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Laboratory Imaging & Photography

Book Description

Laboratory Imaging and Photography: Best Practices for Photomicrography and More is the definitive guide to the production of scientific images. Inside, the reader will find an overview of the theory and practice of laboratory photography, along with useful approaches to choosing equipment, handling samples, and working with microscopic subjects. Drawing from over 150 years of combined experience in the field, the authors outline methods of properly capturing, processing and archiving the images that are essential to scientific research. Also included are chapters on applied close-up photography, artificial light photography and the optics used in today’s laboratory environment, with detailed entries on light, confocal and scanning electron microscopy. A lab manual for the digital era, this peerless reference book explains how to record visual data accurately in an industry where a photograph can serve to establish a scientific fact.

Key features include:

  • Over 200 full-color photographs and illustrations
  • A condensed history of scientific photography
  • Tips on using the Adobe Creative Suite for scientific applications
  • A cheat sheet of best practices
  • Methods used in computational photography

Table of Contents

  1. Cover
  2. Half Title
  3. Title Page
  4. Copyright Page
  5. Table of Contents
  6. About the Author
  7. About the Contributors
  8. About the Series
  9. Acknowledgements
  10. Preface: In the Beginning
  11. Dedication
  12. Introduction: The Imaging Chain
    1. The Product is the Sum of its Parts
    2. The Imaging Chain
    3. Photography Defined
  13. Part I Foundations, Fundamentals, Principles, and Theory
    1. 1 Defining a Science Image
      1. A Frame of Reference for the Image in Science
      2. The Science Image: A Point of Departure
      3. Science Photographs Require a Scale
      4. Photographer’s Intent and Subject Matter
      5. A Picture is Worth a Thousand Words
      6. The Beginnings of Permanent Photographs and Scientific Photography
      7. Making the Invisible Visible
      8. Historical Images and a Contemporary Point of View
      9. Standardized Approaches and Repeatability
      10. Father of Standardized Imaging
      11. Innovators and Technological Progress
      12. Instrumentation
      13. Microscopy and Carl Zeiss
      14. The Invisible Spectrum
      15. Advancements in Film Technology—Kodak, Agfa, Ilford, and Polaroid
      16. Short Duration Light, Electric Flash, and Stroboscopes
      17. Modern Technologies—Digital and Electronic Photography
      18. Scanning Electron Microscopy
      19. Duality of Images
      20. Science Images as Art
      21. Suggested Reading
    2. 2 Human Vision and Perception
      1. The Imaging Room
      2. Seeing
      3. Basic Structures in the Human Visual System
      4. Optics of the Eye and Image Formation
      5. The Physiology of Seeing
      6. Dominant Eye
      7. Visual Perception and the Physiological Aspects of Sight
      8. Perception of Color
      9. Persistence of Vision
      10. Afterimage
      11. Perception of Depth
      12. Adaptation
      13. More on Perception
      14. Mirages or Illusions
      15. Suggested Reading
    3. 3 Applied Physics and Image Formation for the Scientific Photographer
      1. Light
      2. Visibility Requires Contrast, Magnification, and Resolution
      3. Sources
      4. Continuous and Discontinuous Spectrums
      5. Color Temperature
      6. Continuous or Pulsed Emission
      7. Light Behaviors
      8. Lenses
      9. Lenses for Scientific Applications
      10. Photographic Filters
      11. Aberrations
      12. Image Depth of Field
      13. Diffraction
      14. Suggested Reading
    4. 4 Digital Cameras, Digital Images, and Strategies
      1. The Role of the Camera
      2. Camera Components
      3. Camera Modes of Operation
      4. Photographic Exposure
      5. Light Measurement
      6. Shutters
      7. Shutter Effects on Images
      8. Mirrorless Cameras
      9. Sensors
      10. Pixels
      11. Single-shot Area Array Sensors
      12. Multi-shot Area Array Sensors
      13. Sensor Sensitivity ISO, Binning, Gain
      14. Noise: Dark, Shot, Sensor, and Evaluating Noise
      15. Sensor Evaluation
      16. Bit Depth
      17. Color Space
      18. Gamma and Contrast
      19. White Balance
      20. Capture File Formats
      21. Capturing Using Camera Digital Filters
      22. Digital Artifacts: Aliasing
      23. Connecting Devices
      24. Memory Cards
      25. Suggested Reading
  14. Part II Applications, Best Practices, and Methods
    1. 5 The Sample and its Role in Laboratory Photography
      1. The Sample and Photographic Treatments
      2. Preparation for Imaging
      3. Selecting a Sample
      4. Sample Preparation
      5. Isolating the Sample
      6. Controlling Dirt and Extraneous Materials
      7. Handling Samples and Preparation
      8. Wet Specimens: Distilled and De-ionized Water or Other Fluids
      9. Making Chambers and Welled Slides
      10. Staining and Revealing Other Features
      11. Specimen Platforms
      12. Mirrors
      13. Surface Replicas
      14. Backgrounds
      15. The Use of Scales to Indicate Size
      16. Suggested Reading
    2. 6 Basic Laboratory Photography Methods: Close-up Photography, Photomacrography, and Stereomicroscopy
      1. Overview
      2. Close-up Photography
      3. Lenses for Close-up Photography
      4. Focusing, Depth of Field, and Diffraction
