incorporation of a contacting reflective medium. Here, we report the use of a noncontact photoacoustic and laser-ultrasound imaging system that does not require the use of a reflective layer. A simple, robust technique known as gas-coupled laser acoustic detection is used, which has previously been applied to composite material evaluation. This technique has the potential …

Dynamic Dual-Tracer Mri-Guided Fluorescence Tomography To Quantify Receptor Density In Vivo, Scott C. Davis, Kimberley S. Samkoe, Kenneth M. Tichauer, Kristian J. Sexton, Jason R. Gunn, Sophie J. Deharvengt, Tayyaba Hasan, Brian W. Pogue

Dartmouth Scholarship

The up-regulation of cell surface receptors has become a central focus in personalized cancer treatment; however, because of the complex nature of contrast agent pharmacokinetics in tumor tissue, methods to quantify receptor binding in vivo remain elusive. Here, we present a dual-tracer optical technique for noninvasive estimation of specific receptor binding in cancer. A multispectral MRI-coupled fluorescence molecular tomography system was used to image the uptake kinetics of two fluorescent tracers injected simultaneously, one tracer targeted to the receptor of interest and the other tracer a nontargeted reference. These dynamic tracer data were then fit to a dual-tracer compartmental model …

Biomedical Photoacoustic Imaging Using Gas-Coupled Laser Acoustic Detection, Jami Johnson

Student Research Initiative

Several detection methods have been explored for photoacoustic and ultrasound imaging of biological tissues. Piezoelectric transducers are commonly used, which require contact with the sample to be imaged and have limiting bandwidth characteristics. Interferometry detection exhibits improved bandwidth characteristics and resolution, yet generally require complicated optics and the incorporation of a contacting reflective medium. In this paper, we report the use of a noncontact photoacoustic imaging system that does not require the use of a reflective layer. A simple, robust technique known as gas-coupled laser acoustic detection is used, which has previously been applied to evaluation of composite materials. This …

A Gamos Plug-In For Geant4 Based Monte Carlo Simulation Of Radiation-Induced Light Transport In Biological Media, Adam K. Glaser, Stephen C. Kanick, Rongxiao Zhang, Pedro Arce, Brian W. Pogue

Dartmouth Scholarship

We describe a tissue optics plug-in that interfaces with the GEANT4/GAMOS Monte Carlo (MC) architecture, providing a means of simulating radiation-induced light transport in biological media for the first time. Specifically, we focus on the simulation of light transport due to the Čerenkov effect (light emission from charged particle's traveling faster than the local speed of light in a given medium), a phenomenon which requires accurate modeling of both the high energy particle and subsequent optical photon transport, a dynamic coupled process that is not well-described by any current MC framework. The results of validation simulations show excellent agreement with …

Study Of Immobilizing Cadmium Selenide Quantum Dots In Selected Polymers For Application In Peroxyoxalate Chemiluminescence Flow Injection Analysis, Christopher S. Moore

Electronic Theses and Dissertations

Two batches of CdSe QDs with different sizes were synthesized for immobilizing in polyisoprene (PI), polymethylmethacrylate (PMMA), and low-density polyethylene (LDPE). The combinations of QDs and polymer substrates were evaluated for their analytical fit-for-use in applicable immunoassays. Hydrogen peroxide standards were injected into the flow injection analyzer (FIA) constructed to simulate enzyme-generated hydrogen peroxide reacting with bis-(2,4,6-trichlorophenyl) oxalate.

Linear correlations between hydrogen peroxide and chemilumenscent intensities yielded regression values greater than 0.9750 for hydrogen peroxide concentrations between 1.0 x 10^-4 M and 1.0 x 10^-1 M. The developed technique’s LOD was approximately 10 ppm. Variability of the prepared …

Toward Characterization Of Diseased Vascular Structures Using Noncontact Photoacoustic And Laser-Ultrasound Imaging: A Phantom Study, Jami Lynne Johnson

