Delta2D Version 3.4 

Manual

DECODON GmbH

October 2006
Copyright ©2000-2006 DECODON GmbH. DECODON makes no representations, express or implied, with respect to this documentation or the software it describes, including without limitations, any implied warranties of merchantability or fitness for a particular purpose, all of which are expressly disclaimed. Users should recognize that all complex software systems and their documentation contain errors and omissions. DECODON shall not be responsible under any circumstances for providing information on or corrections to errors and omissions discovered at any time in this document or the software it describes, whether or not they are aware of the errors and omissions. DECODON does not recommend the use of the software described in this document for applications in which errors or omissions could threaten life, injury or significant loss. DECODON, the DECODON logo, Delta2D, SmartVectors are trademarks or registered trademarks of DECODON GmbH in Germany and in several other countries all over the world. The use of general descriptive names, trademarks, etc., in this publication, even if the former are not especially identified, is not to be taken as a sign that such names, as understood by the Trade Marks and Merchandise Marks Act, may accordingly be used by anyone. Where those designations appear in this work and DECODON was aware of a trademark claim, the designations follow the capitalization style used by the manufacturer. Linux is a trademark of Linus Torvalds. Apple, Mac, MacOS, Macintosh are trademarks of Apple Computer, Inc., registered in the U.S. and other countries. JAVA and Solaris are registered trademarks of Sun Microsystems, Inc., 901 San Antonio Road, Palo Alto, CA 94303 USA. Microsoft, WINDOWS, NT, PowerPoint, Excel are registered trademarks of Microsoft Corporation. UNIX is a registered trademark of The Open Group. All other products mentioned are trademarks or registered trademarks of their respective companies. Some software products marketed by DECODON GmbH and its distributors may contain proprietary software components of other software vendors.

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 3.4
 2.1 The Example Project
 2.2 Working with Gel Image Pairs
 2.3 Quantitative Data
 2.4 Labels
 2.5 Analysing Projects
 2.6 Instant MS Excel Reports
 2.7 Instant Export to MS PowerPoint
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
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 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 History of Delta2D
 New Features of Delta2D 3.3
 New Features of Delta2D 3.2
 New Features of Delta2D 3.1.3
 New Features of Delta2D 3.1.2
 New Features of Delta2D 3.1
 New Features of Delta2D 3.0
 New Features of Delta2D 2.1
 New Features of Delta2D 2.0
C Contact Information
D Acknowledgments
List of Figures
List of Tables