Imaging Marine Life -- Contents -- Preface -- List of Contributors -- Chapter 1 Under the Eye of Neptune: An Historical Perspective of Marine Creature Imagery -- 1.1 Introduction -- 1.2 Ancient Uses of the Oceans -- 1.2.1 Seafarers -- 1.2.2 The Mediterranean Sea: the cradle of marine biology -- 1.2.2.1 Aristotle and Pliny the Elder, the Founding Fathers -- 1.2.2.2 Understanding the Oceans -- 1.3 From Neptune to Animalcules -- 1.3.1 Age of European Discovery and Exploration -- 1.3.2 Voyages of Exploration and finally Science -- 1.3.3 A Glimpse at the Invisible -- 1.4 The Birth of Oceanography (The Nineteenth Century) -- 1.4.1 Drawing the Jellyfish -- 1.4.2 The H.M.S. Challenger Expedition -- 1.4.3 Stations and Institutions -- 1.5 The Twentieth Century: Institutions and moving images -- 1.5.1 New tools - new images: -- 1.5.2 Jean Painleve -- 1.5.3 The Writers and the Explorers -- 1.5.4 The Future -- 1.6 Time Line of Ocean Imagery -- Further Reading -- Basic Texts -- Source Books -- Ships and Expeditions -- Institutions -- Chapter 2 New Solutions in Underwater Imaging and Vision Systems -- 2.1 Introduction -- 2.2 Underwater Optical Image Formation -- 2.3 Illumination Techniques -- 2.3.1 Illumination Sources -- 2.3.2 Selection of the Light Source Position -- 2.3.3 Illuminating Systems -- 2.4 Laser-Based Techniques -- 2.4.1 Laser Range-Gating (LRG) Methods -- 2.4.2 Laser Line Scan (LLS) Methods -- 2.4.3 Scattered Light Rejection Using Modulation/Demodulation Techniques -- 2.5 Underwater Imaging Infrastructures -- 2.6 Image Improvement via Polarization -- 2.6.1 Extended Range Using Polarization -- 2.6.2 Housing -- 2.6.3 Experimental Evaluation -- 2.7 A Vision System for Underwater Applications -- 2.7.1 The Fugu Vision System -- 2.8 Conclusion -- Acknowledgements -- References.

Chapter 3 Holographic Microscopy of Marine Organisms -- 3.1 Introduction -- 3.2 Advantages of Holographic Microscopy -- 3.3 Past Attempts to Image Microplankton -- 3.4 Point Source Digital In-Line Holographic Microscopy -- 3.4.1 Instruments -- 3.4.2 Image Reconstruction -- 3.4.3 Image Examples -- 3.4.4 Resolution -- 3.4.5 Volume Imaging Challenges -- 3.5 Future Outlook -- References -- Chapter 4 Confocal Laser Scanning Microscopy - Detailed Three-Dimensional Morphological Imaging of Marine Organisms -- 4.1 Introduction -- 4.2 Technical and Methodological Aspects of Confocal Laser Scanning Microscopy -- 4.3 Prerequisites for Generating High-Quality Confocal Laser Scanning Micrographs -- 4.4 Using Autofluorescences for Detailed Three-Dimensional Morphological Imaging -- 4.5 Application of Fluorescence Dyes -- 4.6 Surface Topography Analyses -- 4.7 Future Perspectives -- Acknowledgements -- References -- Chapter 5 Optical Projection Tomography -- 5.1 Introduction -- 5.2 What Is Optical Projection Tomography? -- 5.2.1 Assembly of an OPT System -- 5.2.1.1 Detection Unit -- 5.2.1.2 Illumination Units -- 5.2.1.3 Sample Manipulation Unit -- 5.2.2 Illumination Sources -- 5.2.3 System Capabilities and Limitations -- 5.3 Comparison with Other 3D Microscopy Techniques -- 5.3.1 Confocal Microscopy -- 5.3.2 Two-Photon Microscopy -- 5.4 Sample Preparation -- 5.5 Image Processing and Analysis -- 5.6 Marine Biology Applications -- Acknowledgments -- References -- Chapter 6 Electron Microscopy Techniques for Imaging Marine Phytoplankton -- 6.1 Introduction -- 6.2 Collecting and Processing Specimens -- 6.3 Light Microscopy -- 6.4 Sediment Cyst Surveys -- 6.5 Transmission Electron Microscopy -- 6.6 Scanning Electron Microscopy -- Acknowledgements -- References.

