abstract: Recent new experiments showed that wide-field imaging at millimeter scale is capable of recording hundreds of neurons in behaving mice brain. Monitoring hundreds of individual neurons at a high frame rate provides a promising tool for discovering spatiotemporal features of large neural networks. However, processing the massive data sets is impossible without automated procedures. Thus, this thesis aims at developing a new tool to automatically segment and track individual neuron cells. The new method used in this study employs two major ideas including feature extraction based on power spectral density of single neuron temporal activity and clustering tree to separate overlapping cells. To address issues associated with high-resolution imaging of a large recording area, focused areas and out-of-focus areas were analyzed separately. A static segmentation with a fixed PSD thresholding method is applied to within focus visual field. A dynamic segmentation by comparing maximum PSD with surrounding pixels is applied to out-of-focus area. Both approaches helped remove irrelevant pixels in the background. After detection of potential single cells, some of which appeared in groups due to overlapping cells in the image, a hierarchical clustering algorithm is applied to separate them. The hierarchical clustering uses correlation coefficient as a distance measurement to group similar pixels into single cells. As such, overlapping cells can be separated. We tested the entire algorithm using two real recordings with the respective truth carefully determined by manual inspections. The results show high accuracy on tested datasets while false positive error is controlled within an acceptable range. Furthermore, results indicate robustness of the algorithm when applied to different image sequences. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2016

Damage to the central nervous system (CNS) leads to the generation of an immune response which culminates with the encapsulation of the damaged area. The encapsulation, known as a glial scar, essentially breaks neural signal pathways and blocks signal transmissions to and from the CNS. The effect is the loss of motor and sensory control for the damaged individual. One method that has been used successfully to treat this problem is the use of a brain-machine interface (BMI) which can intercept signals from the brain and use these signals to control a machine. Although there are many types of BMI devices, implantable devices show the greatest promise with the ability to target specific areas of the CNS, with reduced noise levels and faster signal interception, and the fact that they can also be used to send signals to neurons. The largest problem that has plagued this type of BMI device is that the materials that have been used for their construction are not chemically resilient, elicit a negative biological response, or have difficulty functioning for extended periods of time in the harsh body environment. Many of these implantable devices experience catastrophic failure within weeks to months because of these negative factors. New materials must be examined to advance the future utilization of BMI devices to assist people with CNS damage or disease. We have proposed that two semiconductor materials, cubic silicon carbide (3C-SiC) and nanocrystalline diamond (NCD), which should provide solutions to the material biocompatibility problems experienced by implantable BMI devices. We have shown in this study that these two materials show chemical resilience to neuronal cellular processes, and we show evidence which indicates that these materials possess good biocompatibility with neural cell lines that, in the worst case, is comparable to celltreated polystyrene and, in most cases, even surpasses polystyrene. We have utilized 3C-SiC within an electrode device and activated the action potential of differentiated PC12 cells. This work details our initial efforts to modify the surfaces of these materials in order to improve cellular interaction and biocompatibility, and we examine our current and future work on improving our implantable BMI devices.

Indiana University-Purdue University Indianapolis (IUPUI) / This thesis describes a novel method to reversibly and safely block nerve conduction using a low frequency alternating current (LFAC) waveform at 1 Hz applied through a bipolar extrafascicular electrode. This work follows up on observations made on excised mammalian peripheral nerves and earthworm nerve cords. An in-situ electrophysiology setup was used to assess the LFAC waveform on propagating action potentials (APs) within the cervical vagus nerve in anaesthetized Sprague-Dawley rats (n = 12). Two sets of bipolar cuff or hook electrodes were applied unilaterally to the cervical vagus nerve, which was crushed rostral to the electrodes to exclude reflex effects on the animal. Pulse stimulation was applied to the rostral electrode, while the LFAC conditioning waveform was applied to the caudal electrode. The efferent volley, if unblocked, elicits acute bradycardia and hypotension. The degree of block of the vagal stimulation induced bradycardia was used as a biomarker. Block was assessed by the ability to reduce the bradycardic drive by monitoring the heart rate (HR) and blood pressure (BP) during LFAC alone, LFAC with vagal stimulation, and vagal stimulation alone. LFAC applied via a hook electrode (n = 7) achieved 86.6 +/- 11% block at current levels 95 +/- 38 uAp (current to peak). When applied via a cuff electrode (n = 5) 85.3 +/- 4.60% block was achieved using current levels of 110+/-65 uAp. Furthermore, LFAC was explored on larger vagal afferent fibers in larger human sized nerve bundles projecting to effects mediated by a reflex. The effectiveness of LFAC was assessed in an in-situ electrophysiological setup on the left cervical vagus in anaesthetized domestic swine (n = 5). Two bipolar cuff electrodes were applied unilaterally to the cervical vagus nerve, which was crushed caudal to the electrodes to eliminate cardiac effects. A tripolar extrafascicular cuff electrode was placed most rostral on the nerve for recording of propagating APs induced by electrical stimulation and blocked via the LFAC waveform. Standard pulse stimulation was applied to the left cervical vagus to induce the Hering-Breuer reflex. If unblocked, the activation of the Hering-Breuer reflex would cause breathing to slow down and potentially cease. Block was quantified by the ability to reduce the effect of the Hering-Breuer reflex by monitoring the breathing rate during LFAC alone, LFAC and vagal stimulation, and vagal stimulation alone. LFAC achieved 87.2 +/- 8.8% (n = 5) block at current levels of 0.8 +/- 0.3 mAp. Compound nerve action potentials (CNAP) were monitored directly. They show changes in nerve activity during LFAC, which manifests itself as the slowing and amplitude reduction of components of the CNAPs. Since the waveform is balanced, all forward reactions are reversed, leading to a blocking method that is similar in nature to DC block without the potential issues of toxic byproduct production. These results suggest that LFAC can achieve a high degree of nerve block in both small and large nerve bundles, resulting in the change in behavior of a biomarker, in-vivo in the mammalian nervous system at low amplitudes of electrical stimulation that are within the water window of the electrode.

