About Delta2D
How to use this manual
Contents
1 Analyzing Gel Images with Delta2D
 1.1 Setting up Projects
 1.2 Finding Interesting Spots
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
 4.2 Opening, Creating, and Removing Projects
 4.3 Gel Image Groups
 4.4 The Project Manager
 4.5 Connecting the Gel Images by Pairwise Linkage
 4.6 Warping Strategies
 4.7 Different types of Experiments need different Project Setups
 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
 5.2 Configuring the Display Using Rollups
 5.3 Navigating in Images
 5.4 Enhancing the Images View
 5.5 Preferences for Image Preparation
 5.6 Visual Comparison of two Gel Images
 5.7 Warping Gel Images
 5.8 More About Match Vectors
 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
 6.2 Spot Matching on Individual Quantitation
 6.3 Spot Detection and Quantitation Parameters
 6.4 Pixel Based or Modeled Spot Boundaries
 6.5 Edit Spots
7 Working with Spot Annotations
 7.1 Creating a Label
 7.2 Labels and Spots
 7.3 Working with Labels
 7.4 Formatting Labels
 7.5 Creating and Using a Proteome Map with Spot Identifications
 7.6 Support for Protein Identification by Mass Spectrometry
 7.7 Scouts: Finding Information in Web Resources
8 Exploring Analysis Results
 8.1 The Quantitation Tables
 8.2 Working with Spots
 8.3 Gel Image Regions Window
 8.4 Spot Color Coding
 8.5 Expression Profiles Window
 8.6 Statistical Analysis of the Results
 8.7 Generating Reports
 8.8 Exporting Spot Data to Other Applications
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
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
 Create Your Own Pool Before You Start to Work with Delta2D
 Adapt the Memory Settings of Delta2D
 Working with Big Images
 Accurate Scanning Will Be Recompensed
 Working with Different Versions of Delta2D on the Same Data
 Tuning Spot Detection
A Example Files
B Contact Information
C Acknowledgments
List of Figures
List of Tables