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 indeveloping 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.

• ContentsPreface, ixContributors, xiPart I Function and Structural Neurophotonic ImagingChapter 1 ¿ Miniaturized Optical Neuroimaging Systems 3Hang Yu, Janaka Senarathna, Betty M. Tyler, Nitis h V. Thakor, and Arvi nd P. PathakChapter 2 ¿ Functional Imaging with Light-Sheet Microscopy 21Raghav K. Chhetri and Philipp J. KellerChapter 3 ¿ Two-Photon Microscopy in the Mammalian Brain 55Hod Dana and Shy ShohamChapter 4 ¿ Light Field Microscopy for In Vivo Ca2+ Imaging 81Tobi as Nöbauer and Alip asha VaziriChapter 5 ¿ Genetically Encoded Activity Indicators 113Chenchen Song and Thomas KnöpfelChapter 6 ¿ Functional Optoacoustic Imaging 129Daniel RazanskyChapter 7 ¿ Imaging Deep in the Brain with Wavefront Engineering 147Roarke Horstmeyer, Maximi llian Hoffmann, Haowen Ruan, Benjami n Judkewitz,and Changhuei YangChapter 8 ¿ Nanoscopic Imaging to Understand Synaptic Function 173Daniel Choquet and Anne-Sophie HafnerChapter 9 ¿ Chemical Clearing of Brains 191Klaus Becker, Chris tian Hahn, Nina Jährling, Marko Pende,Inna Sabdyusheva-Litsc hauer, Saiedeh Saghafi, Martina Wanis , and Hans-Ulric h DodtChapter 10 ¿ Advanced Light-Sheet Microscopy to Explore BrainStructure on an Organ-Wide Scale 221Ludovic o Silvestri and Francesc o S. PavonePart II Neurophotonic Control and PerturbationChapter 11 ¿ Optogenetic Modulation of Neural Circuits 235Mathias Mahn, Oded Klavi r, and Ofer YizharChapter 12 ¿ Molecular Photoswitches for Synthetic Optogenetics 271Shai Berlin and Ehud Y. IsacoffChapter 13 ¿ Applications of Nanoparticles for Optical Modulation ofNeuronal Behavior 293Chiara Pavi olo, Shaun Gietman, Daniela Duc, Sim on E. Moulton, andPaul R. StoddartChapter 14 ¿ Optical Stimulation of Neural Circuits in Freely MovingAnimals 317Leore R. Heim and Eran StarkChapter 15 ¿ Holographic Optical Neural Interfaces (HONIs) 333Shani Rosen, Shir Paluch, and Shy ShohamChapter 16 ¿ Multi-Photon Nanosurgery 353Anna Letizia Allegra Masc aro and Francesc o Saverio PavonePart III Clinical and Human NeurophotonicsChapter 17 ¿ High Resolution Diffuse Optical Tomography of theHuman Brain 369Muriah D. Wheelock and Adam T. EggebrechtChapter 18 ¿ Human Brain Imaging by Optical Coherence Tomography 399Caroline Magnain, Jean C. Augustinack, Davi d Boas, Bruce Fisc hl, Taner Akkin,Ender Konukoglu, and Hui WangChapter 19 ¿ Acousto-Optic Cerebral Monitoring 439Mic hal Balberg and Revi tal Pery-ShechterChapter 20 ¿ Neurophotonic Vision Restoration 459Adi Schejter Bar-Noam and Shy ShohamChapter 21 ¿ Optical Cochlear Implants 473C.-P. Ric hter, Y. Xu, X. Tan, N. Xia, and N. SuematsuChapter 22 ¿ Label-Free Fluorescence Interrogation of Brain Tumors 503Brad A. Hartl, Shami ra Sridharan, and Laura MarcuChapter 23 ¿ Higher Harmonic Generation Imaging for Neuropathology 527Nikolay Kuzmi n, Sander Idema, Eleonora Aronic a, Philip C. de Witt Hamer,Pieter Wess eling, and Marie Louis e GrootINDEX, 545