Document Outline

• Quantity One®
  • Preface
  • 1 . Introduction
    • 1.1 Overview of Quantity One
    • 1.2 Digital Data and Signal Intensity
    • 1.3 Gel Quality
    • 1.4 Quantity One Workflow
      • 1.4.a Acquire Image
      • 1.4.b Optimize Image
      • 1.4.c Analyze Image
      • 1.4.d Report Results
    • 1.5 Computer Requirements
    • 1.6 Installation
      • 1.6.a Windows
      • 1.6.b Macintosh
    • 1.7 Hardware Security Key (HSK)
      • 1.7.a Windows
      • 1.7.b Macintosh
    • 1.8 Starting the Program
      • 1.8.a Windows
      • 1.8.b Macintosh
    • 1.9 Software License
      • 1.9.a Registering by Internet
      • 1.9.b Registering by Fax or E-mail
      • 1.9.c Entering a Password
    • 1.10 Downloading from the Internet
    • 1.11 Quantity One Basic
    • 1.12 Contacting Bio-Rad
  • 2 . General Operation
    • 2.1 Menus and Toolbars
      • 2.1.a Menu Bar
      • 2.1.b Main Toolbar
      • 2.1.c Status Boxes
      • 2.1.d Secondary Toolbars
      • 2.1.e Quick Guides
      • 2.1.f Right-Click Context Menu
      • 2.1.g Keyboard Commands
    • 2.2 File Commands
      • 2.2.a Opening Images
      • 2.2.b Saving Images
      • 2.2.c Closing Images
      • 2.2.d Revert to Saved
      • 2.2.e Image Info
      • 2.2.f Reduce File Size
    • 2.3 Imaging Device Acquisition Windows
    • 2.4 Exit
    • 2.5 Preferences
      • 2.5.a Misc.
      • 2.5.b Paths
      • 2.5.c Display
      • 2.5.d Toolbar
      • 2.5.e Application
      • 2.5.f Imagers
    • 2.6 User Settings
  • 3 . Viewing and Editing Images
    • 3.1 Magnifying and Positioning Tools
    • 3.2 Density Tools
    • 3.3 Showing and Hiding Overlays
    • 3.4 Multi-Channel Viewer
    • 3.5 3D Viewer
      • 3.5.a Positioning the Image
      • 3.5.b Display Mode
    • 3.6 Image Stack Tool
    • 3.7 Colors
    • 3.8 Transform
      • 3.8.a Transform Subwindows
      • 3.8.b Transform Controls
      • 3.8.c Other Features
    • 3.9 Resizing and Reorienting Images
      • 3.9.a Cropping Images
      • 3.9.b Flipping and Rotating Images
    • 3.10 Whole-Image Background Subtraction
    • 3.11 Filtering Images
      • 3.11.a Filter Wizard
      • 3.11.b Selecting a Filter Directly
    • 3.12 Invert Data
    • 3.13 Text Overlays
    • 3.14 Erasing All Analysis from an Image
    • 3.15 Sort and Recalculate
    • 3.16 Automation Manager
      • 3.16.a Step 1 - Select Template
      • 3.16.b Step 2 - Edit Selected Template
      • 3.16.c Step 3 - Select Images
      • 3.16.d Step 4 - Apply Selected Template
  • 4 . Lanes
    • 4.1 Defining Lanes
      • 4.1.a Lane Frames
      • 4.1.b Editing the Frame
      • 4.1.c Single Lanes
      • 4.1.d Lane Width
      • 4.1.e Lane Profile
    • 4.2 Lane-Based Background Subtraction
      • 4.2.a Profile Trace
      • 4.2.b All Lanes Off
      • 4.2.c All Lanes On (Same Level)
      • 4.2.d Subtraction Varies by Lane
    • 4.3 Compare Lanes
    • 4.4 Lane-based Arrays
  • 5 . Bands
    • 5.1 How Bands Are Identified and Quantified
    • 5.2 Band Detection
      • 5.2.a Detection Parameters
      • 5.2.b Parameter Sets
      • 5.2.c Default Parameters
    • 5.3 Identifying and Editing Individual Bands
      • 5.3.a Identifying Individual Bands
      • 5.3.b Adjusting Bands
      • 5.3.c Deleting Bands
