Imaging in Neuroscience A Laboratory Manual

As imaging technologies have revolutionized research in many areas of biology and medicine, neuroscientists have often pioneered the use of these new visualization techniques. This volume is an essential guide to discovering and implementing these techniques in the neuroscience lab.

Preface to the Book Series
Preface

Section 1: Molecular Tools for Imaging
1. Tracking Receptors Using Individual Fluorescent and Nonfluorescent Nanolabels
Laurent Cognet, Brahim Lounis, and Daniel Choquet
2. Imaging Single Receptors with Quantum Dots
Sabine Lévi, Maxime Dahan, and Antoine Triller
3. Synapto-pHluorins: Genetically Encoded Reporters of Synaptic Transmission
Gero Miesenböck
4. Spatially Resolved Flash Photolysis via Chemical Two-Photon Uncaging
Diana L. Pettit and George J. Augustine
5. Engineering Light-Regulated Ion Channels
Doris L. Fortin, Timothy W. Dunn, and Richard H. Kramer
6. Microbial Opsins: A Family of Single-Component Tools for Optical Control of Neural Activity
Ofer Yizhar, Lief Fenno, Feng Zhang, Peter Hegemann, and Karl Deisseroth
7. Measuring Membrane Voltage with Fluorescent Proteins
Jordan Patti and Ehud Y. Isacoff
8. Imaging Neuronal Activity with Genetically Encoded Calcium Indicators
Lin Tian, S. Andrew Hires, and Loren L. Looger
9. Imaging Synaptic Inhibition with a Genetically Encoded Chloride Indicator
Ken Berglund, Thomas Kuner, Guoping Feng, and George J. Augustine
10. Recombinant Fluorescent Rabies Virus Vectors for Tracing Neurons and Synaptic Connections
Nadin Hagendorf and Karl-Klaus Conzelmann
11. Generating and Imaging Multicolor Brainbow Mice
Tamily A. Weissman, Joshua R. Sanes, Jeff W. Lichtman, and Jean Livet
12. The Use of BAC Transgenic Mice to Label Genetically Defined Cell Populations and the GENSAT Database of Engineered Mouse Strains
Eric F. Schmidt, Laura Kus, Shiaoching Gong, and Nathaniel Heintz

SECTION 2: Axons and Nerve Terminals
13. Presynaptic Calcium Measurements Using Bulk Loading of Acetoxymethyl Indicators
Stephan D. Brenowitz and Wade G. Regehr
14. Imaging Presynaptic Calcium Transients Using Dextran-Conjugated Indicators
Stephan D. Brenowitz and Wade G. Regehr
15. Confocal Spot Detection of Presynaptic Ca2+ Domains
David DiGregorio
16. Ca2+ Uncaging in Nerve Terminals
Olexiy Kochubey and Ralf Schneggenburger
17. Multiple Light Scattering Changes Associated with Secretion from Peptidergic Nerve Terminals
Brian M. Salzberg, Martin Muschol, Paul Kosterin, and Ana Lia Obaid
18. Imaging Synaptic Vesicle Recycling Using FM Dyes
Peer Hoopmann, Silvio O. Rizzoli, and William J. Betz
19. Imaging Exocytosis with Total Internal Reflection Fluorescence Microscopy
Christina Joselevitch, David Zenisek, and David Perrais
20. Interferometric Detection of Action Potentials
Arthur LaPorta and David Kleinfeld
21. Imaging Sodium in Axons and Dendrites
William Ross, Ilya Fleidervish, and Nechama Lasser-Ross
22. Generation and Screening of Mice with Transgenic Neuronal Labeling Controlled by Thy1 Regulatory Elements
Petar Marinković, Leanne Godinho, and Thomas Misgeld

