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P/N 10002940 Rev C
Quantity One
®
User Guide for Version 4.6.3
Windows and Macintosh
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Quantity One User Guide
ii
Bio-Rad Technical Service Department
Phone:
(800) 424-6723
(510) 741-2612
Fax:
(510) 741-5802
E-mail:
LSG.TechServ.US@Bio-Rad.com 
Notice:
No part of this publication may be reproduced or transmitted in any form or by any 
means, electronic or mechanical, including photocopy, recording, or any information 
storage or retrieval system, without permission in writing from Bio-Rad.
Quantity One is a registered trademark of Bio-Rad Laboratories. The Discovery 
Series is a trademark of Bio-Rad Laboratories. All other trademarks and registered 
trademarks are of their respective companies. 
WASTE text engine © 1993–1997 Marco Piovanelli
Limitations of Liability:
Bio-Rad is not responsible for the misinterpretation of results obtained by following 
the instructions in this guide. Whenever possible, you should contact the Technical 
Services Department at Bio-Rad to discuss your results. As with all scientific studies, 
we recommend that you repeat your experiment at least once before making any 
significant conclusions for presentation or publication.
Copyright © 2006 by Bio-Rad Laboratories. All rights reserved.
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Table of Contents
iii
1. Introduction ........................................................................ 1-1
1.1.  Overview of Quantity One .............................................................................. 1-1
1.2.  Digital Data and Signal Intensity .................................................................... 1-2
1.3.  Gel Quality ...................................................................................................... 1-3
1.4.  Quantity One Workflow ................................................................................. 1-4
1.5.  Computer Requirements ................................................................................. 1-5
1.6.  Installation ...................................................................................................... 1-6
1.7.  Software License ............................................................................................ 1-9
1.8.  Downloading from the Internet .................................................................... 1-13
1.9.  Quantity One Basic ....................................................................................... 1-14
1.10.  Contacting Bio-Rad .................................................................................... 1-14
2. General Operation .............................................................. 2-1
2.1.  Menus and Toolbars ....................................................................................... 2-1
2.2.  File Commands ............................................................................................... 2-6
2.3.  Imaging Device Acquisition Windows ......................................................... 2-14
2.4.  Exit ................................................................................................................ 2-15
2.5.  Preferences .................................................................................................... 2-15
2.6.  User Settings ................................................................................................. 2-23
3. Viewing and Editing Images  ............................................. 3-1
3.1.  Magnifying and Positioning Tools ................................................................. 3-1
3.2.  Density Tools .................................................................................................. 3-5
3.3.  Showing and Hiding Overlays ........................................................................ 3-6
3.4.  Multi-Channel Viewer .................................................................................... 3-7
3.5.  3D Viewer ..................................................................................................... 3-10
3.6.  Image Stack Tool .......................................................................................... 3-13
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Quantity One User Guide
iv
3.7.  Colors ............................................................................................................ 3-14
3.8.  Transform ...................................................................................................... 3-17
3.9.  Resizing and Reorienting Images ................................................................. 3-23
3.10.  Whole-Image Background Subtraction ....................................................... 3-29
3.11.  Filtering Images .......................................................................................... 3-33
3.12.  Invert Data ................................................................................................... 3-39
3.13.  Text Overlays .............................................................................................. 3-39
3.14.  Erasing All Analysis from an Image ........................................................... 3-42
3.15.  Sort and Recalculate .................................................................................... 3-42
3.16.  Automation Manager .................................................................................. 3-42
4. Lanes  .................................................................................. 4-1
4.1.  Defining Lanes ................................................................................................ 4-1
4.2.  Lane-Based Background Subtraction .............................................................. 4-9
4.3.  Compare Lanes ............................................................................................. 4-13
4.4.  Lane-based Arrays ........................................................................................ 4-16
5. Bands .................................................................................. 5-1
5.1.  How Bands Are Identified and Quantified ..................................................... 5-2
5.2.  Band Detection ................................................................................................ 5-3
5.3.  Identifying and Editing Individual Bands ..................................................... 5-10
5.4.  Plotting Traces of Bands ............................................................................... 5-12
5.5.  Band Attributes ............................................................................................. 5-13
5.6.  Band Information .......................................................................................... 5-16
5.7.  Gauss-Modeling Bands ................................................................................. 5-18
5.8.  Irregularly Shaped Bands in Lanes ............................................................... 5-21
6. Standards and Band Matching .........................................  6-1
6.1.  Standards ......................................................................................................... 6-1
6.2.  Band Matching .............................................................................................. 6-13
6.3.  Quantity Standards ........................................................................................ 6-24
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Contents
v
7. Volume Tools ..................................................................... 7-1
7.1.  Creating a Volume .......................................................................................... 7-1
