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Contents Imaging in Neuroscience & Development: A Laboratory Manual Dedication, Foreword, Preface, Acknowledgments, Abbreviations, Section 1: Basic Imaging 1 Maintaining Live Cells and Tissue Slices in the Imaging Setup M.E. Dailey, G.S. Marrs, and D. Kurpius 2 Video Microscopy, Video Cameras, and Image Enhancement M. Oshiro, L.A. Moomaw, amd E. Keller 3 The Application of Scientific-grade CCD Cameras to Biological Imaging M. Christenson 4 A practical guide to : Differential interference Contrast (DIC) Imaging of Living Cells N.E. Ziv and J. Schiller 5 A practical guide to : Infrared Videomicroscopy H.-U. Dodt 6 Confocal Microscopy: Principles and Practice A. Fine 7 Principles of Multiphoton-excitation Fluorescence Microscopy W. Denk 8 Two-photon Microscopy for 4D Imaging of Living Neurons S.M. Potter 9 A practical guide to Building a Two-photon Laser Scanning Microscope (TPLSM) J. Mertz 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 11 In vivo Electroporation during Embryogenesis C.E. Krull, R. McLennan, S. O'Connell, Y. Chen, and P.A. Trainor 12 A practical guide to: In Vivo Electroporation of Neurons S.R. Price 13 Single Neuron Labeling using Genetic Methods L. Luo 14 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 15 Imaging Embryonic Development in Caenorhabditis elegans W.A. Mohler and A.B. Isaacson 16 Visualizing Morphogenesis in Frog Embryos L.A. Davidson and J.B. Wallingford 17 In vivo Imaging of Synaptogenesis in the Embryonic Zebrafish J.D. Jontes and S.J. Smith 18 A practical guide to : In ovo imaging of avian embryogenesis P.M. Kulesa and S.E. Fraser 19 A practical guide to: Time-lapse Imaging of the Formation of the Chick Peripheral Nervous System J.C. Kasemeier, F. Lefcort, S.E. Fraser, and P.M. Kulesa 20 Imaging Mouse Embryonic Development E.A.V. Jones, A.-K. Hadjantonakis, and M.E. Dickinson 21 Live Imaging of the Developing Retina C. Lohmann, J. Mumm, J. Morgan, L. Godinho, E. Schroeter, R. Stacy, W.T. Wong, D. Oakley, and R.O.L. Wong 22 A practical guide to: Long-term Two-photon Transcranial Imaging of Synaptic Structures in the Living Brain J. Grutzendler and W.-B. Gan 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 24 Optical Projection Tomography: Imaging 3D Organ Shapes and Gene Expression Patterns in Whole Vertebrate Embryos J. Sharpe 25 Imaging the Development of Neuromuscular Junction M.K. Walsh and J.W. Lichtman 26 A practical guide to: Imaging Synaptogenesis by Measuring Accumulation of Synaptic Proteins C. Dean and P. Scheiffele 27 A practical guide to: Imaging Retinotectal Synaptic Connectivity S. Cohen-Corey 28 A practical guide to: Intrinsic Optical Imaging of Functional Map Development in Mammalian Visual Cortex T. Bonhoeffer and M. Hƒbener Section 3: Calcium Imaging 29 How Calcium Indicators Work S.R. Adams 30 Some Quantitative Aspects of Calcium Fluorimetry E. Neher 31 Calibration of Fluorescent Calcium Indicators F. Helmchen 32 A Single-compartment Model of Calcium Dynamics in Nerve Terminals and Dendrites F. Helmchen and D.W. Tank 33 A practical guide to : Dye loading with Patch Pipettes J. Eilers and A. Konnerth 34 A practical guide to : Calcium Imaging of the Retina C. Lohmann, J. Demas, J.L. Morgan, and R.O.L. Wong 35 Calcium Imaging of Identified Astrocytes in Hippocampal Slices J. Kang, G. Arcuino, and M. Nedergaard 36 A practical guide to: Imaging Microscopic Calcium Signals in Excitable Cells M.B. Cannell, A.J.C. McMorland, and C. Soeller 37 A practical guide to : Monitoring Presynaptic Calcium Dynamics with