    • 5.4 Plotting Traces of Bands
    • 5.5 Band Attributes
    • 5.6 Band Information
    • 5.7 Gauss-Modeling Bands
    • 5.8 Irregularly Shaped Bands in Lanes
      • 5.8.a Contouring Bands
      • 5.8.b Drawing Tools
  • 6 . Standards and Band Matching
    • 6.1 Standards
      • 6.1.a Selecting Predefined Standards
      • 6.1.b Creating New Standards
      • 6.1.c Standards Dialog
      • 6.1.d Standards Regression Curve
      • 6.1.e Displaying Calculated Values
      • 6.1.f Saving, Opening, and Deleting Standards
    • 6.2 Band Matching
      • 6.2.a Editing the Results of Band Matching
      • 6.2.b Band Set Dialog
      • 6.2.c Tips for Gels Without Standards
      • 6.2.d Normalizing for Quantity
      • 6.2.e Graphs of Match Data
    • 6.3 Quantity Standards
      • 6.3.a Creating and Applying a Set of Quantity Standards
      • 6.3.b Calibration Curve
      • 6.3.c Applying the Calibration Curve
      • 6.3.d Generating Standard Bands via a Dilution Series
      • 6.3.e Importing a Calibration Curve
  • 7 . Volume Tools
    • 7.1 Creating a Volume
    • 7.2 Moving, Copying, and Deleting Volumes
    • 7.3 Volume Standards
    • 7.4 Volume Background Subtraction
    • 7.5 Volume Arrays
  • 8 . Colony Counting
    • 8.1 Defining the Counting Region
    • 8.2 Counting the Colonies
    • 8.3 Displaying the Results
    • 8.4 Making and Erasing Individual Colonies
    • 8.5 Using the Histogram to Distinguish Colonies
    • 8.6 Ignoring a Region of the Dish
    • 8.7 Saving/Resetting the Count
    • 8.8 Saving to a Spreadsheet
  • 9 . Differential Display and VNTRs
    • 9.1 Differential Display
      • 9.1.a Normalization
      • 9.1.b Differential Display Searches
    • 9.2 Variable Number Tandem Repeats
  • 10 . Reports
    • 10.1 Report Window
    • 10.2 Lane and Match Reports
    • 10.3 Band Types Report
    • 10.4 1-D Analysis Report
    • 10.5 Similarity Comparison Reports
      • 10.5.a Compare Lane Images
      • 10.5.b Phylogenetic Tree
      • 10.5.c Similarity Matrix
    • 10.6 Volume Analysis Report
      • 10.6.a Volume Report Options
    • 10.7 Volume Regression Curve
    • 10.8 VNTR Report
  • 11 . Printing and Exporting
    • 11.1 Print Image and Print Actual Size
    • 11.2 Page Setup
    • 11.3 Image Report
    • 11.4 Video Print
    • 11.5 Export to TIFF Image
      • 11.5.a Analysis Export Mode
      • 11.5.b Publishing Export Mode
      • 11.5.c Exporting the Image
  • Appendix A Gel Doc 2000
    • A.1 Gel Doc Acquisition Window
    • A.2 Step I. Position Gel
    • A.3 Step II. Select Image Mode
    • A.4 Step III. Acquire Image
    • A.5 Step IV. Optimize Display
    • A.6 Step V. Analysis
    • A.7 Step VI. Select Output
    • A.8 Exposure Status
    • A.9 Options
  • Appendix B ChemiDoc
    • B.1 ChemiDoc Acquisition Window
    • B.2 Step I. Position Gel
    • B.3 Step II. Image Mode
    • B.4 Step III. Acquire Image
    • B.5 Step IV. Optimize Display
    • B.6 Step V. Analysis
    • B.7 Step VI. Select Output
    • B.8 Exposure Status
    • B.9 Options
  • Appendix C ChemiDoc XRS
    • C.1 ChemiDoc XRS Acquisition Window
    • C.2 Step I. Select Application
      • C.2.a. Custom Applications
    • C.3 Step II. Position Gel
    • C.4 Step III. Acquire Image
