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SHORT COURSE 2: Functional, Structural, and Molecular Imaging, and Big Data Analysis Organized by Ed Boyden, PhD, and Kwanghun Chung,NEW PhD COVER TK Short Course 2 Functional, Structural, and Molecular Imaging, and Big Data Analysis Organized by Ed Boyden, PhD, and Kwanghun Chung, PhD Please cite articles using the model: [AUTHOR’S LAST NAME, AUTHOR’S FIRST & MIDDLE INITIALS] (2018) [CHAPTER TITLE] Functional, Structural, and Molecular Imaging, and Big Data Analysis. (Boyden E, Chung K, eds) pp. [xx-xx]. Washington, DC : Society for Neuroscience. All articles and their graphics are under the copyright of their respective authors. Cover graphics and design © 2018 Society for Neuroscience. SHORT COURSE 2 Functional, Structural, and Molecular Imaging, and Big Data Analysis Organized by Ed Boyden, PhD, and Kwanghun Chung, PhD Friday, November 2, 2018 8 a.m.–6 p.m. Location: San Diego Convention Center • Room: 6CF TIME TOPIC SPEAKER 7:30–8 a.m. CHECK-IN Ed Boyden, PhD • Massachusetts Institute of Technology 8–8:10 a.m. Opening Remarks Kwanghun Chung, PhD • Massachusetts Institute of Technology Advanced Optical Methods for Multi-Scale Optical Probing and 8:10–8:50 a.m. Valentina Emiliani, PhD • Paris Descartes University Manipulation of Neural Circuits 8:50–9:30 a.m. Optical Imaging of Neural Ensemble Dynamics in Behaving Animals Mark Schnitzer, PhD • Stanford University 9:30–10:10 a.m. High-Resolution and High-Speed In Vivo Imaging of the Brain Na Ji, PhD • University of California, Berkeley 10:10–10:30 a.m. BREAK High-Speed Volumetric Microscopy and Wide-Field Optical 10:30–11:10 a.m. Elizabeth Hillman, PhD • Columbia University Mapping of Whole-Brain Activity Denoising, Compression, Demixing, and Deconvolution of 11:10–11:50 a.m. Liam Paninski, PhD • Columbia University Functional Imaging Data 11:50 a.m.–12:30 p.m. Connectome Coding Joshua Vogelstein, PhD • Johns Hopkins University 12:30–1:30 p.m. LUNCH — ROOM 25 1:30–2:10 p.m. Holistic Molecular Imaging and Rapid Phenotyping of the Brain Kwanghun Chung, PhD • Massachusetts Institute of Technology 2:10–2:50 p.m. Toward Integrative Optical Interrogation of the Brain Ed Boyden, PhD • Massachusetts Institute of Technology 2:50–3 p.m. Summary and Introduction of Breakout Sessions Ed Boyden, PhD, and Kwanghun Chung, PhD 3–3:15 p.m. BREAK AFTERNOON BREAKOUT SESSIONS • PARTICIPANTS SELECT FIRST DISCUSSION GROUPS AT 3:15 P.M. TIME BREAKOUT SESSIONS SPEAKERS ROOM Kwanghun Chung, PhD, Joshua Vogelstein, 3:15–4:30 p.m. Group 1: 24B Collection and Analysis of Structural and Molecular Data PhD, and Ed Boyden, PhD Elizabeth Hillman, PhD, Liam Paninski, Group 2: 24A Collection and Analysis of Neural and Signaling Dynamics PhD, Ed Boyden, PhD Valentina Emiliani, PhD, Mark Schnitzer, Group 3: 23A Microscopy Technology PhD, and Na Ji, PhD 4:30–4:45 p.m. BREAK AFTERNOON BREAKOUT SESSIONS • PARTICIPANTS SELECT SECOND DISCUSSION GROUPS AT 4:45 P.M. Kwanghun Chung, PhD, and Joshua 4:45–6 p.m. Group 1: 24B Collection and Analysis of Structural and Molecular Data Vogelstein, PhD Elizabeth Hillman, PhD, Liam Paninski, Group 2: 24A Collection and Analysis of Neural and Signaling Dynamics PhD, Ed Boyden, PhD Valentina Emiliani, PhD, Mark Schnitzer, Group 3: 23A Microscopy Technology PhD, and Na Ji, PhD over Table of Contents Agenda .........................................................................3 Introduction .....................................................................5 Expansion Microscopy: Development and Neuroscience Applications Emmanouil D. Karagiannis, PhD, and Edward S. Boyden, PhD ........................7 Holistic Molecular Imaging and Rapid Phenotyping of the Brain Kwanghun Chung, PhD .................................................17 Holographic Illumination for Two-Photon Optogenetics Dimitrii Tanese, PhD, and Valentina Emiliani, PhD ....................................23 High-Speed Recording of Neural Spikes in Awake Mice and Flies with a Fluorescent Voltage Sensor Yiyang Gong, PhD, Cheng Huang, PhD, Jin Zhong Li, DVM, Benjamin F. Grewe, PhD, Yanping Zhang, MD, Stephan Eismann, MS, and Mark J. Schnitzer, PhD ....................41 High-Resolution and High-Speed In Vivo Imaging of the Brain Cristina Rodriguez, PhD, and Na Ji, PhD ............................................52 What Is Connectome Coding? Eric W. Bridgeford, BS, Daniel Sussman, PhD, Vince Lyzinski, PhD, Yichen Qin, PhD, Youngser Park, PhD, Brian Caffo, PhD, Carey E. Priebe, PhD, and Joshua T. Vogelstein, PhD ...................................62 Analysis of Functional Imaging Data at Single-Cellular Resolution Eftychios A. Pnevmatikakis, PhD, and Liam Paninski, PhD ..............................75 High-Speed Volumetric Microscopy and Wide-Field Optical Mapping of Whole-Brain Activity Elizabeth