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Imaging in Neuroscience and Development : A Laboratory Manual
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.
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