7.2.  Volume Labels ................................................................................................ 7-5
7.3.  Volume Features ............................................................................................. 7-7
7.4.  Moving, Copying, and Deleting Volumes ...................................................... 7-8
7.5.  Volume Standards ........................................................................................... 7-8
7.6.  Volume Background Subtraction ................................................................. 7-10
7.7.  Volume Arrays .............................................................................................. 7-12
8. Colony Counting ................................................................ 8-1
8.1.  Defining the Counting Region ........................................................................ 8-2
8.2.  Counting the Colonies .................................................................................... 8-3
8.3.  Displaying the Results .................................................................................... 8-4
8.4.  Making and Erasing Individual Colonies ....................................................... 8-5
8.5.  Using the Histogram to Distinguish Colonies ................................................ 8-6
8.6.  Ignoring a Region of the Dish ........................................................................ 8-8
8.7.  Saving/Resetting the Count ............................................................................ 8-9
8.8.  Saving to a Spreadsheet ................................................................................ 8-10
9
ReadyAgarose™ 96 Plus ................................................... 9-1
9.1.  ReadyAgarose Wizard .................................................................................... 9-1
10. EXQuest Spot Cutter  ....................................................... 10-1
10.1.  Calibration and setup .................................................................................. 10-2
10.2.  Manual Excision ......................................................................................... 10-6
10.3.  Lane/Volume Excision ............................................................................. 10-18
11. Differential Display and VNTRs ...................................... 11-1
11.1.  Differential Display .................................................................................... 11-1
11.2.  Variable Number Tandem Repeats ............................................................. 11-3
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Quantity One User Guide
vi
12. Reports ............................................................................. 12-1
12.1.  Report Window ........................................................................................... 12-1
12.2.  Lane and Match Reports ............................................................................. 12-5
12.3.  Band Types Report ...................................................................................... 12-6
12.4.  1-D Analysis Report .................................................................................... 12-8
12.5.  Similarity Comparison Reports ................................................................... 12-9
12.6.  Volume Analysis Report ........................................................................... 12-20
12.7.  Volume Regression Curve ........................................................................ 12-23
12.8.  VNTR Report ............................................................................................ 12-25
13. Printing and Exporting .................................................... 13-1
13.1.  Print Image .................................................................................................. 13-1
13.2.  Page Setup ................................................................................................... 13-1
13.3.  Print Settings ............................................................................................... 13-1
13.4.  Image Report ............................................................................................... 13-3
13.5.  Video Print .................................................................................................. 13-4
13.6.  Export to TIFF Image ................................................................................. 13-5
13.7.  Exporting a JPEG Image ............................................................................. 13-8
Appendix A.  
Gel Doc EQ ................................................................................ A-1
Appendix B.  
Gel Doc XR ................................................................................ B-1
Appendix C.  
ChemiDoc EQ ........................................................................... C-1
Appendix D.  
ChemiDoc XRS ......................................................................... D-1
Contents
vii
Appendix E.  
GS-800 Imaging Densitometer ................................................ E-1
Appendix F.  
Personal Molecular Imager FX ................................................ F-1
Appendix G.  
Molecular Imager FX Family (FX Pro, FX Pro Plus and Molecular 
FX) .............................................................................................  G-1
Appendix H.  
PharosFX Family (PharosFX and PharosFX Plus) ................ H-1
Appendix I.  
VersaDoc .................................................................................... I-1
Appendix J.  
Other Features .......................................................................... J-1
Appendix K.  
21 CFR Part 11 .......................................................................... K-1
Quantity One User Guide
viii
ix
Preface
1. About This Document
This user guide is designed to be used as a reference in your everyday use of Quantity 
One® Software. It provides detailed information about the tools and commands of 
Quantity One for the Windows and Macintosh platforms. Any platform differences in 
procedures and commands are noted in the text.
This guide assumes that you have a working knowledge of your computer operating 
system and its conventions, including how to use a mouse and standard menus and 
commands, and how to open, save, and close files. For help with any of these 
techniques, see the documentation that came with your computer.
This guide uses certain text conventions to describe specific commands and 
functions.
Some of the illustrations of menus and dialog boxes found in this manual are taken 
from the Windows version of the software, and some are taken from the Macintosh 
version. Both versions of a menu or dialog box will be shown only when there is a 
significant difference between the two.
Example
Indicates
File > Open
Choosing the Open command under the File menu.
Dragging
Positioning the cursor on an object and holding down 
the left mouse button while you move the mouse.
Ctrl+s
Holding down the Control key while typing the letter s.
Right-click/
Left-click/
Double-click
Clicking the right mouse button/
Clicking the left mouse button/
Clicking the left mouse button twice.
Quantity One User Guide
x
2. Bio-Rad Listens
The staff at Bio-Rad are receptive to your suggestions. Many of the new features and 
enhancements in this version of Quantity One are a direct result of conversations with 
our customers. Please let us know what you would like to see in the next version of 
Quantity One by faxing, calling, or e-mailing our Technical Services staff. You can 
also use Solobug (installed with Quantity One) to make software feature requests.
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