Imaging in Neuroscience and Development. a Lab. Manual

Description

As imaging studies have continued to expand in scope and sophistication, this new edition of the highly successful and well–received Imaging Neurons: A Laboratory Manual has expanded to include development, with over twenty new chapters on such topics as MRI microscopy, imaging early developmental events, and labeling single neurons. Chapters on FRET, FCS/ICS, FRAP, hyperresolution microscopy, single molecule imaging, imaging with quantum dots, and imaging gene expression are included. With over forty full chapters, the manual also includes over forty sections of protocols for imaging techniques.

Contents

SECTION 1: BASIC IMAGING

• Chapter 1: Maintaining Live Cells and Tissue Slices in the Imaging Setup
  M.E. Dailey, G.S. Marrs, and D. Kurpius
• Chapter 2: Video Microscopy, Video Cameras, and Image Enhancement
  M. Oshiro, L.A. Moomaw, and E. Keller
• Chapter 3: The Application of Scientific–grade CCD Cameras to Biological Imaging
  M. Christenson
• Chapter 4: A Practical Guide: Differential Interference Contrast Imaging of Living Cells
  N.E. Ziv and J. Schiller
• Chapter 5: A Practical Guide: Infrared Video Microscopy
  H.–U. Dodt, K. Becker, and W. Zieglgänsberger
• Chapter 6: Confocal Microscopy: Principles and Practice
  A. Fine
• Chapter 7: Principles of Multiphoton–excitation Fluorescence Microscopy
  W. Denk
• Chapter 8: Two–Photon Microscopy for 4D Imaging of Living Neurons
  S.M. Potter
• Chapter 9: A Practical Guide: Building a Two–Photon Laser–scanning Microscope
  J. Mertz
• Chapter 10: A Practical Guide: How to Build a Two–Photon Microscope Using a Confocal Scan Head
  V. Nikolenko and R. Yuste

SECTION 2: IMAGING DEVELOPMENT

• Chapter 11: In Vivo Electroporation during Embryogenesis
  C.E. Krull, R. McLennan, S. O’Connell, Y. Chen, and P.A. Trainor
• Chapter 12: A Practical Guide: In Vivo Electroporation of Neurons
  S.R. Price
• Chapter 13: A Practical Guide: Single–Neuron Labeling Using Genetic Methods
  L. Luo
• Chapter 14: A Practical Guide: Ballistic Delivery of Dyes for Structural and Functional Studies of the Nervous System
  W.–B. Gan, J. Grutzendler, R.O. Wong, and J.W. Lichtman
• Chapter 15: A Practical Guide: Imaging Embryonic Development in Caenorhabditis elegans
  W.A. Mohler and A.B. Isaacson
• Chapter 16: Visualizing Morphogenesis in Frog Embryos
  L.A. Davidson and J.B. Wallingford
• Chapter 17: In Vivo Imaging of Synaptogenesis in the Embryonic Zebrafish
  J.D. Jontes and S.J Smith
• Chapter 18: A Practical Guide: In Ovo Imaging of Avian Embryogenesis
  P.M. Kulesa and S.E. Fraser
• Chapter 19: A Practical Guide: Time–lapse Imaging of the Formation of the Chick Peripheral Nervous System
  J.C. Kasemeier, F. Lefcort, S.E. Fraser, and P.M. Kulesa
• Chapter 20: Imaging Mouse Embryonic Development
  E.A.V. Jones, A.–K. Hadjantonakis, and M.E. Dickinson
• Chapter 21: Imaging the Developing Retina
  C. Lohmann, J.S. Mumm, J. Morgan, L. Godinho, E. Schroeter, R. Stacy, W.T. Wong, D. Oakley, and R.O.L. Wong
• Chapter 22: A Practical Guide: Long–term Two–Photon Transcranial Imaging of Synaptic Structures in the Living Brain
  J. Grutzendler and W.–B. Gan
• Chapter 23: In Vivo Time–lapse Imaging of Neuronal Development
  E.S. Ruthazer, K. Haas, A. Javaherian, K. Jensen, W.C. Sin, and H.T. Cline
• Chapter 24: Optical Projection Tomography: Imaging 3D Organ Shapes and Gene Expression Patterns in Whole Vertebrate Embryos
  J. Sharpe
• Chapter 25: Imaging the Development of the Neuromuscular Junction
  M.K. Walsh and J.W. Lichtman
• Chapter 26: A Practical Guide: Imaging Synaptogenesis by Measuring Accumulation of Synaptic Proteins
  C. Dean and P. Scheiffele
• Chapter 27: A Practical Guide: Imaging Retinotectal Synaptic Connectivity
  S. Cohen–Corey
• Chapter 28: A Practical Guide: Intrinsic Optical Imaging of Functional Map Development in Mammalian Visual Cortex
  T. Bonhoeffer and M. Hübener

