COULTER EPICS XL-MCL™ and EPICS XL Flow Cytometer System II Software Getting Started

LEGAL NOTICES

READ ALL PRODUCT MANUALS AND CONSULT WITH COULTER-TRAINED PERSONNEL BEFORE ATTEMPTING TO OPERATE INSTRUMENT.

HAZARDS AND OPERATIONAL PRECAUTIONS AND LIMITATIONS WARNINGS, CAUTIONS, and IMPORTANTS alert you as follows: WARNING CAUTION IMPORTANT

-

Might cause injury. Might cause damage to the instrument. Might cause misleading results.

CAUTION System integrity might be compromised and operational failures might occur if:

This equipment is used in a manner other than specified. Operate the instrument as instructed in the Product Manuals.

You introduce software that is not authorized by Coulter into your computer. Only operate your system’s computer with software authorized by Coulter.

You install software that is not an original copyrighted version. Only use software that is an original copyrighted version to prevent virus contamination.

Coulter Corporation urges its customers to comply with all national health and safety standards such as the use of barrier protection. This may include, but it is not limited to, protective eyewear, gloves, and suitable laboratory attire when operating or maintaining this or any other automated laboratory analyzer. IMPORTANT If you purchased this product from anyone other than Coulter or an authorized Coulter distributor, and, if it is not presently under a Coulter service maintenance agreement, Coulter cannot guarantee that the product is fitted with the most current mandatory engineering revisions or that you will receive the most current informational bulletins concerning the product. If you purchased this product from a third party and would like further information concerning this topic, call Coulter Corporation or its distributor.

REVISION STATUS

Issue A Initial Issue, 1/96 SYSTEM II Software, Version 1.0. Initial issue for customer distribution. Issue B, 12/98 Complete revision. SYSTEM II Software, Version 3.0. Includes new quality control features, patient report export feature, and user-defined run time reports.

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.

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CONTENTS

LEGAL NOTICES, ii REVISION STATUS, iii INTRODUCTION, xi USING YOUR XL AND XL-MCL FLOW CYTOMETER MANUALS, xi ABOUT THIS MANUAL, xii CONVENTIONS, xiii Description of Reporting Units, xiii ICONS, xiv 1

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CONTROLS AND INDICATORS, 1 1.1

XL AND XL-MCL FLOW CYTOMETRY SYSTEM, 1

1.2

CYTOMETER INDICATOR PANELS, 2 Cytometer Ready and Laser On Indicators, 2 Sample Flow Rate Indicators, 3 Signal Amplitude Indicators, 3

1.3

CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER), 4 Operating Mode Buttons, 4 Level Sense and Flow Indicators: XL-MCL Flow Cytometer, 5 Level Sense and Flow Indicators: XL Flow Cytometer, 5 Sample Stage Area, 5

1.4

MCL (MULTI-TUBE CAROUSEL LOADER), 6

1.5

WORKSTATION, 6 Computer, 7

1.6

POWER SUPPLY, 8

1.7

PRINTER (OPTIONAL), 8

LEARNING THE BASICS, 9 2.1

LEARNING THE BASIC OPERATING TECHNIQUES, 9

2.2

USING THE SAMPLE STAGE, 9 Test Tube and Sample Requirements, 9 Putting a Tube on the Sample Stage, 10 Removing a Tube from the Sample Stage, 13

2.3

USING THE MCL (XL-MCL FLOW CYTOMETER ONLY), 14 Carousels, 14 Putting Sample Tubes in a Carousel, 14 Putting a Carousel in the MCL, 14 Removing a Carousel from the MCL, 16 Bar-Code Labels, 17

v

CONTENTS

Putting a Bar-Code Label on a Sample Tube, 17

3

vi

2.4

USING THE MOUSE, 18 Selecting Screen Items, 18 Symbols for Selecting Menu Items, 18 Symbols for Selecting Screen Buttons, 19

2.5

MOVING BETWEEN SCREENS, 20

2.6

USING YOUR NETWORK WORKSTATION AND SERVER, 20

SOFTWARE OVERVIEW, 21 3.1

APPLICATIONS MENU, 21 Description of the Applications, 21 Screen Features, 21

3.2

ACQUISITION APPLICATION, 22 Acquisition Setup Screen Menu, 22 Acquisition Protocol Menu, 23 Acquisition Screen Buttons, 23 Histogram Display Buttons, 23 File Buttons, 23 Acquisition Buttons, 24 Display and Region Buttons, 24 Output Options Window, 25 Cytometer Control Windows, 25 Counters and Stops Window, 25 Signal Window, 26 Discriminators Window, 26 Color Compensation Window, 26

3.3

LISTMODE APPLICATION, 27 Listmode Setup Menu, 27 Listmode Screen Buttons, 28 Histogram Display Buttons, 28 Replay Options Buttons, 28 Output and Region Buttons, 28

