Laboratory Imaging & 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