Contents

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 Protein–Labeled 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 Deflector-Based 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. Structure–Function 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 C–Based 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 Hemodynamic–Based 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

  “The most important feature of the manual is the protocol provided, and sometimes variations on the protocol. These are clearly written...and most chapters include trouble-shooting hints, which are most helpful....We expect this manual to be highly useful for both students and researchers.”
      —The Quarterly Review of Biology