1 Strategy for Analyzing Gel Images with Delta2D
2 Install and start Delta2D
 2.1 Available Computing Platforms
 2.2 Installation Steps for Microsoft Windows
 2.3 Start Delta2D
 2.4 License Registration
 2.5 Adjusting Memory Settings
 2.6 Checking for Software Updates
 2.7 Updating an Existing Installation of Delta2D
3 Workflow of Delta2D 4.0
 3.1 Setup Project
   Create or Open a Project
   Add Groups and Gel Images to the Groups
 3.2 Setup Gel Image Warping
 3.3 Create Direct Warpings
 3.4 Create the Consensus Spot Pattern
   Fuse Images
   Detect and Edit Spots on Fused Image
   Transfer Spots
    Transfer Spot Shapes to Other Gel Images
   Spot Matching
 3.5 Analyze Expression Profiles
 3.6 Present Results
   Generating Reports
    Project Summary
    Spot Album
    Spot Quantities
    Modifying, Saving, and Printing Reports
 3.7 Exporting Results to Other Applications
   Instant MS Excel^TMReports
   Instant Export to MS PowerPoint^TM
4 Main Menu and Toolbars
 4.1 The Main Menu
 4.2 The Main Toolbar
5 The Windows
 5.1 Workflow
 5.2 Project Explorer
   Gel Groups
   Gel Image Pairs
    Gel Image Pair Status
   Different Kinds of Projects
    Standard (Single Channel) Experiments
    DIGE Experiments Using Internal Standard
    Delta2D and DIGE
    Other Multiplex Experiments without Internal Standard
    Delta2D and other Multiplex Experiments
 5.3 Light Table
   Adding a Group
   Adding Gel Images to a Group
 5.4 Warping Setup
   Warping Strategies
 5.5 Dual View
   The Dual View Menu
   The Dual View Toolbar
   The Dual View Tool Panel
   The Status Bar
   Navigating in Images
   Configuring the Display Using Rollups
    The Colors Rollup
    The Overlays Rollup
    The Navigator Rollup
    The Zoom Rollup
    The Expression Profile Rollup
    The 3D Spots Rollup
    The pI/MW Calibration Rollup
   Controlling Background Display
   The Histograms Dialog
    Histograms or Amplitude Rescaling?
    Automatic Histogram Equalization
    Manual Histogram Equalization
    Manually Adjusting the Balance Between Two Images
    Modifying the Histogram for a Single Image
    Managing the Histograms Dialog
    About the Histogram Adjustment Process
   Using Colors: The Color Schemes Dialog
   Warping Gel Images
    Saving the Warped Image
    Setting Match Vectors
    Questions and Answers About Warping
   The Spot Detection and Quantitation Dialog
    Spot Detection Parameters
    Spot Shapes: Pixel Based or Modeled
    Spot Editing
   Spot Quantitation and Matching
 5.6 Quantitation Table
   The Quantitation Table Menu
   The Quantitation Table Toolbar
   Changing the Table Layout
   Table Properties
 5.7 Gel Image Regions
 5.8 Expression Profiles
 5.9 Color Coding
   Color Coding by Subsets
   Color Coding by Min/Max
 5.10 Job Manager
 5.11 Analysis
   Getting a High Level Overview of Expression Data - Heat Maps
   Discovering Patterns in Expression Profiles
   Finding differentially expressed proteins: Statistical Tests
   Working with Sets of Spots
   Statistical Analysis is Integrated with Image Analysis
   Overview of Statistical Methods
 5.12 Project Matrix
 5.13 Arrange Windows
6 The Gel Pool
 6.1 Adding Gel Images to the Pool
 6.2 Assigning Gel Image Attributes
7 Image Fusion
8 Working with Spots
 8.1 Sorting and Selecting Spots
 8.2 Selecting Spots in the Dual View
 8.3 Hiding Spots
 8.4 Canceling Spots
 8.5 Marking Spots
 8.6 Counting
 8.7 Filtering
   Example: Showing Spots Whose Quantities Differ by More Than a Factor of Two
 8.8 Scatter Plots
 8.9 Spot Picking
   The Generic File Format
   The Molecular Dynamics^TMFile Format
   The Genomic Solutions^TMFile Format
   The Ettan Spot Handling WorkStation^TMFile Format
   What if my Picker is not Supported?
9 Working with Spot Annotations
 9.1 Creating a Label
   Changing the Text of a Label
   Moving a Label
   Label Snap
   Greek Symbols in Labels
 9.2 Labels and Spots
   Creating and editing labels in the Quantitation Table
    Sorting and Searching for Labels
 9.3 Working with Labels
   Individual Labels
    Deleting a Label
    Adjusting a Label
    Moving a Label to Another Image
    Working with Scout Data
    Information at a Glance
 9.4 Formatting Labels
   The Label Formats Dialog
    Managing the Label Formats Dialog
    Saving Label Data
    Specifying Label Formats
    Coloring Labels
    Saving Label Formats
    Loading Label Formats
 9.5 Creating and Using a Proteome Map with Spot Identifications
 9.6 Support for Protein Identification by Mass Spectrometry
   Automatically Creating Labels in the Dual View
   Automatically Create Labels in the Quantitation Tables
   Automatically Replace Labels with Names of Identified Proteins
 9.7 Scouts: Finding Information in Web Resources
   Accessing Scout Data
10 Options
 10.1 Delta2D
   Match Vectors
   Spots
   3D Spots
   Labels
   Tables
   Projects
   Image Preparation
 10.2 General
   License
   Files
   Appearance
   Updates
   Windows
   Web
 10.3 Memory
 10.4 Keymap
   Global Keymap
   Window-specific keymaps
    Keyboard Shortcuts in the Dual View
11 Advanced Topic: Scripting
 11.1 File Commands
 11.2 Image Processing Commands
 11.3 Commands for Controlling Windows
 11.4 Remote Control Commands
12 Advanced Topic: Greyscale Calibration
13 Useful Tips
A Example Files
B Contact Information
C Acknowledgments
D Lists of Figures and Tables, Index