Instructions for Use Kaluza Analysis Flow Cytometry Software A75667AD January 2014 Manufactured by Beckman Coulter, Inc. 250 S. Kraemer Blvd. Brea, CA 92821 U.S.A. Kaluza Analysis Software Instructions for Use PN A75667AD ( January 2014) Beckman Coulter, the stylized logo and Kaluza are trademarks of Beckman Coulter, Inc and are registered in the USPTO Windows®, Windows Vista®, Excel®, and PowerPoint® are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. HASP® is a registered trademark of SafeNet, Inc. Oki® is a registered trademark of Oki Electric Industry Co., Ltd. Tesla® is a registered trademark of Nvidia, Inc. in the U.S. and/or other countries. Copyright © 1990-2007 Info-ZIP. All rights reserved. Info- ZIP retains the right to use the names "Info-ZIP," "Zip," "UnZip," "UnZipSFX," "WiZ," "Pocket UnZip," "Pocket Zip," and "MacZip" for its own source and binary releases. The definitive version of the Info-ZIP license document should be available at: ftp://ftp.info-zip.org/pub/infozip/license.html indefinitely and a copy at: http://www.info-zip.org/pub/infozip/license.html. All other trademarks, service marks, products, or services are trademarks or registered trademarks of their respective holders. © 2009 - 2014 Beckman Coulter, Inc. Find us on the World Wide Web at: www.beckmancoulter.com Made in USA Printed in USA Revision History This document applies to the latest software listed and higher versions. When a subsequent software version changes the information in this document, a new issue will be released to the Beckman Coulter website. For labeling updates, go to www.beckmancoulter.com and download the most recent manual or system help for your instrument. Initial Issue A, 09/2009 Software Version 1.0 Issue AB, 06/2010 Software Version 1.1 • Updated the following sections in the Introduction to Kaluza Analysis Software chapter: Application Menu Options Basic Editing for Plots, and Sheet Items Color Precedence Pane Components of the Main Workspace File/Protocol File Compatibility System Requirements • Updated the following sections in the Data Analysis chapter: Accounting for Autofluorescence Applying a Protocol to a Raw Data Set Choosing Scale Type Establishing Color Precedence of Gates Gate Statistics Table Generating Compensation and Autofluorescence Vector Values Importing a Compensation File Kaluza File Type Summary Merge Data Sets Overlay Plots Setting Up Statistics Saving a Compensation File Setting Up Radar Plots Setting Up Tree Plots Updating Content within the Parameters Pane Using Kaluza with Other Applications Using the Coloring Menu Viewing Gate Logic • Added Appendix A, Statistics. • Added Appendix B, Quick Reference Sheet. • Added the Index. Issue AC, 09/2011 Software Version 1.2 Complete revision; therefore, change bars are not applicable. A75667AD iii Revision History Issue AD, 01/2014 Software Version 1.3 Change bars indicate updated or new content. Sections containing change bars are as follows: • Chapter 1, Introduction to Kaluza Analysis Software: — Overview — Getting Started — Main Workspace — Selecting Sheet Items • Chapter 2, Data Analysis — Kaluza Analysis Files — Protocols — Composite Protocols — Plots & Tables — Gates & Tools — Parameters — Compensation — Using Kaluza Analysis With Other Applications • Chapter 3, Sheet Setup — Using Sheets — Using the Sheet Tab Bar — Report Sheet • APPENDIX A, Statistics • APPENDIX B, Quick Reference Sheet • APPENDIX C, Frequently Asked Questions • Added APPENDIX D, Troubleshooting iv A75667AD Safety Notice Read all product manuals and consult with Beckman Coulter-trained personnel before attempting to use this product. Do not attempt to perform any procedure before carefully reading all instructions. Always follow product labeling and manufacturer’s recommendations. If in doubt as to how to proceed in any situation, contact Beckman Coulter. Product Alerts WARNING This computer program is protected by international copyright and patent laws. Unauthorized copying, use, distribution, transfer, or sale is a violation of those laws that may result in civil or criminal penalties. This computer program may also be subject to additional restrictions contained in a license granted by Beckman Coulter, Inc. to the authorized user of this computer program or to the authorized owner or other authorized user of the system onto which this computer program is installed. Any violation of the license provisions may result in additional civil penalties, including an injunction and damages. Please refer to the computer program or system agreement or to the computer program or system documentation for the terms and conditions of that license. CAUTION If you purchased this product from anyone other than Beckman Coulter or an authorized