SECTION 3: Spines and Dendrites
23. Correlated Light and Electron Microscopy of Green Fluorescent ProteinLabeled Dendrites and Axons
Graham W. Knott
24. Stimulated Emission Depletion (STED) Imaging of Dendritic Spines
Katrin I. Willig and U. Valentin Nägerl
25. Two-Photon Uncaging Microscopy
Masanori Matsuzaki and Haruo Kasai
26. Acousto-Optical DeflectorBased Patterned Ultraviolet Uncaging of Neurotransmitter for the Study of Neuronal Integration
Eugene F. Civillico, Shy Shoham, Daniel H. O'Connor, Dmitry V. Sarkisov, and Samuel S.-H. Wang
27. Two-Photon Calcium Imaging of Dentritic Spines
Roberto Araya, Jesse H. Goldberg, and Rafael Yuste
28. Imaging Calcium Waves and Sparks in Central Neurons
William N. Ross and Satoshi Manita
29. Dendritic Voltage Imaging
Knut Holthoff, Marco Canepari, Kaspar Vogt, Arthur Konnerth, and Dejan Zecevic
30. Two-Photon Sodium Imaging in Dendritic Spines
Christine R. Rose
31. Transcranial Two-Photon Imaging of the Living Mouse Brain
Jaime Grutzendler, Guang Yang, Feng Pan, Christopher N. Parkhurst, and Wen-Biao Gan
32. Imaging Neocortical Neurons through a Chronic Cranial Window
Anthony Holtmaat, Vincenzo de Paola, Linda Wilbrecht, Josh T. Trachtenberg, Karel Svoboda, and Carlos Portera-Cailliau

SECTION 4: Neurons and Circuits In Vitro
33. Maintaining Live Cells and Tissue Slices in the Imaging Setup
Michael E. Dailey, Glen S. Marrs, and Dana Kurpius
34. Calcium Imaging in Neuronal Endoplasmic Reticulum
Natasha Solovyova and Alexei Verkhratsky
35. Dye Loading with Whole-Cell Recordings
Hartmut Schmidt and Jens Eilers
36. A Single-Compartment Model of Calcium Dynamics in Nerve Terminals and Dendrites
Fritjof Helmchen and David W. Tank
37. Imaging Action Potentials with Calcium Indicators
Rafael Yuste, Jason MacLean, Joshua Vogelstein, and Liam Paninski
38. StructureFunction Analysis of Genetically Defined Neuronal Populations
Alexander Groh and Patrik Krieger
39. Infrared-Guided Neurotransmitter Uncaging on Dendrites
Hans-Ulrich Dodt, Matthias Eder, Anja Schierloh, and Walter Zieglgänsberger
40. Uncaging Calcium in Neurons
Kerry R. Delaney and Vahid Shahrezaei
41. An Optical Fiber-Based Uncaging System
Karl Kandler, Tuan Nguyen, Jihyun Noh, and Richard S. Givens
42. Multiphoton Stimulation of Neurons and Spines
Hajime Hirase, Volodymyr Nikolenko, and Rafael Yuste
43. Circuit Mapping by Ultraviolet Uncaging of Glutamate
Gordon M.G. Shepherd
44. Two-Photon Mapping of Neural Circuits
Volodymyr Nikolenko, Elodie Fino, and Rafael Yuste
45. All-Optical In Situ Histology of Brain Tissue with Femtosecond Laser Pulses
Philbert S. Tsai, Pablo Blinder, Jeffrey A. Squier, and David Kleinfeld
46. Ballistic Delivery of Dyes for Structural and Functional Studies of the Nervous System
Wen-Biao Gan, Jaime Grutzendler, Rachel O. Wong, and Jeff W. Lichtman

