1 Analyzing Gel Images with Delta2D
 1.1 Setting up Projects
 1.2 Finding Interesting Spots
   Identifying Interesting Spots by their Appearance
   Finding Interesting Spots in a Scatter Plot
   Identify Interesting Spots by Their Expression Profile
   Filtering for Interesting Expression Profiles
2 A Quick Tour of Delta2D 3.6
3 Install and start Delta2D
 3.1 Available Computing Platforms
 3.2 Installation Steps for Microsoft Windows
 3.3 Start Delta2D
 3.4 Registration
 3.5 Adjusting Memory Settings
 3.6 Checking for Software Updates
 3.7 Updating an Existing Installation of Delta2D
4 Working with Analysis Projects
 4.1 The Gel Pool
   Adding Gel Images to the Pool
   Assigning Gel Image Attributes
 4.2 Opening, Creating, and Removing Projects
 4.3 Gel Image Groups
   Creating a New Group
   Adding Gel Images to a Group
 4.4 The Project Manager
 4.5 Connecting the Gel Images by Pairwise Linkage
   Status Icons
 4.6 Warping Strategies
 4.7 Different types of Experiments need different Project Setups
   Standard (Single Channel) Experiments
   DIGE Experiments Using Internal Standard
   Other Multiplex Experiments without Internal Standard
    Delta2D and other Multiplex Experiments
 4.8 Image Fusion
 4.9 Transfer Spots Shapes to Other Gel Images
 4.10 Performing Analysis Jobs in the Background
 4.11 Spot Detection and Quantitation Options
5 Warping 2D Gel Images
 5.1 The Gel Image Pair View
   The Tool Panel
   The Icon Bar
   The Status Bar
 5.2 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
   The Rollups Menu
 5.3 Navigating in Images
 5.4 Enhancing the Images View
   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
 5.5 Preferences for Image Preparation
 5.6 Visual Comparison of two Gel Images
 5.7 Warping Gel Images
   Automatic Warping
    Improving the Results of Automatic Warping
   Do a Global Warp
   Do an Exact Warp
    Add More Match Vectors if Necessary
 5.8 More About Match Vectors
    Match Vector Snap
    Creating Match Vectors by Double Click
   Saving the Match Map
   Saving the Warped Image
 5.9 Preferences for Match Vectors
 5.10 Defining a Warp Strategy for the Complete Project
 5.11 Interpretation of the Dual Channel Image
 5.12 Questions and Answers About Warping
 5.13 Using Color
6 Spot Quantitation and Matching
 6.1 The Quantitation Dialog
   Quantifying One Single Gel
   Individual Quantitation for Both Gel Images
 6.2 Spot Matching on Individual Quantitation
 6.3 Spot Detection and Quantitation Parameters
   Configuring the Local Background Region
   Configuring the Average Spot Size
   Configuring the Weak Spot Sensitivity
   Saving and Loading Sets of Options
 6.4 Pixel Based or Modeled Spot Boundaries
 6.5 Edit Spots
   Adding a Spot
   Splitting a Spot in Two
   Joining two Spots
   Removing a Manually Edited Spot
7 Working with Spot Annotations
 7.1 Creating a Label
   Changing the Text of a Label
   Moving a Label
   Label Snap
   Greek Symbols in Labels
 7.2 Labels and Spots
   Creating and editing labels in the quantitation table
    Sorting and Searching for Labels
 7.3 Working with Labels
   All Labels on a Gel
   Individual Labels
    Deleting  a  Label
    Adjusting  a  Label
    Moving  a  Label  to  Another  Image
    Working with Scout Data
    Information at a Glance
 7.4 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
 7.5 Creating and Using a Proteome Map with Spot Identifications
 7.6 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
 7.7 Scouts: Finding Information in Web Resources
   Accessing Scout Data
8 Exploring Analysis Results
 8.1 The Quantitation Tables
   Single Gel Tables
   Multi Gel Tables
   The Statistics Table
   Changing the Table Layout
   Table Properties
 8.2 Working with Spots
   Sorting and Selecting Spots
   Selecting Spots in the Gel Image Pair View
   Hiding Spots
   Canceling Spots
   Marking Spots
   Counting
   Filtering
    Example: Showing Spots Whose Quantities Differ by More Than a Factor of Two
   Scatter Plots
 8.3 Gel Image Regions Window
 8.4 Spot Color Coding
   Color Coding by Subsets
   Color Coding by Min/Max
   Example: Color Coding Spots by Subsets
 8.5 Expression Profiles Window
 8.6 Statistical Analysis of the Results
   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
 8.7 Generating Reports
   Project Summary
   Spot Album
   Spot Quantities
   Modifying, Saving, and Printing Reports
 8.8 Exporting Spot Data to Other Applications
   Spot Picking
    The Generic File Format
    The Molecular Dynamics File Format
    The Genomic Solutions File Format
    The Ettan Spot Handling WorkStation File Format
    What if my Picker is not Supported?
   Instant MS Excel Reports
   Instant Export to MS PowerPoint
9 Preferences
 9.1 Image Preparation
 9.2 Files
 9.3 Match Vectors
 9.4 Spots
 9.5 Labeling
 9.6 Tables
 9.7 Appearance
 9.8 Projects
 9.9 Memory
 9.10 3D Spots
 9.11 License
10 Keyboard Shortcuts
 10.1 Keyboard Shortcuts in the Project Manager Window
 10.2 Keyboard Shortcuts in the Gel Image Pair View Window
 10.3 Keyboard Shortcuts Depending on Tool
   Match Map Tool
   Segments Tool
   Zoom Tool
   Labels Tool
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: Grayscale Calibration
13 Useful Tips
A Example Files
B Contact Information
C Acknowledgments