3.4

MULTIGRAPH APPLICATION, 29 Multigraph Screen Menu, 29 Multigraph Screen Buttons, 30 Histogram Display Buttons, 30 Mode Buttons, 30 Save and Print Buttons, 30

3.5

REPORTS APPLICATION, 31 Reports Screen Menu, 31

3.6

QC APPLICATION, 32 QC Screen Menu, 32

3.7

UTILITIES APPLICATION, 33 Utilities Screen Menu, 33

3.8

POP-UP WINDOWS, 34

3.9

FILE MENU, 36 PN 4237238B (December 1998)

CONTENTS

3.10 USING THE KEYBOARD, 37 Utility Keys, 37 Histogram Display Keys, 37 Acquisition Keys, 37 Selecting Menu Items with the Cursor Keys, 38 Keyboard Shortcuts/Hot Keys, 38 3.11 RESPONDING TO PROMPTS AND MESSAGES, 39 Prompts, 39 Clearing the Prompt from the Screen, 39 Using the Default Information, 39 Entering Information, 39 Editing the Default or the Information You Type, 39 Messages, 40 Acknowledging a Message, 40 3.12 ADJUSTING CYTOMETER SETTINGS, 40 Acquisition Cytosettings Screen, 41 4

5

CREATING PROTOCOLS, 43 4.1

WHAT IS A PROTOCOL?, 43

4.2

CREATING AND EDITING PROTOCOLS, 43

4.3

SELECTING SIGNALS, 44 Naming Signals, 44 Erasing Signals, 45 Selecting and Assigning AUX, 46 Editing AUX Parameter, 47 Selecting and Assigning Ratio Parameter, 47 Selecting and Assigning TIME Parameter, 49 Activating PRISM in Acquisition, 50 Activating PRISM in Listmode, 50

4.4

DEFINING HISTOGRAMS, 51 Assigning Parameters and Titles to Histograms, 51 Erasing Parameters and Histograms, 53 Specifying Histogram Options, 53 Histogram Resolution, 54 Positives Analysis, 54

4.5

SPECIFYING FUNCTION OPTIONS, 55

4.6

SAVING OR UPDATING A PROTOCOL, 56 Saving a Protocol, 56

USING REGIONS, 57 5.1

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REGION TYPES, 57 Acquisition Regions, 57 Region List, 57 One-Parameter Histogram Regions, 58 Numeric and Linear Regions, 58

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CONTENTS

Two-Parameter Histogram Regions, 58 Numeric and Rectilinear Regions, 58 Quad-stat Region, 59 Amorphous Region, 59 5.2

CHANGING THE CURSOR MODE, 60

5.3

ASSIGNING REGIONS, 60 Assigning Gates to Histograms, 61 Assigning a Region as a Gate, 62 Gating Equations, 64 Sequential Gating, 64

5.4

CELL-SEEKER (AUTOGATING) REGIONS, 65 Assigning Autogating Regions, 66

5.5

CELL-TRACKER REGIONS, 66 Assigning Cell-Tracker Regions, 66

5.6

PRISM EQUATION REGIONS, 67 Assigning Prism Equations, 67

5.7

LISTMODE GATING, 68 Assigning Listmode Gates, 68 Activating Listmode Gating, 69 Assigning Negative Listmode Gates, 69

5.8

PRIME REGIONS, 69 Assigning Prime Regions, 69

5.9

MAPPING REGIONS, 70

5.10 CALIBRATION REGIONS, 71 5.11 QC REGIONS, 71 Assigning a QC Region, 72 5.12 LOT NUMBER REGIONS, 72 6

viii

CREATING PANELS, 73 6.1

WHAT IS A PANEL?, 73

6.2

PANEL PROTOCOL ASSIGNMENTS, 74 Primary Assignment, 75 Control Assignment, 75 Secondary Assignment, 75 Next Assignment, 75 Passing Cytometer Settings in a Panel, 75 Passing Regions in a Panel, 76 Passing Region Names in a Panel, 76 Gating in a Panel, 76 Cell-Seeker (Autogating) Regions in a Panel, 76 Passing Other Regions in a Panel, 76

6.3

CREATING A PANEL, 77 Selecting Protocols, 77 Making Assignments and Ordering Protocols, 78 PN 4237238B (December 1998)

CONTENTS

Saving a Panel, 79 Adding Panels, 80 Adding Protocols, 81 7

THE OPERATING SYSTEM, 83 7.1

THE XL OR XL-MCL FLOW CYTOMETER AND THE MS-DOS® OPERATING SYSTEM, 83 Restarting the Software from the MS-DOS Operating System, 83

7.2

THE XL OR XL-MCL FLOW CYTOMETER AND MICROSOFT® WINDOWS™ SOFTWARE, 84

INDEX, 85 TRADEMARKS

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CONTENTS

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INTRODUCTION

This introductory section contains the following topics:

Using your COULTER EPICS XL and XL-MCL Flow Cytometer Manuals

About this Manual

Conventions

Icons.