Boise State University Theses and Dissertations

Visualizing and characterizing atherosclerotic plaques is important in determining the vulnerability of a plaque to rupture. To evaluate rupture risk, several compositional factors should be evaluated, including inflammation, the presence and size of lipid pools, thickness of the fibrous cap, and calcification. Currently, a need exists for an imaging modality that can detect each of these factors in a safe, noninvasive manner with high resolution and contrast at clinically relevant depths. Photoacoustic imaging is a growing field that has the potential to improve plaque diagnosis. Spectroscopic methods have shown promise toward detection of constituents of plaque with unique optical absorption …

Delayed Thrombus Resolution And Fibroproliferative Vascular Wound Healing From Deficiency Of Type Iii Collagen: A Paradoxical Mechanism For Tissue Fragility, Amy J. Reid

Dissertations and Theses (Open Access)

Vascular Ehlers-Danlos syndrome is a heritable disease of connective tissue caused by mutations in COL3A1, conferring a tissue deficiency of type III collagen. Cutaneous wounds heal poorly in these patients, and they are susceptible to spontaneous and catastrophic rupture of expansible hollow organs like the gut, uterus, and medium-sized to large arteries, which leads to premature death. Although the predisposition for organ rupture is often attributed to inherent tissue fragility, investigation of arteries from a haploinsufficient Col3a1 mouse model (Col3a1^+/-) demonstrates that mutant arteries withstand even supraphysiologic pressures comparably to wild-type vessels. We hypothesize that injury …

A Microfluidic Pretreatment Isoelectric Focusing Dc-Field Assisted H-Filter For The Separation Of Charged Particles, Cameron Sean Carroll

Biomedical Engineering

Microfluidic devices are small portable diagnostic chips that allow for analysis of a biologic sample at relatively low cost. This makes them ideal for settings where a hospital is unavailable. The microfluidic pretreatment isoelectric focusing DC-field assisted H-filter is a device that allows for the separation of differently charged particles in a biologic sample. It does this by employing the concepts of diffusion, electrophoresis, and isoelectric focusing. This is perfect for isolation of a desired analyte or separation of waste from a sample in order to achieve better diagnostic results. The device was first modeled mathematically and visually using Comsol. …

Picture Of A Chelate In Exchange: The Crystal Structure Of Nahodotma, A 'Semi'-Hydrated Chelate, Katherine M. Payne, Edward J. Valente, Silvio Aime, Mauro Botta, Mark Woods

Chemistry Faculty Publications and Presentations

Crystallography generally only provides static structural information. This can render it an ineffective technique for probing dynamic solution state processes. A crystal of HoDOTMA affords unique structures that effectively represent that of a lanthanide tetra-acetate chelate mid-way through the water exchange process.

Automated Point-Of-Care Image Processing Methodology For The Diagnosis Of Malaria, Michael B. Jorgensen

Master's Theses

Malaria has profoundly influenced human history for over four thousand years and despite numerous attempts at eradication, the prevention, diagnosis, and treatment of malaria have been largely ineffective. More than five hundred million people are affected by malaria every year resulting in over one million deaths. Drug resistance development by the parasite has diminished the effectiveness of numerous treatment options due, in part, to overtreatment of negative patients based on insufficient clinical algorithms and diagnostic methods. The goal of this research was to develop an image analysis algorithm to diagnose malaria with a high degree of sensitivity and specificity in …

Scanning In Situ Spectroscopy Pplatform For Imaging Surgical Breast Tissue Specimens, Venkataramanan Krishnaswamy, Ashley M. Laughney, Wendy A. Wells, Keith D. Paulsen, Brian W. Pogue

Dartmouth Scholarship

A non-contact localized spectroscopic imaging platform has been developed and optimized to scan 1 x 1 cm² square regions of surgically resected breast tissue specimens with ~150-micron resolution. A color corrected, image-space telecentric scanning design maintained a consistent sampling geometry and uniform spot size across the entire imaging field. Theoretical modeling in ZEMAX allowed estimation of the spot size, which is equal at both the center and extreme positions of the field with ~5% variation across the designed waveband, indicating excellent color correction. The spot sizes at the center and an extreme field position were also measured experimentally using the …