M. C. Hillman, PhD ....................................................86 Introduction We find ourselves in an era of great innovation in neuroscience that is yielding a constant stream of new molecular reporters of neural activity, novel microscope architectures, and new strategies for acquiring and analyzing large physiological, molecular, and anatomical datasets. How can these technologies be deployed in the service of making the highest-impact discoveries in both basic and applied neuroscience? With the help of a number of excellent faculty at the cutting edge of the invention and application of novel tools, we have designed this course to explore the basic principles underlying how such technologies work as well as practical considerations for adopting and integrating these methods into neuroscience. Our experts will cover a broad range of topics in their lectures, including the imaging of neural ensemble dynamics, multiscale optogenetic manipulation of circuits, high-resolution in vivo imaging, and multiscale structural and molecular phenotyping techniques. We will also review methods for extracting information from the large-scale functional, structural, and molecular imaging datasets that result. During the breakout sessions, our experts and teaching assistants (TAs) will discuss each technology in depth and go over detailed protocols, with the goal of enabling attendees to intelligently select the best technological path and rapidly adopt the technologies. We will also discuss examples that show how these technologies can be integrated into a streamlined experiment to study a given scientific question in the fundamental or translational realm. Our experts (listed in alphabetical order) include pioneers of optical methods for studying the brain, who will discuss the following topics: Ed Boyden will discuss how integrating optical tools for reading neural activity, writing neural activity, and mapping the connectivity of the brain might be unified to enable new kinds of structure–function linkage in neuroscience experimentation. Kwanghun Chung will discuss a series of technologies including CLARITY, SWITCH, MAP, stochastic electrotransport, SHIELD, and eFLASH (unpublished) that enable integrated multiscale imaging and molecular phenotyping of both animal tissues and human clinical samples. Valentina Emiliani will discuss the powerful intersection of three-dimensional (3D) parallel holographic illumination for the single-cell- targeted optogenetic control of neurons, and the development of novel opsins with high-performance characteristics for mediating such control. She will explore the optical principles underlying such microscopy systems, as well as practical considerations governing the most suitable manipulation approaches for given problems. Elizabeth Hillman will discuss swept confocally aligned planar excitation (SCAPE) microscopy (a form of light-sheet microscopy that uses a single stationary objective lens to perform high-speed 3D microscopy of a diversity of neuroscientifically relevant systems) and wide- field optical mapping (WFOM) for imaging neural activity and brain hemodynamics across the whole dorsal cortex in awake, behaving mice. Na Ji will present wavefront shaping techniques that enable the imaging of neural circuits with higher resolution, greater depth, and faster speed than before, including examples that enable synapse-level spatial resolution imaging throughout the entire depth of the cortex, and a volumetric microscopy strategy with a novel video rate (~30 Hz). Liam Paninski will discuss methods for extracting information from single-cell resolution calcium and voltage imaging data, including denoising, demixing, and deconvolving approaches to extract estimates of voltage and spiking activity from video data. Mark Schnitzer will present recent advances from his lab that are allowing the measurement of neural codes across large scales and optical readout of neural voltage oscillations. These advances include miniature microscopes, new forms of two-photon microscopy, and novel fiber optic methods for transmembrane electrical measurements performed optically (TEMPO). In the context of neural coding, Josh Vogelstein will discuss “connectome coding”—the characterization of the relationship between past environments and stimuli (even past experiences of ancestors encoded in the genome) and current neural connectivity. Introduction 6 In summary, our speakers will cover the dynamical readout, dynamical control, and the anatomical NOTES and molecular mapping of the brain, as well as the computational analysis of the datasets thus acquired. We anticipate that students will emerge from the course with not just new technical insights, but also the ability to think across technologies and scales
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