Structural and Functional Biomedical Imaging Using Polarization-Based Optical Coherence Tomography

University of Minnesota Ph.D. dissertation. August 2015. Major: Biomedical Engineering. Advisor: Taner Akkin. 1 computer file (PDF); x, 103 pages.Biomedical imaging has had an enormous impact in medicine and research. There are numerous imaging modalities covering a large range of spatial and temporal scales, penetration depths, along with indicators for function and disease. As these imaging technologies mature, the quality of the images they produce increases to resolve finer details with greater contrast at higher speeds which aids in a faster, more accurate diagnosis in the clinic. In this dissertation, polarization-based optical coherence tomography (OCT) systems are used and developed to image biological structure and function with greater speeds, signal-to-noise (SNR) and stability. OCT can image with spatial and temporal resolutions in the micro range. When imaging any sample, feedback is very important to verify the fidelity and desired location on the sample being imaged. To increase frame rates for display as well as data throughput, field-programmable gate arrays (FPGAs) were used with custom algorithms to realize real-time display and streaming output for continuous acquisition of large datasets of swept-source OCT systems. For spectral domain (SD) OCT systems, significant increases in signal-to-noise ratios were achieved from a custom balanced detection (BD) OCT system. The BD system doubled measured signals while reducing common term. For functional imaging, a real-time directed scanner was introduced to visualize the 3D image of a sample to identify regions of interest prior to recording. Elucidating the characteristics of functional OCT signals with the aid of simulations, novel processing methods were also developed to stabilize samples being imaged and identify possible origins of functional signals being measured. Polarization-sensitive OCT was used to image cardiac tissue before and after clearing to identify the regions of vascular perfusion from a coronary artery. The resulting 3D image provides a visualization of the perfusion boundaries for the tissue that would be damaged from a myocardial infarction to possibly identity features that lead to fatal cardiac arrhythmias. 3D functional imaging was used to measure functional retinal activity from a light stimulus. In some cases, single trial responses were possible; measured at the outer segment of the photoreceptor layer. The morphology and time-course of these signals are similar to the intrinsic optical signals reported from phototransduction. Assessing function in the retina could aid in early detection of degenerative diseases of the retina, such as glaucoma and macular degeneration

Functional and Categorical Analysis of Waveshapes Recorded on Microelectrode Arrays

Dissociated neuronal cell cultures grown on substrate integrated microelectrode arrays (MEAs) generate spontaneous activity that can be recorded for up to several weeks. The signature wave shapes from extracellular recording of neuronal activity display a great variety of shapes with triphasic signals predominating. I characterized extracellular recordings from over 600 neuronal signals. I have preformed a categorical study by dividing wave shapes into two major classes: (type 1) signals in which the large positive peak follows the negative spike, and (type 2) signals in which the large positive peak precedes the negative spike. The former are hypothesized to be active signal propagation that can occur in the axon and possibly in soma or dendrites. The latter are hypothesized to be passive which is generally secluded to soma or dendrites. In order to verify these hypotheses, I pharmacologically targeted ion channels with tetrodotoxin (TTX), tetraethylammonium (TEA), 4-aminopyridine (4-AP), and monensin

Microstimulation and multicellular analysis: A neural interfacing system for spatiotemporal stimulation

Willfully controlling the focus of an extracellular stimulus remains a significant challenge in the development of neural prosthetics and therapeutic devices. In part, this challenge is due to the vast set of complex interactions between the electric fields induced by the microelectrodes and the complex morphologies and dynamics of the neural tissue. Overcoming such issues to produce methodologies for targeted neural stimulation requires a system that is capable of (1) delivering precise, localized stimuli a function of the stimulating electrodes and (2) recording the locations and magnitudes of the resulting evoked responses a function of the cell geometry and membrane dynamics. In order to improve stimulus delivery, we developed microfabrication technologies that could specify the electrode geometry and electrical properties. Specifically, we developed a closed-loop electroplating strategy to monitor and control the morphology of surface coatings during deposition, and we implemented pulse-plating techniques as a means to produce robust, resilient microelectrodes that could withstand rigorous handling and harsh environments. In order to evaluate the responses evoked by these stimulating electrodes, we developed microscopy techniques and signal processing algorithms that could automatically identify and evaluate the electrical response of each individual neuron. Finally, by applying this simultaneous stimulation and optical recording system to the study of dissociated cortical cultures in multielectode arrays, we could evaluate the efficacy of excitatory and inhibitory waveforms. Although we found that the proximity of the electrode is a poor predictor of individual neural excitation thresholds, we have shown that it is possible to use inhibitory waveforms to globally reduce excitability in the vicinity of the electrode. Thus, the developed system was able to provide very high resolution insight into the complex set of interactions between the stimulating electrodes and populations of individual neurons.Ph.D.Committee Chair: Stephen P. DeWeerth; Committee Member: Bruce Wheeler; Committee Member: Michelle LaPlaca; Committee Member: Robert Lee; Committee Member: Steve Potte

Anatomical Organization of the Extended Amygdala

The concept of the extended amygdala proposed by de Olmos and Heimer suggests that the central (CEA) and medial nuclei of the amygdala (MEA) and the bed nucleus of stria terminalis (BST) are parts of a contiguous cellular column of neurons with similar anatomical connectivity and functional output (Olmos; and Heimer; 1999). An alternative hypothesis proposed by Larry Swanson suggests that the CEA/MEA and BST are ventral differentiations of the striatum and pallidum, together forming a striatopallidal circuit that participates in a cortical reentrant loop (Swanson and Petrovich 1998, Swanson 2000). In support of the extended amygdala concept, connections between the amygdala and BST are topographically-organized, suggesting the presence of discrete channels for information processing. Furthermore, results from several studies indicate that lesions of the amygdala or BST often produce experimental results that are quite similar (Zardetto-Smith, Beltz et al. 1994, Newman 1999, Tanimoto, Nakagawa et al. 2003, Nakagawa, Yamamoto et al. 2005, Deyama, Nakagawa et al. 2007). On the other hand, the concept of the extended amygdala has been challenged by results from behavioral studies that suggest a dissociation of CEA and BST functions in mediating behavioral processes associated with fear, anxiety (Walker and Davis 1997, Fendt, Endres et al. 2003, Walker, Toufexis et al. 2003, Sullivan, Apergis et al. 2004), social defeat (Jasnow, Davis et al. 2004), social interaction (Cecchi, Khoshbouei et al. 2002) and ethanol self-administration (Funk, O'Dell et al. 2006). The studies in this dissertation were designed to test some of the assumptions proposed by the extended amygdala concept by more closely examining the similarities of extended amygdala circuits. In the first study, we tested the hypothesis proposed by de Olmos and Heimer that “all or most of the central extended amygdala would share similar inputs” (de Olmos and Heimer 1999). In the second study, we examined multisynaptic BST circuits that project to CEA and MEA to determine if BST circuits were maintained within topographically-organized channels. Our findings reveal several organizational principles for the anatomical relationship of the amygdala and BST subnuclei and suggest new theories for how extended amygdala circuits process information