Preface to the Book Series ................................... xiii
1 Introduction ................................................. 1
James Sharpe and Rachel O. Wong
SECTION 1. MODEL SYSTEMS
2 Live Imaging of Caenorhabditis elegans Embryogenesis ........ 11
Zhirong Bao and John I. Murray
3 Live Imaging of Drosophila Development ...................... 23
Jessica R.K. Seifert and Ruth Lehmann
4 Live Imaging of Zebrafish Development ....................... 49
Leanne Godinho
5 Live Imaging of Cells and Tissues in Xenopus Embryos ........ 69
John B. Wallingford
6 Live Imaging of Avian Embryos ............................... 85
Paul M. Kulesa and Scott E. Fraser
7 Live Imaging of Mouse Embryos .............................. 101
Monica D. Garcia, Ryan S. Udan, Anna-Katerina
Hadjantonakis, and Mary E. Dickinson
SECTION 2. CELLS
Labeling Cells for Live Cell Imaging
8 Electroporation of Chick and Mouse Embryos ................. 119
Catherine E. Krull, Fengyun Su, Mary E. Swartz, Johann
Eberhart, Rebecca McLennan, Yaxiong Chen, and Paul
A. Trainor
9 Single-Cell Electroporation in Xenopus ..................... 143
Xue Feng Liu and Kurt Haas
10 Single-Neuron Labeling Using Genetic Methods ............... 157
J. Sebastian Espinosa, Joy S. Tea, and Liqun Luo
11 Ballistic Labeling of Developing Retinal Neurons ........... 177
Josh L. Morgan and Daniel Kerschensteiner
12 Multicolor Brainbow Imaging in Zebrafish ................... 191
Y. Albert Pan, Jean Livet, Joshua R. Sanes, Jeff W.
Lichtman, and Alexander F. Schier
13 Genetic Labeling of Neurons in Mouse Brain ................. 199
Z. Josh Huang, Hiroki Taniguchi, Miao He, and Sandra
Kuhlman
Cell Fate, Differentiation, and Migration
14 Live Imaging of Neuroblast Lineages within Intact
Larval Brains in Drosophila ................................ 217
Clemens Cabernard and Chris Q. Doe
15 Visualizing Cell Contacts and Cell Polarity in
Caenorhabditis elegans Embryos ............................. 229
Timothy Walston and Jeff Hardin
16 In Vivo Birthdating in Zebrafish ........................... 245
Y. Albert Pan, Sophie J.C. Caron, and Alexander
F. Schier
17 Imaging Retinal Progenitor Lineages in the Developing
Zebrafish Retina ........................................... 253
Patricia Jusuf, William A. Harris, and Lucia Poggi
18 Imaging the Development of the Fish Lateral-Line System .... 271
Kevin Schuster and Alain Chysen
19 Imaging Cell Migration in Chick Explant Cultures ........... 291
Jennifer C. Kasemeier-Kulesa, Frances Lefcort, Scott
E. Fraser, and Paul M. Kulesa
20 Imaging Cell Movements in Egg Cylinder Stage Mouse
Embryos .................................................... 299
Shankar Srinivas
21 Marking Cells for Imaging Analysis of Morphogenetic
Behavior and Cell Fates in Mouse Embryos ................... 311
Nicolas Fossat, David A.F. Loebel, Vanessa Jones,
Poh-Lynn Khoo, Heidi Bildsoe, and Patrick P.L. Tam
22 Visualizing Spatiotemporal Dynamics of Multicellular
Cell-Cycle Progressions .................................... 331
Asako Sakaue-Sawano and Atsushi Miyawaki
23 Time-Lapse Imaging of Fluorescently Labeled Live Cells
in the Embryonic Mammalian Forebrain ....................... 341
Stephen C. Noctor
Imaging Circuit Formation in the Nervous System
24 Imaging Calcium Transients in Developing Xenopus Spinal
Neurons .................................................... 357
Nicholas C. Spitzer, Laura N. Borodinsky and Cory
M. Root
25 Imaging Axon Pathfinding in Xenopus and Zebrafish
In Vivo .................................................... 373
Louis Leung and Christine E. Holt
26 Axons and Dendrites: In Vivo Time-Lapse Imaging of
Neuronal Development in Xenopus ............................ 387
Edward S. Ruthazer, Anne Schohl, Neil Schwartz, Aydin
Tavakoli, Marc Tremblay, and Hollis T. Cline
27 In Vivo Imaging of Synaptogenesis in Zebrafish ............. 405
James D. Jontes and Michelle R. Emond
28 Live Imaging of Developing Retinal Circuits ................ 417
Philip R. Williams, Joshua L. Morgan, Daniel
Kerschensteiner, and Rachel O.L. Wong
29 Imaging the Developing Mammalian Neuromuscular Junction
In Vivo .................................................... 435
Stephen C. Turney Mark K. Walsh, and Jeff W. Lichtman
30 Live Imaging of Developing Hippocampal Neurons in
Culture .................................................... 449
Stefanie Kaech, Chun-Fang Huang, and Gary Banker
31 Imaging of Synapse Formation and Function in Neuronal
Cell Cultures by Quantitative Immunocytochemistry .......... 467
Camin Dean and Peter Scheiffele
32 Simultaneous Imaging of Structural Plasticity and
Calcium Dynamics in Developing Dendrites and Axons ......... 479
Friederike Siegel and Christian Lohmann
33 Simultaneous Patch-Clamping and Calcium Imaging in
Developing Dendrites ....................................... 491
Thomas Kleindienst and Christian Lohmann