SECTION 3: CALCIUM IMAGING

• Chapter 29: How Calcium Indicators Work
  S.R. Adams
• Chapter 30: Some Quantitative Aspects of Calcium Fluorimetry
  E. Neher
• Chapter 31: Calibration of Fluorescent Calcium Indicators
  F. Helmchen
• Chapter 32: A Single–Compartment Model of Calcium Dynamics in Nerve Terminals and Dendrites
  F. Helmchen and D.W. Tank
• Chapter 33: A Practical Guide: Dye Loading with Patch Pipettes
  J. Eilers and A. Konnerth
• Chapter 34: A Practical Guide: Calcium Imaging of the Retina
  C. Lohmann, J. Demas, J.L. Morgan, and R.O.L. Wong
• Chapter 35: Calcium Imaging of Identified Astrocytes in Hippocampal Slices
  J. Kang, G. Arcuino, and M. Nedergaard
• Chapter 36: Imaging Microscopic Calcium Signals in Excitable Cells
  M.B. Cannell, A.J.C. McMorland, and C. Soeller
• Chapter 37: Monitoring Presynaptic Calcium Dynamics with Membrane–permeant Indicators
  W.G. Regehr
• Chapter 38: A Practical Guide: Two–Photon Calcium Imaging of Spines and Dendrites
  J.H. Goldberg and R. Yuste
• Chapter 39: A Practical Guide: Measurement of Free Ca2+ Concentration in the Lumen of Neuronal Endoplasmic Reticulum
  N. Solovyova and A. Verkhratsky
• Chapter 40: Imaging Intracellular Calcium–concentration Microdomains at a Chemical Synapse
  R. Llinás and M. Sugimori
• Chapter 41: Monitoring Intramitochondrial Calcium with Rhod–2
  M. Hoth and R.S. Lewis
• Chapter 42: Generation of Controlled Calcium Oscillations in Nonexcitable Cells
  R.E. Dolmetsch and R.S. Lewis
• Chapter 43: A Practical Guide: High–Speed Imaging of Calcium Waves in Neurons in Brain Slices
  W.N. Ross, T. Nakamura, S. Watanabe, M.E. Larkum, and N. Lasser–Ross
• Chapter 44: A Practical Guide: Imaging Action Potentials with Calcium Indicators
  J.N. MacLean and R. Yuste
• Chapter 45: Imaging Calcium Transients in Developing Xenopus Spinal Neurons
  N.C. Spitzer, L.N. Borodinsky, and C.M. Root

SECTION 4: PHOTOACTIVATION

• Chapter 46: Basics of Photoactivation
  G.C.R. Ellis–Davies
• Chapter 47: Two–Photon Uncaging Microscopy
  H. Kasai, M. Matsuzaki, and G.C.R. Ellis–Davies
• Chapter 48: A Practical Guide: Chemical Two–Photon Uncaging
  D.L. Pettit and G.J. Augustine
• Chapter 49: A Practical Guide: Uncaging with Visible Light, Inorganic Caged Compounds
  L. Zayat, L. Baraldo, and R. Etchenique
• Chapter 50: A Practical Guide: Infrared–guided Laser Stimulation of Neurons in Brain Slices
  H.–U. Dodt, M. Eder, A. Schierloh, and W. Zieglgänsberger
• Chapter 51: Uncaging Calcium in Neurons
  K.R. Delaney and V. Shahrezaei
• Chapter 52: A Practical Guide: Building a Simple Uncaging System
  K. Kandler, G. Kim, and B. Schmidt
• Chapter 53: Ca2+ Uncaging in Nerve Terminals
  R. Schneggenburger
• Chapter 54: Direct Multiphoton Stimulation of Neurons and Spines
  H. Hirase, V. Nikolenko, and R. Yuste

