Handbook of Neurophotonics

Francesco S. Pavone is full professor at the University of Florence in the Department of Physics and at the European Laboratory for Non-Linear Spectroscopy (LENS), and group leader at the Biophotonics Laboratories. He obtained a PhD in optics in 1993 and spent two years as postdoctoral fellow at the Ecole Normale Superieure with the group of Claude Cohen Tannoudjy (Nobel Prize, 1997). His research group is involved in developing new microscopy techniques for high-resolution and high-sensitivity imaging, and laser manipulation purposes. These techniques have been applied in singlemolecule biophysics, single-cell imaging, and optical manipulation. He is also engaged in tissue imaging research, for which nonlinear optical techniques have been applied to skin and neural tissue imaging. He is the author of more than 100 peer-reviewed journal articles, has delivered more than 60 invited talks. He coordinates various European projects and has organized international congresses. He is director of the international PhD program at LENS. He is on the editorial board of the journal Neurophotonics and is a principal investigator for the Human Brain Project, an EU Flagship initiative. Shy Shoham is an Associate Professor at the Department of Biomedical Engineering in the Technion - Israel Institute of Technology. He was born in Rehovot, Israel, and holds a B.Sc. degree in Physics from Tel Aviv University and a Ph.D. in Bioengineering from the University of Utah. After completing his Ph.D., he was a Lewis-Thomas postdoctoral fellow at the department of Molecular Biology, Princeton University. In 2005 he joined the Technion's faculty of Biomedical Engineering, where he established the Neural Interface Engineering laboratory. His lab focuses on the development of implant-less retinal prostheses aimed at restoring vision loss from outer-retinal degenerative diseases, and on developing advanced technologies for acoustic neuromodulation, microscopic neuro-imaging and for bioengineering brain-like tissues. He is a recipient of a starting grant from the European Research Council, and of the Daniel Shiran and Juludan awards for engineering advances in bio-medicine, and is a member of the editorial boards of Journal of Neural Engineering, and of Translational Vision Science & Technology.

Contents

Preface, ix

Contributors, xi

Part I Function and Structural Neurophotonic Imaging

Chapter 1 ◾ Miniaturized Optical Neuroimaging Systems 3

Hang Yu, Janaka Senarathna, Betty M. Tyler, Nitis h V. Thakor, and Arvi nd P. Pathak

Chapter 2 ◾ Functional Imaging with Light-Sheet Microscopy 21

Raghav K. Chhetri and Philipp J. Keller

Chapter 3 ◾ Two-Photon Microscopy in the Mammalian Brain 55

Hod Dana and Shy Shoham

Chapter 4 ◾ Light Field Microscopy for In Vivo Ca2+ Imaging 81

Tobi as Nöbauer and Alip asha Vaziri

Chapter 5 ◾ Genetically Encoded Activity Indicators 113

Chenchen Song and Thomas Knöpfel

Chapter 6 ◾ Functional Optoacoustic Imaging 129

Daniel Razansky

Chapter 7 ◾ Imaging Deep in the Brain with Wavefront Engineering 147

Roarke Horstmeyer, Maximi llian Hoffmann, Haowen Ruan, Benjami n Judkewitz,

and Changhuei Yang

Chapter 8 ◾ Nanoscopic Imaging to Understand Synaptic Function 173

Daniel Choquet and Anne-Sophie Hafner

Chapter 9 ◾ Chemical Clearing of Brains 191

Klaus Becker, Chris tian Hahn, Nina Jährling, Marko Pende,

Inna Sabdyusheva-Litsc hauer, Saiedeh Saghafi, Martina Wanis , and Hans-Ulric h Dodt

Chapter 10 ◾ Advanced Light-Sheet Microscopy to Explore Brain

Structure on an Organ-Wide Scale 221

Ludovic o Silvestri and Francesc o S. Pavone

Part II Neurophotonic Control and Perturbation

Chapter 11 ◾ Optogenetic Modulation of Neural Circuits 235

Mathias Mahn, Oded Klavi r, and Ofer Yizhar

Chapter 12 ◾ Molecular Photoswitches for Synthetic Optogenetics 271

Shai Berlin and Ehud Y. Isacoff

Chapter 13 ◾ Applications of Nanoparticles for Optical Modulation of

Neuronal Behavior 293

Chiara Pavi olo, Shaun Gietman, Daniela Duc, Sim on E. Moulton, and

Paul R. Stoddart

Chapter 14 ◾ Optical Stimulation of Neural Circuits in Freely Moving

Animals 317

Leore R. Heim and Eran Stark

Chapter 15 ◾ Holographic Optical Neural Interfaces (HONIs) 333

Shani Rosen, Shir Paluch, and Shy Shoham

Chapter 16 ◾ Multi-Photon Nanosurgery 353

Anna Letizia Allegra Masc aro and Francesc o Saverio Pavone

Part III Clinical and Human Neurophotonics

Chapter 17 ◾ High Resolution Diffuse Optical Tomography of the

Human Brain 369

Muriah D. Wheelock and Adam T. Eggebrecht

Chapter 18 ◾ Human Brain Imaging by Optical Coherence Tomography 399

Caroline Magnain, Jean C. Augustinack, Davi d Boas, Bruce Fisc hl, Taner Akkin,

Ender Konukoglu, and Hui Wang

Chapter 19 ◾ Acousto-Optic Cerebral Monitoring 439

Mic hal Balberg and Revi tal Pery-Shechter

Chapter 20 ◾ Neurophotonic Vision Restoration 459

Adi Schejter Bar-Noam and Shy Shoham

Chapter 21 ◾ Optical Cochlear Implants 473

C.-P. Ric hter, Y. Xu, X. Tan, N. Xia, and N. Suematsu

Chapter 22 ◾ Label-Free Fluorescence Interrogation of Brain Tumors 503

Brad A. Hartl, Shami ra Sridharan, and Laura Marcu

Chapter 23 ◾ Higher Harmonic Generation Imaging for Neuropathology 527

Nikolay Kuzmi n, Sander Idema, Eleonora Aronic a, Philip C. de Witt Hamer,

Pieter Wess eling, and Marie Louis e Groot

INDEX, 545