SECTION 5: Neurons and Circuits In Vivo
47. Two-Photon Targeted Patching and Electroporation In Vivo
Michael Häusser and Troy W. Margrie
48. Imaging with Voltage-Sensitive Dyes: Spike Signals, Population Signals, and Retrograde Transport
Bradley Baker, Xin Gao, Brian S. Wolff, Lei Jin, Lawrence B. Cohen, Chun X. Bleau, and J.-y. Wu
49. In Vivo Two-Photon Calcium Imaging Using Multicell Bolus Loading of Fluorescent Indicators
Nathalie L. Rochefort, Christine M. Grienberger, and Arthur Konnerth
50. In Vivo Local Dye Electroporation for Ca2+ Imaging and Neuronal-Circuit Tracing
Shin Nagayama, Max L. Fletcher, Wenhui Xiong, Xiaohua Lu, Shaoqun Zeng, and Wei R. Chen
51. In Vivo Two-Photon Calcium Imaging in the Visual System
Kenichi Ohki and R. Clay Reid
52. Three-Dimensional Imaging of Neuronal Network Activity
Björn M. Kampa, Werner Göbel, and Fritjof Helmchen
53. High-Speed Two-Photon Calcium Imaging of Neuronal Population Activity Using Acousto-Optic Deflectors
Benjamin F. Grewe and Fritjof Helmchen
54. Calcium Imaging in the Drosophila Olfactory System with a Genetic Indicator
Cory M. Root, Allan M. Wong, Jorge Flores, and Jing W. Wang
55. Calcium Imaging in the Intact Olfactory System of Zebrafish and Mouse
Rainer W. Friedrich
56. Calcium Imaging in Populations of Olfactory Neurons by Planar Illumination Microscopy
Timothy E. Holy
57. Functional Neuron-Specific Expression of Genetically Encoded Fluorescent Calcium Indicator Proteins in Living Mice
Matthias Heindorf and Mazahir T. Hasan
58. Chronic Calcium Imaging of Neurons in the Visual Cortex Using a Troponin CBased Indicator
Alexandre Ferrão Santos and Mark Hübener
59. Two-Photon Chloride Imaging Using MQAE In Vitro and In Vivo
Yury Kovalchuk and Olga Garaschuk
60. Intrinsic Optical Imaging of Functional Map Development in Mammalian Visual Cortex
Tobias Bonhoeffer and Mark Hübener

SECTION 6: Glia
61. Imaging Astrocytic Calcium and Vacuole-Like Vesicles
Jian Kang
62. Monitoring Exocytosis in Astrocytes with Total Internal Reflection Fluorescence Microscopy
Paola Bezzi and Andrea Volterra
63. In Vivo Labeling of Cortical Astrocytes with Sulforhodamine 101
Axel Nimmerjahn and Fritjof Helmchen
64. In Vivo Imaging of Structural and Functional Properties of Astrocytes
Takahiro Takano, Daniel Christensen, and Maiken Nedergaard
65. Imaging Calcium Waves in Cerebellar Bergmann Glia
Michael Beierlein
66. In Vivo Calcium Imaging of Cerebellar Astrocytes with Synthetic and Genetic Indicators
Bernd Kuhn, Tycho M. Hoogland, and Samuel S.-H. Wang
67. Two-Photon Imaging of Neurons and Glia in the Spinal Cord In Vivo
Heinz Steffens, Fabien Nadrigny, and Frank Kirchhoff
68. Imaging Microglia in Brain Slices and Slice Cultures
Michael E. Dailey, Ukpong Eyo, Leah Fuller, John Hass, and Dana Kurpius
69. Two-Photon Imaging of Astrocytic and Neuronal Excitation in Cerebellar Cortex of Awake Mobile Mice
Axel Nimmerjahn and Mark J. Schnitzer