The Role Of Tissue Sound Speed As A Surrogate Marker Of Breast Density, Mark Sak

Wayne State University Dissertations

Breast density is one of the strongest predictors of breast cancer risk as women with the densest breasts have a three- to five-fold increase in risk compared to women with the least dense breasts. Breast density is currently measured by using mammography, the current gold standard for breast imaging. There are many shortcomings to using mammography to measure breast density, including the use of ionizing radiation. Ultrasound tomography (UST) does not use ionizing radiation and can create tomographic breast sound speed images. These sound speed images are useful because breast density is proportional to sound speed. The purpose of this …

Compressed Sensing And Joint Acquisition Techniques In Mri, Rouhollah Hamtaei

Wayne State University Theses

The relatively long scan times in Magnetic Resonance Imaging (MRI) limits some clinical applications and the ability to collect more information in a reasonable period of time. Practically, 3D imaging requires longer acquisitions which can lead to a reduction in image quality due to motion artifacts, patient discomfort, increased costs to the healthcare system and loss of profit to the imaging center. The emphasis in reducing scan time has been to a large degree through using limited k-space data acquisition and special reconstruction techniques. Among these approaches are data extrapolation methods such as "constrained reconstruction" techniques, data interpolation methods such …

Noninvasive Near-Infrared Diffuse Optical Monitoring Of Cerebral Hemodynamics And Autoregulation, Ran Cheng

Theses and Dissertations--Biomedical Engineering

Many cerebral diseases are associated with abnormal cerebral hemodynamics and impaired cerebral autoregulation (CA). CA is a mechanism to maintain cerebral blood flow (CBF) stable when mean arterial pressure (MAP) fluctuates. Evaluating these abnormalities requires direct measurements of cerebral hemodynamics and MAP. Several near-infrared diffuse optical instruments have been developed in our laboratory for hemodynamic measurements including near-infrared spectroscopy (NIRS), diffuse correlation spectroscopy (DCS), hybrid NIRS/DCS, and dual-wavelength DCS flow-oximeter. We utilized these noninvasive technologies to quantify CBF and cerebral oxygenation in different populations under different physiological conditions/manipulations. A commercial finger plethysmograph was used to continuously monitor MAP. For investigating …

Recovering Local Neural Tract Directions And Reconstructing Neural Pathways In High Angular Resolution Diffusion Mri, Ning Cao

Theses and Dissertations--Computer Science

Magnetic resonance imaging (MRI) is an imaging technique to visualize internal structures of the body. Diffusion MRI is an MRI modality that measures overall diffusion effect of molecules in vivo and non-invasively. Diffusion tensor imaging (DTI) is an extended technique of diffusion MRI. The major application of DTI is to measure the location, orientation and anisotropy of fiber tracts in white matter. It enables non-invasive investigation of major neural pathways of human brain, namely tractography. As spatial resolution of MRI is limited, it is possible that there are multiple fiber bundles within the same voxel. However, diffusion tensor model is …

Automatic Detection Of Polypoid Skin Lesions: The Squash Sign, Saurabh G. Karnik

Masters Theses

“Earlier detection of malignant melanoma can save lives. Automatic in-vivo methods of melanoma detection including smart-phone applications are now available, but specificity is low, i.e. too many benign lesions are detected as possible melanomas. Polypoids, elevated and rounded lesions are one class of benign lesions. These raised lesions with piecewise circular borders, predominantly intradermal nevi and cutaneous polyps (IDNs), are always benign. Variegated coloring present in polypoid lesions can lead physicians to perform an unneeded biopsy. Contact dermatoscope plates with gel squash these lesions, leaving a “squash sign” marker of benignancy which can be automatically detected. We present a method …

Significance And Analysis Of Milia-Like Cysts In Dermoscopy Skin Lesion Images, Sneha K. Mahajan

Masters Theses

“Milia-like cysts (MLCs) are dermoscopic structures frequently observed in seborrheic keratoses(SKs), which are the most common type of skin lesions. Diverse appearances of these skin lesions make them difficult to differentiate from melanoma, a deadly type of skin cancer. Classified by size into two main groups, starry MLCs and cloudy MLCs, the presence of these structures in a skin lesion has been known to help differentiate benign lesions from melanoma. Though the presence of cloudy MLCs is not exclusively associated with SKs, they can be a useful tool to differentiate SKs from melanoma. This research study determines the statistical occurrence …