Beckman Coulter distributor, and it is not presently under a Beckman Coulter service maintenance agreement, Beckman Coulter cannot guarantee that the product is fitted with the most current mandatory engineering revisions or that you will receive the most current information bulletins concerning the product. If you purchased this product from a third party and would like further information concerning this topic, call your Beckman Coulter Representative. A75667AD v Safety Notice Product Alerts vi A75667AD Contents Revision History, iii Safety Notice,v Introduction to Kaluza Analysis,1-1 Overview,1-1 Product Description,1-1 Distinguishing Features,1-1 Radial Menus,1-1 Tree Plot,1-2 Comparison Plot,1-3 Radar Plots ,1-3 Radar Plot with Gates,1-5 Logicle Scale,1-5 Interactive Report Sheet,1-6 Getting Started,1-6 File/ Protocol File Compatibility,1-6 System Requirements,1-6 Launching Kaluza Analysis Software,1-7 Command-line Switches to Kaluza Analysis,1-7 Using the License Key,1-8 Setting-Up a Computer Using a Single License Key,1-8 Setting-Up Computers Using a Network License Key,1-8 License Key Troubleshooting,1-9 User Preferences and Security,1-9 Components of the Main Workspace,1-10 Tooltips,1-11 Warning and Information Messages,1-11 Right-Click Options,1-12 Using Radial Menus,1-12 Drag and Drop,1-13 Pop-up Menu Set-Up,1-13 Indication of Option Availability,1-14 System Performance,1-14 Main Workspace,1-14 Application Menu,1-14 vii Contents Application Menu Options,1-15 Quick-Access Toolbar,1-22 Application Title Bar,1-23 Analysis List,1-24 Multi-Selecting Files,1-26 Importing Files by Dragging into Analysis List,1-27 Changing the Sequence of Analysis List Rows,1-28 Replacing or Importing a Data Set or Protocol into an Analysis List Row,1-28 Applying Data Sets to a Composite or Compensation Composite File,1-29 Clear Analysis List,1-30 Save Analysis List,1-30 Attributes Panes,1-31 Attributes Pane,1-32 Parameters Pane,1-32 Compensation Pane,1-33 Color Precedence Pane,1-33 Display Options for the Analysis List and Attributes Pane,1-34 Hiding a Component Pane,1-34 Displaying a Component Pane,1-35 Selecting the Data Set in a Composite,1-36 Hiding the Attributes Pane,1-36 Displaying the Attributes Pane,1-37 Resizing the Analysis List or Attributes Panes,1-37 Resizing Attribute Component Panes,1-37 Ribbon,1-38 Switching Active Ribbon Tabs,1-38 Hiding the Ribbon Toolbar,1-38 Restoring the Ribbon Toolbar,1-38 Using the Ribbon Toolbars,1-38 Plots & Tables Tab,1-39 Gates & Tools Tab,1-39 Edit Tab,1-40 Page Layout Tab,1-41 Sheet Tab Bar,1-42 Basic Editing for Plots, Gates, and Sheet Items,1-42 Selecting Sheet Items,1-44 Data Analysis,2-1 Kaluza Analysis Files,2-1 Protocols,2-2 Creating a New Protocol,2-2 Saving a Protocol,2-3 Saving an Analysis,2-4 Applying a Protocol to a Raw Data Set,2-4 Resolving Parameter Mismatch,2-5 Applying a Different Protocol to an Analysis Entry,2-6 viii Contents Composite Protocols,2-6 Creating a New Composite Protocol,2-6 Saving a Composite Analysis,2-7 Setting Up a Composite Protocol,2-8 Add All Plots ,2-8 Overlay Plots in a Composite Protocol,2-8 Changing the Data Set Associated with a Plot in a Composite Protocol,2-8 Gating in Composite Protocol,2-9 Copying Compensation to Other Data Sets,2-10 Saving a Composite Protocol,2-11 Arranging Data Sets,2-11 Freeform Arrangement,2-12 By Data Set Arrangement,2-12 Plots & Tables,2-13 Histograms,2-13 Setting Up Histograms,2-13 Merged Data Histogram,2-15 Comparison Plots,2-16 Setting Up Comparison Plots,2-17 Dot, Density, and Contour Plots,2-21 Dot Plot,2-21 Density Plot,2-21 Contour Plot,2-22 Setting Up Dot, Density, and Contour Plots,2-22 Tree Plots,2-25 Setting Up Tree Plots,2-25 Radar Plots,2-28 Gating on a Radar Plot and Population Statistics,2-29 Setting Up Radar Plots,2-29 Overlay Plots,2-29 Setting Up Overlay Plots,2-31 Overlay Marker,2-33 Add All Plots,2-35 Gate Statistics Table,2-36 Information Table,2-38 Adding Plots to the Plot Sheet,2-41 Plot Set-Up,2-41 Editing Plots,2-41 Setting Up Statistics,2-42 Setting Up Plot Display,2-44 Using the Gates & Tools Plot Radial Menu,2-47 Setting Up Plot Data,2-49 Using the Coloring Menu,2-50 Gates & Tools,2-53 Viewing Gate Logic,2-54 Linear Gates,2-54 Quadrant Gates,2-55 Hinged Quadrant Gates,2-56 ix Contents Polygon Gates,2-57 Freehand Gates,2-58 Rectangle Gates,2-59 Ellipse Gates,2-60 Boolean Gates,2-60 Setting Up Gates,2-63 Editing Gates,2-63 Setting Up Gate Display,2-64 Adding a New Gate,2-67 Data Menu,2-67 Resizing, Reshaping, and Moving Gates,2-71 Methods for Applying Gates to Plots,2-71 Establishing Color Precedence of Gates,2-72 Tools,2-77 Annotation Tool,2-78 Overlay Marker,2-78 Selection Tool,2-78 Parameters,2-79 Changing the Parameters Pane Display ,2-80 Updating