Date of Award

May 2018

Degree Type


Degree Name

Master of Science



First Advisor

Ramin Pashiae

Committee Members

Chiu T Law, Yongjin Sung


To further understand neural disorders as well as recognize complexities of normal brain functionality continuously drives the development and implementation of new research instruments and techniques. In neuroscience research one difficulty that these instruments face is accessing subcortical regions with minimal invasiveness. While electrode based deep brain stimulation (DBS) has been a primary technique in research it has also become an accepted alleviation method for some neurological diseases such as Parkinson’s, epilepsy, and depression in severe cases. However, there are possible side effects that may arise from the lack of cell targeting in electrical stimulation.

Optogenetics, uses proteins from microbial opsins to make cell populations of interest sensitive to light exposure. These proteins allow us to use light of appropriate wavelengths to manipulate the activity of targeted neurons when successfully expressed. In optogentic practice target cells are also co-expressed with fluorescence bio-markers in order to evaluate the level of light sensitivity in the cells population of interest. Detection and imaging of these fluorescence molecules have motivated the development of new devices however, there is still a limitation on these instruments for deep brain fluorescence imaging including the limitations on invasiveness, resolution, and penetration depth.

This project strives to address the need for the development of a practical and cost-efficient device to find the location of maximum light sensitivity and measure the spatial distribution of fluorescence molecules in deep brain regions. This goal is achieved by proposing a novel optoelectronic design that uses only a relatively thin (200um) penetrating and rotating side-firing fiber to scan the brain tissue and collect data sets. These data sets are processed in a computer to reconstruct images displaying the distribution of fluorescence molecules in a cylindrical volume surrounding the fiber. The main benefits of this design are the simplicity of the hardware and experimental protocols since the procedure is only minimally invasive and image development is performed by computer algorithms and image reconstruction subroutines.