SECTION 5: ADVANCED IMAGING AND SPECIAL APPLICATIONS

• Chapter 55: A Practical Guide: Imaging Microglia in Live Brain Slices and Slice Cultures
  D. Kurpius and M.E. Dailey
• Chapter 56: Single and Multiphoton Fluorescence Recovery after Photobleaching
  E. Brown, A. Majewska, and R.K. Jain
• Chapter 57: All–Optical, In Situ Histology of Neuronal Tissue with Ultrashort Laser Pulses
  P.S. Tsai, B. Friedman, C.B. Schaffer, J.A. Squier, and D. Kleinfeld
• Chapter 58: Imaging with Voltage–sensitive Dyes: Spike Signals, Population Signals, and Retrograde Transport
  E.K. Kosmidis, L.B. Cohen, C.X. Falk, J.–Y. Wu, and B.J. Baker
• Chapter 59: Dendritic Voltage Imaging
  M. Djurisic, S. Antic, and D. Zecevic
• Chapter 60: Second Harmonic Imaging of Membrane Potential
  A.C. Millard, A Lewis, and L.M. Loew
• Chapter 61: Imaging Synaptic Vesicle Dynamics with Styryl Dyes
  S.O. Rizzoli, U. Becherer, J. Angleson, and W.J. Betz
• Chapter 62: A Practical Guide: Imaging FM Dyes in Brain Slices
  A.R. Kay
• Chapter 63: A Practical Guide: Imaging Zinc in Brain Slices
  A.R. Kay
• Chapter 64: A Practical Guide: Imaging Exocytosis with Total Internal Reflection Microscopy
  D. Zenisek and D. Perrais
• Chapter 65: A Practical Guide: Measuring Light–scattering Changes Associated with Secretion from Nerve Terminals
  B.M. Salzberg, M. Muschol, and A.L. Obaid
• Chapter 66: Imaging with Quantum Dots
  J.K. Jaiswal, E.R. Goldman, H. Mattoussi, and S.M. Simon
• Chapter 67: Imaging Single Receptors with Quantum Dots
  S. Lévi, M. Dahan, and A. Triller
• Chapter 68: A Practical Guide: Tracking Receptors by Imaging Single Molecules
  L. Cognet, B. Lounis, and D. Choquet
• Chapter 69: A Practical Guide: Imaging Sodium in Dendrites
  W. Ross, J.C. Callaway, and N. Lasser–Ross
• Chapter 70: A Practical Guide: Two–Photon Sodium Imaging in Dendritic Spines
  C.R. Rose
• Chapter 71: Two–Photon Imaging of Chloride
  O. Garaschuk and A. Konnerth
• Chapter 72: A Practical Guide: Interferometric Detection of Action Potentials
  A. LaPorta and D. Kleinfeld
• Chapter 73: A Practical Guide: Intrinsic Optical Signal Imaging in Brain Slices
  B.A. MacVicar and S.J. Mulligan

