A SYSTEMATIC CHARACTERIZATION OF FIBER PHOTOMETRY FOR OPTICAL INTERROGATION OF NEURAL CIRCUIT DYNAMICS By MAY MANSY A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2019 © 2019 May Mansy To my mother, for empowering me To my father, for supporting me To my daughter, for bringing out the best in me To my husband, for always being by my side To my family, who fill me with pride ACKNOWLEDGMENTS The true treasures of life are in the people, who stand by us through thick and thin, and who never cease to believe in us. I have been tremendously blessed to have the most wonderful people in my life, who have contributed directly and indirectly to the completion of this dissertation. I would like to start by giving huge thanks to my academic advisor, Dr. Karim Oweiss, for granting me the opportunity to pursue a Ph.D. in his lab and for his unwavering efforts to support and guide me over the past six years. I’m immensely grateful for all the valuable pieces of advice and teachable lessons that improved my critical and analytical thinking as well as the guidance Dr. Oweiss endowed me throughout the years of my research. Additionally, I would like to thank Dr. Oweiss for always giving me the opportunity to attend various scientific research conferences and for encouraging me to engage in activities that nurtured my personal and professional development. Sincere gratitude also goes to the members of my committee, Dr. Kevin Otto, Dr. Thomas Foster, Dr. Minghzou Ding and Dr. Brandi Ormerod for their valuable feedback, advice and continuous support. Furthermore, I would like to express my genuine appreciation to the graduate advisor of my Ph.D. program, Dr. Cherie Stabler, who has always been there for me and who never ceased to believe in me. I would like to thank Dr. Stabler for all the eye-opening, enlightening and very up-lifting discussions we had. Next, I would like to express my thanks to Dr. Brandi Ormerod not just for always empowering me and for the many valuable pieces of advice, but also for being the first to help me discover my teaching talent. A token of appreciation also goes to Dr. Marwan Abdellah for the opportunity to collaborate with the Blue Brain Project at EPFL, which made a major part of this dissertation possible. 4 I will now turn to the amazing members of the Oweiss lab. It was a real pleasure to work and interact with each one of the current and former members of the Oweiss lab. Brandey Andersen, who was more than just a lab colleague and friend, and who always helped me find my way. Islam Badreldin who never fell short of providing technical advice for any technical challenge. Dr. Ali Ibrahim who taught me perseverance. Ben Goolsby who always reminded me to calm down and who always helped review my writing tasks. Joseph Canzano for the fruitful scientific chats and brainstorming sessions that always helped me critique my thinking and identify shortcomings of my research. Dr. Narayan Subramanian, for teaching me about immuno-histochemical techniques, helping me course-correct when I lost track and get up when I hit rock-bottom. Rebeca Castro for helping me collect my data during the last phase of my PhD, Naoki Sawahashi for helping resolve some challenging technical issue I faced towards the end of my degree, and all the other wonderful members who shaped my experience at the Oweiss lab: Hong-Jae Kim, Phillip Navarro, Mehrdad Hashemi, Joseph Succar, Michael Brodowski, Abduraham Siddiqi, Kyle Sheller. I would like to express my sincere gratitude to mentor, Dr. Yifei Dai, for offering me the opportunity of an internship at Exactech, for being a constant source of support and empowerment and for the abundant guidance and advice during my job-hunting phase. I would also like to acknowledge Dr. Erin Patrick for being a great teaching partner and mentor. I’d like to thank Dr. Patrick for teaching me about teaching, for her valuable feedback on my performance and for providing the ultimate guide on how to pursue a career in teaching. Furthermore, I would like to express my deepest appreciation to Professor William Mcelroy for teaching me things beyond “Engineering Leadership”, providing precious tips and advice, and for always checking on me. 5 I would also like to express my appreciation to all the administrative staff members who helped me with filing paperwork, placing orders for my research supplies, installing new equipment, delivering mail and maintaining my workstation: Kathryn Thompson, Jason Kawaja, Marcy Lee, Ray McClure, Quashawn Durant, Kimberly Depue, Michelle Evern, Myra Edwards, Amanda Redinger, Victor De La Cruz and Kaitlynn Gravely. I would like to thank my husband, partner and best friend Islam Badreldin, for being my safe place, for being by my side and for always taking care of the things that I get on my nerves. I deeply appreciate his support and back up during my downtimes and during my times of stress. I would like to thank my daughter, Noor, for teaching me how to value and enjoy every minute of every day and for bringing out the best in me with the simplest of words. Her endless questions and curiosity about the world make me learn new things and acquire new ways to teach her about them. The final token of sincere gratitude goes to my siblings and my loving parents for their endless love, care, and support. I can’t thank them enough for instigating high moral standards and discipline in me, for allowing me to be who I am, and for always having my back. 6 TABLE OF CONTENTS page ACKNOWLEDGMENTS ........................................................................................................... 4 LIST OF TABLES .................................................................................................................... 10 LIST OF FIGURES .................................................................................................................. 11 LIST OF ABBREVIATIONS.................................................................................................... 13 ABSTRACT ............................................................................................................................. 14 CHAPTER 1 INTRODUCTION ............................................................................................................. 16 Centuries of Choreographed Synergy ................................................................................. 16 Dissertation Overview ........................................................................................................ 24 2 BACKGROUND AND MOTIVATION ............................................................................. 25 Let there be Light ............................................................................................................... 25 … and there was Light ....................................................................................................... 25 The Origin of Light ..................................................................................................... 26 The Light Duality ........................................................................................................ 26 Basics of Illumination ........................................................................................................ 29 Parameters of Light ..................................................................................................... 31 Radiometric Quantities ................................................................................................ 32 Basics of Optics .......................................................................................................... 33 Propagation of Light .......................................................................................................... 37 Propagation in an Optic Fiber ...................................................................................... 37 Propagation in Neural Tissue ....................................................................................... 38 Fundamentals of Fluorescence............................................................................................ 41 Optical Interrogation of Neural Circuity ............................................................................. 46 Optical Actuators ........................................................................................................ 47 Optical Sensors ........................................................................................................... 49 Comparison of Fluorescent Imaging Techniques ................................................................ 52 Two-Photon Imaging ................................................................................................... 52 Single-Photon Micro-endoscopy.................................................................................. 54 Single-Photon Fiber Photometry .................................................................................. 54 Motivation and Research Aims ........................................................................................... 58 Significance ................................................................................................................ 60 Research Aims ............................................................................................................ 60 3 SPATIAL CHARACTERIZATION OF THE DETECTION VOLUME ............................