      5. Creating Camera-to-Subject Alignment
      6. Selecting the Best Aperture Possible
      7. Exposure Compensation and Determination
      8. Photomacrography
      9. Bellows and Laboratory Set-ups
      10. True Macro Lenses and Optical Considerations
      11. Other Lenses that Can Be Used for Magnifications 2:1 and Higher
      12. Setting up the System
      13. Exposure Compensation
      14. Exposure Factor Equations
      15. Depth of Field
      16. Stereo Photomicroscopes
      17. Suggested Reading
    3. 7 Advanced Laboratory Photography Methods: Making Things Visible
      1. Introduction
      2. Fluorescence
      3. Photographing with the Invisible Spectrum
      4. Polarized Light
      5. Schlieren Photography
      6. Scanners as Cameras
      7. Peripheral Photographs
      8. Stereo Photography and Anaglyphs
      9. Stroboscopy
      10. Suggested Reading
    4. 8 A Primer for Lighting Small Laboratory Subjects
      1. Light and Lighting
      2. Making Good Light
      3. White and Neutral Backgrounds
      4. Making Contrast
      5. Reducing Contrast
      6. Axial Lighting
      7. Laboratory Glassware
      8. Metal and Tent Lighting
      9. Immersion
      10. A Working Summary
      11. Suggested Reading
    5. 9 Light Microscopy
      1. Foundations and Brightfield Methods
      2. Fundamentals of Magnified Images
      3. Optical Magnification
      4. Optical Elements in a Light Microscope
      5. Numerical Aperture
      6. Fundamentals of Operating a Light Microscope
      7. Photographing using a Light Microscope
      8. Instrument Cameras
      9. DSLR Cameras
      10. More Advanced Methods that Produce Contrast
      11. Setting Up Darkfield
      12. Differential Interference Contrast
      13. Fluorescence
      14. Phase Contrast
      15. Polarized Light
      16. Rheinberg Differential Colorization
      17. Suggested Reading
    6. 10 Confocal Microscopy
      1. Introduction
      2. Why Confocal?
      3. Types of Confocal Microscopes
      4. Fluorescence Microscopy and Confocal Methods
      5. How a Confocal Microscope Works
      6. Balance and Compromises Required for Forming a Good 2D Image
      7. Hardware Choices
      8. Overview of Instrument Controls and Software
      9. 3D Imaging
      10. Considerations for Making a Good Z-Stack
      11. Consideration for Live Cell Imaging
      12. Advanced Techniques
      13. Suggested Reading
    7. 11 Scanning Electron Microscopy
      1. Introduction
      2. History
      3. Modern Machines
      4. Theory and Design of the Instrument
      5. The Nature of an Electron in a Vacuum
      6. Electron Source Design
      7. Electron Microscopy Optics
      8. Astigmatization
      9. The Electron Aperture
      10. Resolution in an SEM
      11. Signal-to-Noise Ratio
      12. Scan Rotation
      13. Specimen Charging
      14. Maximizing Resolution
      15. Sample Preparation
      16. Critical Point Drying
      17. Sputter Coating
      18. Conclusion
      19. Suggested Reading
    8. 12 Ethical Considerations in Scientific Photography: Why Ethics?
      1. The Need for Protocols
      2. The Image as Data
      3. Manipulation and Disclosure
      4. Manipulation by Specimen Selection
      5. Manipulation by Hardware Settings
      6. Manipulation by Imaging Technique
      7. Manipulation by Software
      8. Manipulation by Presentation
      9. Forensic Examination: Uncovering Digital Image Fraud
      10. Industry Oversight
      11. Consequences
      12. Conclusions
      13. Suggested Reading
    9. 13 Considerations and Methods for Image Processing in Science
      1. Introduction
      2. Terminology: Manipulation, Enhancement, Clarification
      3. Software
      4. Basic Color Theory
      5. Fundamental Digital Color Models
      6. Channels
      7. Layers
      8. Fundamental/Global Image Editing Methods
      9. Selection and Tools Overview
      10. Image Editing Tools Overview
      11. Contrast and Color Balance Corrections
      12. Converting RGB files to B&W (Grayscale)
      13. Sharpening
      14. Noise Reduction Using Photoshop Software
      15. Noise Reduction Using the Camera Raw Convertor
      16. Combining Separate Fluorescence Images
      17. Pseudo-coloring B&W Images
      18. Creating a Composite Image for Publication
      19. The Type Tool
      20. Basic Shapes
      21. Preparing Files for Publication
      22. Suggested Reading
    10. 14 Applications of Computational Photography for Scientist Photographers
      1. Batch Processing
      2. Making an Action
      3. Increased Depth of Field Methods
      4. Making Image Focus Slices
      5. Global Image Processing of Files Used in Computational Images
      6. Widefield High Resolution or Image Mapping
      7. Methods
      8. High Dynamic Range Images
      9. Time-based Imaging
      10. Suggested Reading
    11. 15 Best Practices
      1. Introduction
      2. The Laboratory and Environmental Conditions
      3. Optimizing the Camera’s Settings
      4. Cleaning a Lens
      5. Monitors and Video Displays
      6. Color Management
      7. Software, Upgrades, and Optimizing the Computer
      8. Image Workflow, Folders, and Naming Files
      9. Archiving, Data Redundancy, and Backing Up
      10. Planning for Data Loss and Failures
      11. Digital Housekeeping
      12. Keeping Things Tuned Up
      13. Smartphone Photography
      14. Social Media
      15. Conclusion
      16. Suggested Reading
  15. A Cheat Sheet for Best Practices
  16. Index