Laboratory Imaging & Photography: Best Practices for Photomicrography & More, 1st Edition (Paperback) book cover

Laboratory Imaging & Photography

Best Practices for Photomicrography & More, 1st Edition

By Michael Peres

Routledge

370 pages

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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

Reviews

"The book is both comprehensive and accessible to photographers at all levels. Each topic is approached without expectation of previous knowledge from the reader or any photographic snobbery. For example, whether you are reading about comparisons between focal plane, sync speed, leaf and electronic shutters or how to apply an un-sharpen mask in Photoshop, everything is written in an easy-to-digest way for photographers of all backgrounds. [It] provides theoretical content to underpin many of the day-to-day practices of a medical photographer. Other practising clinical photographers will find the book reaffirms much of their current knowledge, while enhancing their understanding in some areas and potentially providing an introduction to unfamiliar techniques.

The underlying feeling I had throughout reading this book was ‘why couldn’t this book have been available while I was studying?’ I will certainly be using the book as part of my continuing professional development for many years to come."

—Simon Brinkworth, Medical Illustration, Marlborough Hill Workshops, Bristol, UK © 2018 The Institute of Medical Illustrators

Table of Contents

Acknowledgements

Preface: The Beginning

Introduction: The Imaging Chain

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

Criteria for Good Photography

Science Photographs require a Scale

Photographer’s Intent and Subject Matter

A picture is worth a thousand words

The beginnings of permanent photographs and scientific photography

Making the Invisible visible

Historical images and Contemporary Point of View

Standardized Approaches and Repeatability

Father of Standardized Imaging

Innovators and technological progress

Instrumentation

Microscopy and Carl Zeiss

The Invisible Spectrum

Advancement of Film Technology – Kodak. Agfa, Ilford and Polaroid

Short Duration Light, Electric Flash and Stroboscopes

Modern Technologies - Digital and Electronic Photography

Scanning Electron Microscopy

Confocal Microscope

Duality of Images

Science Images as Art

Chapter 2

Human Vision and Perception

The Human Visual System

The Imaging Room

Seeing

Basic Structure of the Human Visual System

Optics of the Eye and Image Formation

Physiology of Seeing

Dominant Eye

Visual Perception and the Physiological of Sight

Perception of color

Persistence of Vision

Afterimage

Perception of Depth

Adaption

More on Perception

Illusions

Chapter 3

Applied Physics and Image Formation for the Scientific Photographer

Visibility requires Contrast, Magnification, and Resolution

Light & Illumination

Sources and Spectrums

Continuous and Discontinuous Spectrums

Color temperature

Light behaviours

Reflection

Refraction

Dispersion

Interference

Lenses

Lenses for Scientific Applications

Fundamental optics

Teleconverters

Working Distance

Close up Lenses

Supplementary Lenses

Mirror Lenses

Telecentric Lenses

Photographic Filters

Polarizing Filters

Neutral Density Filters

Aberrations

Curvature of the Field

Chromatic Aberrations

Depth of Field

Diffraction

Chapter 4

Digital Cameras, Digital Images, and Strategies

The role of the camera

Camera Components

Shutters

Modes of Operation

Manual

Automatic

Secondary Modes of Operation

Photographic Exposure

Light measurement

Types of Shutters

Focal Plane Shutters

Syncing with electronic flash

Electronic shutters

Shutter affects on subjects

Vibration affects

Mirrorless cameras

Sensors

Pixels

Single shot cameras

Scanning arrays

Multi-shot arrays

Sensor sensitivity ISO, Binning, Gain

Noise production, dark, shot, sensor and evaluating

Sensor evaluation

Bit depth

Color space

Gamma

White balance

Spectral sensitivity

Capture file formats

Other file formats

Filters

Sharpening

Color reproduction

Noise reduction

Digital Artifacts

Connecting devices

Memory cards

Applications, Best Practices and Methods

Chapter 5

The Sample and its Role in Laboratory Photography

Laboratory Photography Overview

The Sample and Treatment

Treatment

Preparation

Selecting a Sample

Isolating the sample

Objects and characteristics

Isolating the subject

Composition

Handling samples, preparation and treatments

Staining and other contrast producing factors

Wet samples and immersion methods

Making chambers

Specimen Tables

Surface replicas

White, Black or Gray Backgrounds

Use of Scales to indicate size

Chapter 6

Basic Laboratory Photography Methods:

Close-Up Photography, Photomacrography, and Stereomicroscopy

Overview of Close-up Photography

Close- Up Methods

Lenses for Close-Up Photography

Supplementary Lenses

Extension Tubes

Focusing, Depth of Field, and Diffraction

Creating Camera to Subject Alignment

Selecting the Aperture

Exposure in Close-Up applications

Photomacrography

Introduction

Bellows and Laboratory Set-Ups

True Macro Lenses and Optical Considerations

Other lenses that can be used for magnifications 2:1 and higher

Setting up a Macro System

Exposure Compensation

Exposure Factor equations

Depth of Field

Stereo Microscopes

Photographing with a stereomicroscope

Chapter 7

Advanced Laboratory Photography Methods – Making Things Visible

Introduction

I- Fluorescence

Jablonski diagram

Ultraviolet and Short Wave Blue Excitation

The Fluorescence System

II - Photographing with the Invisible spectrum

Basic Problems

Energy Sources

Cameras

Lenses

Filters

Focusing

Live View or Auto-focus

Exposure Determination

Increasing the ISO

Noise Reduction Filters

Work tethered

Multiple Discharges for Electronic Flash

Other Strategies

III - Polarized light

Seeing internal structure

The System

IV - Schlieren

Photographing Schlieren Images

V - Scanners as Cameras

Scanner Settings

Using Descreen

Unsharp Masking

Imaging Objects on a Scanner

VI - Peripheral Photography

VII - Stereo and Anaglyphs

Making a Stereo Pair

Making an Anaglyph

VIII - Stroboscopy

Chapter 8

A Primer for Lighting Small Laboratory Subjects

There is light and then there is lighting

Making good light

White and Neutral Backgrounds

Making Contrast

Reducing Contrast

Axial lighting

Glassware

Metal and tent lighting

Immersion methods

A Working Summary

Chapter 9

Light Microscopy

I - Foundations and brightfield methods

Introduction

Fundamentals of Magnified Images

Optical Magnification

Optical Elements on a Light Microscope

Eyepieces

Prism

Photo or Imaging System Lenses

Substage Condendsers

Objectives

Numerical Aperture

Forming Images - Diffraction and Resolution

More on Numerical Aperture

Objective Corrections

Fundamentals useful in Operating a Light Microscope

Setting the Eyepieces

Focusing

Very Small Working Distances

Interpupillary Distances

Looking into the Body Tube

Nosepiece or Turrets

Adjusting the Substage Condenser

Setting the Field Diaphragm

Lamp

Setting the Aperture Diaphragm

Establishing Proper Brightfield or Kohler Illumination

More on Kohler

Photographing using a Light Microscope

Instrument Cameras

DSLR cameras

Attaching a Camera to a Microscope

II: Advanced Methods

Darkfield

Differential Interference Contrast

Fluorescence

Phase Contrast

Polarized light

Rheinberg Differential Colorization Technique

Chapter 10

Confocal Microscopy

by James Hayden

Introduction

Why Confocal ?