Membrane-permeant Indicators W.G. Regehr 38 A practical guide to : Two-Photon Calcium Imaging of Spines and Dendrites J.H. Goldberg and R. Yuste 39 A practical guide to : Measurements of Free Ca2+ Concentration in the Lumen of Neuronal Endoplasmic Reticulum N. Solovyova and A. Verkhratsky 40 A practical guide to: Imaging Intracellular Calcium-concentration Microdomains at a Chemical Synapse R. Llinçs and M. Sugimori 41 A practical guide to: Monitoring Intramitochondrial Calcium with Rhod-2 M. Hoth and R.S. Lewis 42 A practical guide to: Generation of Controlled Calcium Oscillations in Nonexcitable Cells R.E. Dolmetsch and R.S. Lewis 43 A practical guide to: High-Speed Imaging of Calcium Waves in Neurons in Brain W.N. Ross, T. Nakamura, S. Watanabe, M.E. Larkum, and N. Lasser-Ross 44 A practical guide to: Imaging Action Potentials with Calcium Indicators J.N. MacLean and R. Yuste 45 Imaging Calcium Transients in Developing Xenopus Spinal Neurons N.C. Spitzer, L.N. Borodinsky, and C.M. Root Section 4: Photoactivation 46 Basics of Photoactivation G.C.R. Ellis-Davies 47 A practical guide to: Two-photon Uncaging Microscopy H. Kasai, M. Matsuzaki, and G.C.R. Ellis-Davies 48 A practical guide to : Chemical Two-photon Uncaging D.L. Pettit and G.J. Augustine 49 A practical guide to: Uncaging with Visible Light ( Inorganic Caged Compounds L. Zayat, L. Beraldo, and R. Etchenique 50 A practical guide to : Infrared-guided Laser Stimulation of Neurons in Brain Slices H.-U. Dodt, M. Eder, A. Schierloh, and W. Zieglgènsberger 51 Uncaging Calcium in Neurons KR. Delaney and V. Shahrezaei 52 A practical guide to : Building a Simple Uncaging System K. Kandler, G. Kim, and B. Schmidt 53 A practical guide to : Ca2+ Uncaging in Nerve Terminals R. Schneggenburger 54 A practical guide to: Direct Multi-photon Stimulation of Neurons and Spines H. Hirase, V. Nikolenko, and R. Yuste Section 5: Advanced Imaging and Special Applications 55 A practical guide to : Imaging Microglia in Live Brain Slices and Slice Cultures D. Kurpius and M.E. Dailey 56 Single and Multiphoton Fluorescence Recovery after Photobleaching (FRAP) E. Brown, A. Majewska, and R.K. Jain 57 A practical guide to : 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 58 Imaging with Voltage-sensitive Dyes: Spike Signals, Population Signals, and Retrograde Transport E. Kosmidis, L.B. Cohen, C.X. Falk, J.-Y. Wu, and B. Baker 59 A practical guide to : Dendritic Voltage Imaging M. Djurisic, S. Antic, and D. Zecevic 60 Second Harmonic Imaging of Membrane Potential A.C. Millard, A Lewis and LM. Loew 61 Imaging Synaptic Vesicle Dynamics with Styryl Dyes S.O. Rizzoli, U. Becherer, J. Angleson, and W.J. Betz 62 A practical guide to : Imaging FM Dyes in Brain Slices A.R. Kay 63 A practical guide to: Imaging Zinc in Brain Slices A.R. Kay 64 Imaging Exocytosis with Total Internal Reflection Microscopy D. Zenisek and D. Perrais 65 A practical guide to : Measuring the Multiple Light Scattering Changes Associated with Secretion from Peptidergic Nerve Terminals B.M. Salzberg, M. Muschol, and A.L. Obaid 66 Imaging with Quantum Dots J.K. Jaiswal, E.R. Goldman, H. Mattoussi, and S.M. Simon 67 A practical guide to: Imaging Single Receptors with Quantum Dots S. LÄvi, M. Dahan, and A. Triller 68 A practical guide to : Tracking Receptors by Optical Imaging of Single Molecules L. Cognet, B. Lounis, and D. Choquet 69 A practical guide to : Imaging Sodium in Dendrites W. Ross, J.C. Callaway, and N. Lasser-Ross 70 A practical guide to : Two-photon Sodium Imaging in Dendritic Spines C.R. Rose 71 A practical guide to : Two-photon Imaging of Chloride O. Garaschuk and A. Konnerth 72 A practical guide to: Interferometric Detection of Action Potentials A. LaPorta and D. Kleinfeld 73 A practical guide to: Intrinsic Optical Signal Imaging in Brain Slices B.A. MacVicar and S.J. Mulligan Section 6: Genetically Engineered Fluorescent Probes 74 Indicators Based on Fluorescence Resonance Energy Transfer R.Y. Tsien 75 Cellular Imaging of Bioluminescence J.D. Plautz and S.A. Kay 76 Introduction of Green Fluorescent Protein into Hippocampal Neuron 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 77 A practical guide to : Grene Fluorescent Proteins for Measuring Voltage M.S. Siegel and E.Y. Isacoff 78 Genetic Probes for Calcium Dynamics A. Miyawaki, T. Nagai, and H. Mizuno 79 A practical guide to: Targeted Recombinant Aequorins T. Pozzan and R. Ruzzuto 80 A practical guide to : Imaging Synaptic Inhibition with Clomeleon, A Genetically Encoded Chloride Indicator K. Berglund, R.L. Dunbar, P. Lee, G. Feng, and G.J. Augustine 81 A practical guide to : Synapto-pHluorins: Genetically Encoded Reporters of Synaptic Transmission G. MiesenbÜck 82 Imaging Gene Expression in Live Cells and Tissues R.E. Dolmetsch, N. Gomez, E. Green, and E.A. Nigh 83 A practical guide to: Imaging Olfactory Activity in Drosophila CNS with a Calcium-sensitive Green Fluorescent Protein A.M. Wong, J. Flores, J.W. Wang 84 A practical guide to: Tracking Molecules in Intact Zebrafish R. Armisen, M.R. Gleason, J.R. Fetcho, and G. Mandel Section 7: In vivo Imaging 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 86 A practical guide to: A 2-Photon Fiberscope for Imaging in Freely Moving Animals F. Helmchen and W. Denk 87 A practical guide to: In vivo Two-photon Calcium Imaging using Multi-cell Bolus Loading O. Garaschuk and A. Konnerth 88 A practical guide to: In Vivo Calcium Imaging in the Fly Visual System A. Borst, W. Denk, and J. Haag 89 Intrinsic Signal Imaging in the Neocortex: Implications for Hemodynamic Based Functional Imaging A. Grinvald, D. Sharon, H. Slovin, and I. Vanzetta 90 A practical guide to: Voltage-sensitive-dye Imaging in the Neocortical Activity A. Grinvald, D. Sharon, A. Sterkin, H. Slovin, and R. Hildesheim 91 A practical guide to: Whole-cell Recording and Voltage-sensitive Dye Imaging In vivo C. Petersen 92 A practical guide to: In Vivo Imaging of Tumors E. Brown, L.L. Munn, D. Fukumura, and R.K. Jain 93 A practical guide to: Two-photon Imaging of Cortical Microcirculaton D. Kleinfeld and W. Denk 94 A practical guide to: Imaging Neuronal Activity with Calcium Indicators in Larval Zebrafish J.R. Fetcho Section 8: Principles and Instrumentation 95 Microscopy and Microscope Optical Systems F. Lanni and H.E. Keller 96 Practical Limits to Resolution in Fluorescence Light Microscopy E.H.K. Stelzer 97 Lasers for Multiphoton Microscopy F.W. Wise 98 Acousto-optic Tunable Filters for Microscopy E.S. Wachman 99 A practical guide to: Arc Lamps and Monochromators for Fluorescence Microscopy R. Uhl 100 The Use of Liquid-crystal Tunable Filters for Fluorescence Imaging K.R. Spring 101 Fluorescence Grating Imager Systems for Optical-sectioning Microscopy F. Lanni 102 Analysis of Dynamic Optical Imaging Data B. Pesaran, A.T. Stornborger, N. Nishimura, D. Kleinfeld, and P.P. Mitra APPENDICES Glossary Electromagnetic Spectrum Microscopy: Lenses, Filters, and Emission/Excitation Spectra Cautions Index
Library of Congress Subject Headings for this publication:
Neurons -- Laboratory manuals.
Microscopy -- Laboratory manuals.
Developmental neurophysiology -- Laboratory manuals.