Chapter 7 Looking Inside Marine Organisms with Magnetic Resonance and X-ray Imaging -- 7.1 Introduction -- 7.2 Magnetic Resonance Imaging -- 7.2.1 Experimental Setup -- 7.2.2 Hardware Improvements -- 7.2.3 Contrast -- 7.2.4 Applications -- 7.2.4.1 Anatomical MRI -- 7.2.4.2 Functional MRI -- 7.2.4.3 Diffusion Tensor Imaging or Diffusion MRI (DTI) -- 7.2.4.4 MEMRI or Manganese-Enhanced Magnetic Resonance Imaging -- 7.3 X-Ray Microtomography -- 7.3.1 Sources -- 7.3.1.1 Laboratory-Based Setups -- 7.3.1.2 Synchrotron-Based Setups -- 7.3.2 Sample Stage -- 7.3.3 Detector -- 7.3.4 Forward Problem (Contrast Formation) -- 7.3.5 Tomographic Reconstruction -- 7.3.5.1 2D Filtered Back-Projection -- 7.3.5.2 Image Quality and Artifacts -- 7.3.5.3 3D Image Reconstruction -- 7.4 Synchrotron laminography -- 7.4.1 Introduction -- 7.4.2 Image Reconstruction -- 7.4.3 Example Applications -- 7.5 Absorption Imaging -- 7.5.1 Natural Contrast -- 7.5.2 Staining Contrast -- 7.6 Phase-Contrast Imaging -- 7.6.1 Introduction -- 7.6.2 Free-Space Propagation Methods (Holotomography) -- 7.6.3 Analyzer-Based Imaging -- 7.6.3.1 Applications -- 7.6.4 X-Ray Grating Interferometry -- 7.6.4.1 Introduction -- 7.6.4.2 Performance Characteristics and Applications -- 7.7 Applications (Post-treatment) -- 7.7.1 Segmentation - Visualization Methods -- 7.7.1.1 Main Visualization Methods -- 7.7.1.2 Classification and Segmentation -- 7.7.2 Numeric Simulation - Testing Hypotheses on Adaptive Evolution in Marine Vertebrates Using 3D Imaging Tools -- 7.8 Conclusion -- Acknowledgements -- References -- Chapter 8 Imaging Marine Life with a Thin Light-Sheet -- 8.1 Introduction -- 8.2 Fluorescence Microscopy Methods -- 8.2.1 Fluorescence -- 8.2.2 Epi-Fluorescence Wide-Field Microscopy -- 8.2.3 Confocal Laser Scanning Fluorescence Microscopy.

8.2.4 Other Approaches for Optical Sectioning -- 8.3 Light-Sheet Fluorescence Microscopy -- 8.3.1 Concept -- 8.3.2 Implementations and Instruments -- 8.3.2.1 Illumination Unit -- 8.3.2.2 Detection Unit -- 8.3.2.3 Sample Chamber and Movement Unit -- 8.3.3 Spatial Resolution -- 8.3.4 Sample Mounting -- 8.3.5 Upright LSFM: an Alternative Configuration with Simplified Sample Mounting -- 8.4 Advantages of LSFM -- 8.5 How to Improve LSFM Imaging -- 8.6 Different Ways to Generate a Light-Sheet -- 8.6.1 Digital Scanned Light-Sheet Microscope -- 8.6.2 Incoherent Structured Illumination -- 8.6.3 Two-Photon Excitation -- 8.6.4 Bessel Beams -- 8.7 Application Examples -- 8.8 LSFM Combined with Other Fluorescence Techniques -- 8.9 Light-Sheet Fluorescence Microscopy for Marine Biology -- 8.10 Summary and Outlook -- References -- Chapter 9 Ex-situ Macro Photography of Marine Life -- 9.1 Introduction -- 9.2 The Exposure -- 9.2.1 Shutter Speed -- 9.2.2 Aperture -- 9.2.3 ISO Value -- 9.2.4 Depth of Field (DoF) -- 9.2.5 Camera Settings -- 9.2.6 What Is a Good Exposure? -- 9.3 Using Flashes -- 9.3.1 Controlling Exposure -- 9.3.2 Positioning and Shaping the Light -- 9.4 Equipment -- 9.4.1 Camera -- 9.4.2 Lenses -- 9.4.3 Flashes -- 9.4.4 Flash Accessories and Lighting Gear -- 9.4.5 Aquarium Setup -- 9.4.6 Other Accessories -- 9.5 Macro Photography of Marine Life -- 9.5.1 Setting up the Camera -- 9.5.2 Positioning the Flashes -- 9.5.2.1 Lighting Small Animals -- 9.5.2.2 Lighting Bigger Animals -- 9.5.2.3 Water Quality -- 9.6 After the Photographic Shoot -- 9.6.1 File Formats -- 9.6.2 Post-processing Workflow -- 9.6.3 Selecting Images -- 9.7 Animal Care -- 9.7.1 Collecting -- 9.7.2 Handling and Imaging -- Acknowledgements -- References -- Chapter 10 Automated Image Processing in Marine Biology -- 10.1 Introduction.

10.2 Methods of Planktonic Community Analysis -- 10.2.1 General Methods -- 10.2.2 Semi-automated Options -- 10.3 Semi-automated Planktonic Community Analysis -- 10.3.1 Work Flow of Analysis -- 10.3.1.1 Sample Collection -- 10.3.1.2 Image Capture -- 10.3.1.3 Importation and Segmentation -- 10.3.1.4 Classifier Generation -- 10.3.1.5 Classification -- 10.4 Future Directions -- 10.5 Conclusion -- References -- Index.