34 Imaging Synaptic Protein Dynamics in the Cerebral Cortex
In Vitro and In Vivo ....................................... 499
Robby M. Weimer, Travis C. Hill, Andrew M. Hamilton,
and Karen Zito
35 In Vivo Imaging of Axonal and Dendritic Structures in
Developing Cortex .......................................... 513
Alberto Cruz-Martin and Carlos Portera-Cailliau
SECTION 3. DYNAMIC TISSUES AND ORGANS
36 Quantifying the Bicoid Morphogen Gradient in Living Fly
Embryos .................................................... 523
Alexander H. Morrison, Martin Scheeler, Julien Dubuis,
and Thomas Gregor
37 Quantitative Imaging of Morphogen Gradients in
Drosophila Imaginal Discs .................................. 533
Anna Kicheva, Laurent Holtzer, Ortrud Wartlick, Thomas
Schmidt, and Marcos González-Gaitán
38 Methods to Investigate Molecular Mechanisms and Cellular
Mechanics Responsible for Morphogenesis in Xenopus
laevis Embryos ............................................. 551
Hye Young Kim and Lance A. Davidson
39 Notochord Formation in Zebrafish ........................... 569
Samantha J. England and Richard J. Adams
40 High-Resolution, Multiphoton Time-Lapse Imaging of Early
Chick Embryos .............................................. 581
Octavian Voiculescu and Claudio D. Stern
41 Four-Dimensional Fluorescent Imaging of Embryonic Quail
Development ................................................ 593
Christie A. Canaria and Rusty Lansford
42 Imaging Kidney Development ................................. 605
Frank Costantini, Tomoko Watanabe, Benson Lu, Xuan Chi,
and Shankar Srinivas
43 Practical Considerations for Long-Term Time-Lapse
Imaging of Epithelial Morphogenesis in Three-Dimensional
Organotypic Cultures ....................................... 623
Andrew J. Ewald
44 High-Speed Optical Coherence Tomography Imaging of the
Beating Avian Embryonic Heart .............................. 647
Shi Gu, Michael W. Jenkins, Michiko Watanabe, and Andrew
M. Rollins
45 Imaging Mouse Embryonic Cardiovascular Development ......... 659
Irina V. Larina, Monica D. Garcia, Tegy J. Vadakkan,
Kirill V. Larin, and Mary E. Dickinson
46 Micro-Ultrasound and Its Application to Longitudinal
Studies of Mouse Eye Development and Disease ............... 669
F. Stuart Foster and Allison S. Brown
SECTION 4. WHOLE EMBRYOS: GENE EXPRESSION, PHENOTYPING, AND
DATABASES
47 Quantitative Imaging of Gene Expression in Drosophila
Embryos .................................................... 683
Svetlana Surkona, Ekaterina Myasnikova, Konstantin N.
Kozlov, Andrei Pisarev, John Reinitz, and Maria Samsonova
48 Three-Dimensional Morphology and Gene Expression Mapping
for the Drosophila Blastoderm .............................. 699
David W. Knowles
49 From Confocal Imaging to 3D Model: A Protocol for
Creating 3D Digital Replicas of Ascidian Embryos ........... 711
François B. Robin, Delphine Dauga, Olivier Tassy, Daniel
Sobral, Fabrice Daian, and Patrick Lemaire
50 Preparation of Fixed Xenopus Embryos for Confocal
Imaging .................................................... 729
John B. Wallingford
51 Optical Projection Tomography of Vertebrate Embryo
Development ................................................ 739
Laura Quintana and James Sharpe
52 X-Ray Microtomographic Imaging of Vertebrate Embryos ....... 753
Brian D. Metscher
53 Episcopic Three-Dimensional Imaging of Embryos ............. 765
Timothy J. Mohun and Wolfgang J. Weninger
54 High-Throughput Analysis of Mouse Embryos by Magnetic
Resonance Imaging .......................................... 777
Simon D. Bamforth, Jürgen E. Schneider, and Shoumo
Bhattacharya
55 MRI in Developmental Biology and the Construction of
Developmental Atlases ...................................... 789
Seth W. Ruffins and Russell E. Jacobs
56 Automated Lineage and Expression Profiling in Live
Caenorhabditis elegans Embryos ............................. 799
John Isaac Murray and Zhirong Bao
57 Imaging the Development of Entire Zebrafish and
Drosophila Embryos with Digital Scanned Laser Light-Sheet
Fluorescence Microscopy (DSLM) ............................. 815
Philipp J. Keller, Annette D. Schmidt, Jochen Wittbrodt,
and Ernst H.K. Stelzer
SECTION 5. APPENDICES
1 Electromagnetic Spectrum ................................... 827
Marilu Hoeppner
2 Fluorescence Microscopy Filters and Excitation/Emission
Spectra .................................................... 829
3 Safe Operation of a Fluorescence Microscope ................ 833
George McNamara
4 Microscope Objective Lenses ................................ 835
5 Resources for Live Imaging of Drosophila ................... 837
6 Glossary of Imaging Terms .................................. 845
7 Cautions ................................................... 855
Index ......................................................... 863
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