Types of Confocal Microscopes

Fluorescence Microscopy and Confocal Methods

Fluorescent Markers

Choosing and Working with Fluorophores

How a Confocal Microscope Works

Balance and Compromises required for forming a Good 2D image

Hardware Considerations

Lasers

Detectors

Overview of Instruments Controls and Software

Laser Power

Detector Settings

Simultaneous of Sequential Acquisition

Gain and Offset

Pinhole Size and Resolution

Spatial Resolution and Format

Scanning Speed

Bidirectional Scanning

Digital Zoom

Bit depth

Averaging / Signal to Noise

Accumulation

3D imaging

Considerations for Creating an Effective Z stack

Consideration for Live Cell Imaging

Advanced techniques

Chapter 11

Scanning Electron Microscopy

by Ted Kinsman

Introduction

History

Modern Machines

Theory and Design of Instruments

The Nature of an Electron in a Vacuum

Electron Source

Electron Microscopy Optics

Astigmatization

The Electron Aperture

Resolution in a SEM

Signal to Noise Ratio

Scan Rotation

Specimen Charging

Maximizing Resolution

Sample Preparation

Critical Point Drying

Sputter Coating

Chapter 12

Ethical Considerations in Scientific Photography: Why Ethics?

by James Hayden

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

Chapter 13

Considerations and Methods for Image Processing in Science

by Staffan Larsson

Introduction

Terminology: Manipulation, Enhancement, Clarification

Software

Image J

GIMP

Adobe Photoshop

Basic Color Theory

Fundamental Digital Color Models

Channels

Layers

Fundamental Image Editing Methods in Science

Monitor Calibration

Selection tools and tools overview

Image Size

Image Editing Tools Overview

Selection Image editing tools

Pixel Adjustment Tools

Image Processing

I - Contrast and Color Balance Corrections

Method: Setting a white and black point

Method: Changing contrast using Levels

Method: Using Curves

II - Converting RGB files to Grayscale

Method: Grayscale

Method: Split Channels

Method: Channel Mixer

Method: Black and White Adjustment Layer

III – Sharpening

Method: Unsharp Masking

Method: High Band Pass Filter

Noise reduction using Adobe Camera RAW

Method: Eliminating Luminance Noise

Method: Despeckle

Method: Smart Blur Filter

Method: Reducing Noise using the Reduce Noise Filter

V – Noise Reduction using the Camera Raw Convertor Software

Method: Using the Camera RAW Module

VI - Combining fluorescent images

VII - Pseudo-coloring B & W images

VIII - Making composite images

Method: Making a Composite File

IX- Type and the Text Tool

X - Shapes

XI - Preparing files for Publication

Method: converting RGB to CMYK

Method: Evaluating a CMYK images Black Point

Profiles

Proofing

Gamut Warning

Chapter 14

Applications of Computational Photography for Scientist Photographers

Image editing and Batch Processing

Making actions

Increased DOF

Making Image Slices

Global Image Processing

Z Stack file processing using Adobe® Photoshop

Z Stack file processing using Helicon Focus®

Z Stack file processing using Zerene Stacker

Wide field high resolution

Methods

Global Image Processing

Creating the Image Map

High Dynamic Range Images

Making Photographic Exposures for HDR

Blending the Images

Time based imaging

Photographic Considerations

Intervalometers

Making the Photographs

Chapter 15

Best Practices

Introduction

More Thoughts about Best Practices and Workflow

The Laboratory and Environmental conditions

Cleanliness is imperative

Optimizing Camera’s Settings

Cleaning A Lens

Monitors and video displays

Color Management

Software, upgrades and Optimizing a Computer

Image Workflow, Folders, and Naming Files

Archiving, Data Redundancy, and Backing Up

Planning for Data loss and Disk Failure

Digital housekeeping

Keeping things Tuned Up

Smart phone photography

Social Media

Conclusion

Best Practices Cheat Sheet

About the Author

Michael Peres is the editor-in-chief of The Focal Encyclopedia of Photography, 4th Edition, and former chair of the biomedical photographic communications department at the Rochester Institute of Technology. Since 1986, he has taught photomicrography, biomedical photography and other applications of photography used in science. Prior to joining the RIT faculty, Peres worked at Henry Ford Hospital and the Charleston Division of West Virginia University as a medical photographer. He is the recipient of the RIT Eisenhart Outstanding Teaching Award and the Schmidt Medal for Lifetime Achievement in the Field of Biocommunications.

About the Series

Applications in Scientific Photography

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MED019000
MEDICAL / Diagnostic Imaging
PHO000000
PHOTOGRAPHY / General
PHO018000
PHOTOGRAPHY / Techniques / General