Quantity One® User Guide for Version 4.6.3 Windows and Macintosh P/N 10002940 Rev C Quantity One User Guide Bio-Rad Technical Service Department Phone: (800) 424-6723 (510) 741-2612 Fax: (510) 741-5802 E-mail: [email protected] 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. ii Table of Contents 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 iii Quantity One User Guide 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 iv Contents 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 ........................................................................................