This thesis describes a novel method to reversibly and safely block nerve conduction using a low frequency alternating current (LFAC) waveform at 1 Hz applied through a bipolar extrafascicular electrode. This work follows up on observations made on excised mammalian peripheral nerves and earthworm nerve cords. An<i> in-situ</i> electrophysiology setup was used to assess the LFAC<br>waveform on propagating action potentials (APs) within the cervical vagus nerve in anaesthetized Sprague-Dawley rats (n = 12). Two sets of bipolar cuff or hook electrodes were applied unilaterally to the cervical vagus nerve, which was crushed rostral to the electrodes to exclude reflex effects<br>on the animal. Pulse stimulation was applied to the rostral electrode, while the LFAC conditioning waveform was applied to the caudal electrode. The efferent volley, if unblocked, elicits acute bradycardia and hypotension. The degree of block of the vagal stimulation induced bradycardia<br>was used as a biomarker. Block was assessed by the ability to reduce the bradycardic drive by monitoring the heart rate (HR) and blood pressure (BP) during LFAC alone, LFAC with vagal stimulation, and vagal stimulation alone. LFAC applied via a hook electrode (n = 7) achieved 86.6 +/- 11% block at current levels 95 +/- 38 uAp (current to peak). When applied via a cuff electrode (n = 5) 85.3 +/- 4.60% block was achieved using current levels of 110 +/- 65 uAp. Furthermore, LFAC was explored on larger vagal afferent fibers in larger human sized nerve bundles projecting to effects mediated by a reflex. The effectiveness of LFAC was assessed in an <i>in-situ</i> electrophysiological setup on the left cervical vagus in anaesthetized domestic swine (n = 5). Two bipolar cuff electrodes were applied unilaterally to the cervical vagus nerve, which was crushed caudal to the electrodes to eliminate cardiac effects. A tripolar extrafascicular cuff electrode was placed most rostral on the nerve for recording of propagating APs induced by<br>electrical stimulation and blocked via the LFAC waveform.<br>Standard pulse stimulation was applied to the left cervical vagus to induce the Hering-Breuer reflex. If unblocked, the activation of the Hering-Breuer reflex would cause breathing to slow down and potentially cease. Block was quantified by the ability to reduce the effect of the Hering-Breuer<br>reflex by monitoring the breathing rate during LFAC alone, LFAC and vagal stimulation, and vagal stimulation alone. LFAC achieved 87.2 +/- 8.8% (n = 5) block at current levels of 0.8 +/- 0.3 mAp. Compound nerve action potentials (CNAP) were monitored directly. They show changes<br>in nerve activity during LFAC, which manifests itself as the slowing and amplitude reduction of components of the CNAPs. Since the waveform is balanced, all forward reactions are reversed, leading to a blocking method that is similar in nature to DC block without the potential issues of<br>toxic byproduct production. These results suggest that LFAC can achieve a high degree of nerve block in both small and large nerve bundles, resulting in the change in behavior of a biomarker, <i>in-vivo </i>in the mammalian nervous system at low amplitudes of electrical stimulation that are within the water window of the electrode.<br>