SECTION 6: GENETICALLY ENGINEERED FLUORESCENT PROBES

• Chapter 74: Indicators Based on Fluorescence Resonance Energy Transfer
  R.Y. Tsien
• Chapter 75: Cellular Imaging of Bioluminescence
  J.D. Plautz and S.A. Kay
• Chapter 76: Introduction of Green Fluorescent Protein into Hippocampal Neurons through Viral Infection
  R. Malinow, Y. Hayashi, M. Maletic–Savatic, S.H. Zaman, J.–C. Poncer, S.–H. Shi, J.A. Esteban, P. Osten, and K. Seidenman
• Chapter 77: Green Fluorescent Proteins for Measuring Voltage
  M.S. Siegel and E.Y. Isacoff
• Chapter 78: Genetic Probes for Calcium Dynamics
  A. Miyawaki, T. Nagai, and H. Mizuno
• Chapter 79: A Practical Guide: Targeted Recombinant Aequorins
  T. Pozzan and R. Rizzuto
• Chapter 80: A Practical Guide: Imaging Synaptic Inhibition with Clomeleon, a Genetically Encoded Chloride Indicator
  K. Berglund, R.L. Dunbar, P. Lee, G. Feng, and G.J. Augustine
• Chapter 81: A Practical Guide: Synapto–pHluorins—Genetically Encoded Reporters of Synaptic Transmission
  G. Miesenböck
• Chapter 82: Imaging Gene Expression in Live Cells and Tissues
  R.E. Dolmetsch, N. Gomez–Ospina, E. Green, and E.A. Nigh
• Chapter 83: Imaging Olfactory Activity in Drosophila CNS with a Calcium–sensitive Green Fluorescent Protein
  A.M. Wong, J. Flores, and J.W. Wang
• Chapter 84: Tracking Molecules in Intact Zebrafish
  R. Armisen, M.R. Gleason, J.R. Fetcho, and G. Mandel

SECTION 7: IN VIVO IMAGING

• Chapter 85: Long–Term, High–Resolution Imaging of Neurons in the Neocortex In Vivo
  A.J.G.D. Holtmaat, L. Wilbrecht, A. Karpova, C. Portera–Cailliau, B. Burbach, J.T. Trachtenberg, and K. Svoboda
• Chapter 86: A Two–Photon Fiberscope for Imaging in Freely Moving Animals
  F. Helmchen and W. Denk
• Chapter 87: A Practical Guide: In Vivo Two–Photon Calcium Imaging Using Multicell Bolus Loading
  O. Garaschuk and A. Konnerth
• Chapter 88: A Practical Guide: In Vivo Calcium Imaging in the Fly Visual System
  A. Borst, W. Denk, and J. Haag
• Chapter 89: Intrinsic Signal Imaging in the Neocortex: Implications for Hemodynamic–based Functional Imaging
  A. Grinvald, D. Sharon, H. Slovin, and I. Vanzetta
• Chapter 90: Voltage–sensitive Dye Imaging of Neocortical Activity
  A. Grinvald, D. Sharon, A. Sterkin, H. Slovin, and R. Hildesheim
• Chapter 91: A Practical Guide: Whole–Cell Recording and Voltage–sensitive Dye Imaging In Vivo
  C. Petersen
• Chapter 92: A Practical Guide: In Vivo Imaging of Tumors
  E. Brown, L.L. Munn, D. Fukumura, and R.K. Jain
• Chapter 93: Two–Photon Imaging of Cortical Microcirculation
  D. Kleinfeld and W. Denk
• Chapter 94: Imaging Neuronal Activity with Calcium Indicators in Larval Zebrafish
  J.R. Fetcho

SECTION 8: PRINCIPLES AND INSTRUMENTATION

• Chapter 95: Microscopy and Microscope Optical Systems
  F. Lanni and H.E. Keller
• Chapter 96: Practical Limits to Resolution in Fluorescence Light Microscopy
  E.H.K. Stelzer
• Chapter 97: Lasers for Multiphoton Microscopy
  F.W. Wise
• Chapter 98: Acousto–optic Tunable Filters for Microscopy
  E.S. Wachman
• Chapter 99: A Practical Guide: Arc Lamps and Monochromators for Fluorescence Microscopy
  R. Uhl
• Chapter 100: The Use of Liquid–Crystal Tunable Filters for Fluorescence Imaging
  K.R. Spring
• Chapter 101: Fluorescence Grating Imager Systems for Optical–sectioning Microscopy
  F. Lanni
• Chapter 102: Analysis of Dynamic Optical Imaging Data
  B. Pesaran, A.T. Sornborger, N. Nishimura, D. Kleinfeld, and P.P. Mitra

Appendices

• 1. Electromagnetic Spectrum
• 2. Microscopy: Lenses, Filters, and Emission/Excitation Spectra
• 3. Cautions

Index