      • C.4.a. Exposure Status
    • C.5 Options
      • C.5.a. Imaging Area
      • C.5.b. Reminder
      • C.5.c. Dark Subtraction
      • C.5.d. Save Options
      • C.5.e. Auto-scale Transform
      • C.5.f. Auto Exposure Threshold
    • C.6 Other Features
  • Appendix D GS-700 Imaging Densitometer
    • D.1 GS-700 Acquisition Window
    • D.2 Step I. Select Application
    • D.3 Step II. Select Scan Area
    • D.4 Step III. Select Resolution
    • D.5 Acquire the Image
    • D.6 Calibration
      • D.6.a Editing the Step Tablet
      • D.6.b Calibration Settings
    • D.7 Other Options
  • Appendix E GS-710 Imaging Densitometer
    • E.1 GS-710 Acquisition Window
    • E.2 Step I. Select Application
    • E.3 Step II. Select Scan Area
    • E.4 Step III. Select Resolution
    • E.5 Calibration
      • E.5.a Editing the Step Tablet
      • E.5.b Calibration Settings
    • E.6 Acquire the Image
    • E.7 Other Options
  • Appendix F GS-800 Imaging Densitometer
    • F.1 GS-800 Acquisition Window
    • F.2 Step I. Select Application
    • F.3 Step II. Select Scan Area
    • F.4 Step III. Select Resolution
    • F.5 Calibration
      • F.5.a Step Tablet Values
      • F.5.b Other Calibration Settings
    • F.6 Acquire the Image
    • F.7 Other Options
  • Appendix G Fluor-S MultiImager
    • G.1 Fluor-S Acquisition Window
    • G.2 Step I. Select Application
    • G.3 Step II. Position/Focus
    • G.4 Step III. Set Exposure Time
    • G.5 Acquire the Image
    • G.6 Options
      • G.6.a Dark Subtraction Type
      • G.6.b Live Exposure Mode
      • G.6.c Save
      • G.6.d Imaging Area Size
      • G.6.e Auto-scale Transform
    • G.7 Other Features
  • Appendix H Fluor-S MAX MultiImager
    • H.1 Fluor-S MAX Acquisition Window
    • H.2 Step I. Select Application
    • H.3 Step II. Position/Focus
    • H.4 Step III. Set Exposure Time
    • H.5 Acquire the Image
    • H.6 Options
      • H.6.a Dark Subtraction Type
      • H.6.b Live Exposure Mode
      • H.6.c Save
      • H.6.d Imaging Area Size
      • H.6.e Auto-scale Transform
    • H.7 Other Features
  • Appendix I Personal Molecular Imager FX
    • I.1 Personal FX Acquisition Window
    • I.2 Step I. Select Scan Area
    • I.3 Step II. Select Resolution
    • I.4 Acquire the Image
    • I.5 Options
  • Appendix J Molecular Imager FX Family (FX Pro, FX Pro Plus and Molecular FX)
    • J.1 FX Acquisition Window
    • J.2 Step I. Select Application
      • J.2.a Selecting a Channel
      • J.2.b Selecting an Application
    • J.3 Step II. Select Scan Area
    • J.4 Step III. Select Resolution
    • J.5 Acquire the Image
    • J.6 Options
  • Appendix K VersaDoc
    • K.1 VersaDoc Acquisition Window
    • K.2 Step I. Select Application
      • K.2.a. Selecting a Channel
      • K.2.b. Selecting an Application
    • K.3 Step II. Position/Focus
    • K.4 Step III. Set Exposure Time
    • K.5 Acquire the Image
    • K.6 Options
      • K.6.a. Dark Subtraction Type
      • K.6.b. Save
      • K.6.c. Imaging Area Size
      • K.6.d. Auto-scale Transform
    • K.7 Other Features
  • Appendix L CrossPlatform File Exchange
    • L.1 Macintosh to PC
    • L.2 PC to Macintosh
  • Appendix M Other Features
    • M.1 Categories and Attributes
    • M.2 Gel Layout