Laboratory imaging and photography : best practices for photomicrography and more

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