SECTION 7: Brain Dynamics and Behavior
70. Automated Imaging and Analysis of Behavior in Caenorhabditis elegans
Eviatar Yemini, Rex A. Kerr, and William R. Schafer
71. In Vivo Dendritic Calcium Imaging in the Fly Visual System
Alexander Borst, Winfried Denk, and Jürgen Haag
72. Imaging Neuronal Activity and Motor Behavior in Zebrafish
Germán Sumbre and Mu-Ming Poo
73. Confocal Calcium Imaging of Neuronal Activity in Larval Zebrafish
Joseph R. Fetcho
74. Voltage-Sensitive Dye Imaging of Neocortical Activity
Amiram Grinvald, David B. Omer, Dahlia Sharon, Ivo Vanzetta, and Rina Hildesheim
75. Voltage-Sensitive Dye Imaging of Cortical Spatiotemporal Dynamics in Awake Behaving Mice
Carl C.H. Petersen
76. Two-Photon Imaging of Neural Activity in Awake Mobile Mice
Daniel Dombeck and David Tank
77. Imaging Neuronal Population Activity in Awake and Anesthetized Rodents
David S. Greenberg, Damian J. Wallace, and Jason N.D. Kerr
78. Miniaturization of Two-Photon Microscopy for Imaging in Freely Moving Animals
Fritjof Helmchen, Winfried Denk, and Jason N.D. Kerr
79. Optogenetics: Opsins and Optical Interfaces in Neuroscience
Antoine R. Adamantidis, Feng Zhang, Luis de Lecea, and Karl Deisseroth
80. Optogenetics in Freely Moving Mammals: Dopamine and Reward
Feng Zhang, Hsing-Chen Tsai, Raag D. Airan, Garret D. Stuber, Antoine R. Adamantidis, Luis de Lecea, Antonello Bonci, and Karl Deisseroth
81. In Vivo Calcium Recordings and Channelrhodopsin-2 Activation through an Optical Fiber
Helmuth Adelsberger, Christine Grienberger, Albrecht Stroh, and Arthur Konnerth
82. Fiber-Optic Calcium Monitoring of Dendritic Activity In Vivo
Masanori Murayama and Matthew Larkum
83. Imaging the Neocortex Functional Architecture Using Multiple Intrinsic Signals: Implications for HemodynamicBased Functional Imaging
Amiram Grinvald, Dahlia Sharon, David Omer, and Ivo Vanzetta

SECTION 8: Brain Pathology
84. Two-Photon Imaging of Blood Flow in Cortex
Jonathan D. Driscoll, Andy Y. Shih, Patrick J. Drew, Gert Cauwenberghs, and David Kleinfeld
85. Optically Induced Occlusion of Single Blood Vessels in Neocortex
Andy Y. Shih, Nozomi Nishimura, John Nguyen, Beth Friedman, Patrick D. Lyden, Chris B. Schaffer, and David Kleinfeld
86. Two-Photon Imaging of Neuronal Structural Plasticity in Mice during and after Ischemia
Timothy H. Murphy
87. Two-Photon Imaging of Microglia in the Mouse Cortex In Vivo
Axel Nimmerjahn
88. Two-Photon Imaging of Immune Cells in Neural Tissue
Raluca Niesner, Volker Siffrin, and Frauke Zipp
89. Two-Photon Imaging of Structure and Function in Alzheimer's Disease
Michal Arbel-Ornath, Monica Garcia-Alloza, Kishore V. Kuchibhotla, Tara Spires-Jones, and Brian J. Bacskai
90. Two-Photon Imaging of Neural Networks in a Mouse Model of Alzheimer's Disease
Gerhard Eichhoff and Olga Garaschuk
91. Imaging Tumors in the Brain
Kelley S. Madden, Martha L. Zettel, Ania K. Majewska, and Edward B. Brown
92. Fluorescent Molecular Tomography of Brain Tumors in Mice
Nikolaos C. Deliolanis and Vasilis Ntziachristos

SECTION 9: APPENDICES
1. Electromagnetic Spectrum
Marilu Hoeppner
2. Fluorescence Microscopy Filters and Excitation/Emission Spectra
3. Safe Operation of a Fluorescence Microscope
George McNamara
4. Microscope Objective Lenses
5. Glossary of Imaging Terms
6. Cautions
Index