USING YOUR XL AND XL-MCL FLOW CYTOMETER MANUALS Use the Reference manual for in-depth information on the principles of flow cytometry, information about what your system does, the methods it uses, its specifications, and information on installation, safety, and system options. Use the Getting Started manual to become familiar with the controls and indicators for your system and to learn about protocols, regions, panels, and the basic skills you need to operate the system. This manual also has an overview of the software. Use the Operator’s Guide for the day-to-day running of your instrument. Go through the detailed step-by-step procedures of startup, quality control (QC), running samples, analyzing data, printing reports, reviewing QC data, and shutdown. Use the Data Management manual for instructions on how to export, save, copy, move, archive, and delete files. It also has information about the types of files your system creates and uses, instructions for working with QC features, and instructions for setting up the report template that you use to create your patient reports. Use the Special Procedures and Troubleshooting manual to clean, replace, or adjust a component of the instrument. The Troubleshooting tables and error messages are at the back of the manual. Use the Operating Summary as a quick reference for basic procedures. Use the Master Index to easily locate a topic in any of your manuals. Use the User's Comment Card in the Reference manual to give us your comments about the manual and ways to improve it.

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INTRODUCTION

ABOUT THIS MANUAL Your EPICS XL and XL-MCL Flow Cytometer Getting Started manual has information on the skills and concepts you need to learn before operating the instrument. It also contains an overview of the system software. This information is organized as follows:

xii

Chapter 1, Controls and Indicators Describes the parts of the instrument used during normal operation and how you interact with them.

Chapter 2, Learning the Basics Contains instructions for basic operating techniques, loading samples, using the MCL, and using the mouse.

Chapter 3, Software Overview Contains illustrations, descriptions for each software screen and instructions for using the screen buttons and keyboard.

Chapter 4, Creating Protocols Contains instructions on creating, editing and saving protocols, defining histograms, creating regions, assigning gates and adjusting cytometer settings.

Chapter 5, Using Regions Contains information on region types and instructions for creating, assigning and editing regions.

Chapter 6, Creating Panels Contains information on what panels and worklists are and how to use them to process batches of samples.

Chapter 7, The Operating System Contains instructions on starting the XL and XL-MCL software from the MS-DOS® operating system and warnings about Microsoft® Windows™ and XL and XL-MCL software.

Index Use the Index to easily locate specific information in this manual.

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CONVENTIONS

CONVENTIONS This manual uses the following conventions: Throughout this manual your EPICS XL or XL-MCL flow cytometer is referred to as the system. Italics indicate screen messages. Bold indicates a menu item.

Courier font indicates text you have to type using the keyboard. indicates a key (such as Enter ). + indicates that the two keys listed (such as Alt + F2 ) are linked for a specific function and must be pressed in this sequence: 1.

Press down on the first key listed and while continuing to press it, press down on the second key listed.

2.

Release both keys at the same time.

indicates to press and release the first key listed then press and release the next key listed. For example, Y Enter .

F1

File  Save

Select the Save item on the File menu.

[OKAY]

Use the mouse to click on the screen button labeled [OKAY].

through F12

Special function keys.

Description of Reporting Units Unless otherwise stated, all parameter units are shown in the US unit format (cells/µL) throughout the manuals.

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INTRODUCTION

ICONS Press and release the left mouse button.

Move the mouse without pressing either button.

Press and hold the right mouse button while moving the mouse.

Press and release the right mouse button.

Press and hold the left mouse button while moving the mouse. Operational check.

Turn off the system at the computer.

Turn on the system at the computer.

Power Supply.

No fluid.

Close the Power Supply door.

Open the Power Supply door.

Call your Coulter Representative.

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CONTROLS AND INDICATORS 1

1.1

XL AND XL-MCL FLOW CYTOMETRY SYSTEM CONTROLS AND 1 INDICATORS

COMPUTER WORKSTATION CYTOMETER CYTOMETER

FS

READY

SS

LASER

ON

SAMPLE FLOW

AUX

FL1 FL2

LOW MED HIGH

FL3 FL4

®

MCL OPTION

TM

TM

POWER SUPPLY MODULE

7029077D

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®

1

CONTROLS AND INDICATORS

1.2

CYTOMETER INDICATOR PANELS CYTOMETER

READY

LASER

ON

FS SS

AND INDICATORS 1 CONTROLS

AUX

FL1

SAMPLE FLOW

FL2

LOW MED HIGH

FL3 FL4

CYTOMETER READY

LASER

FS SS

ON

SAMPLE FLOW

LOW MED HIGH

AUX

FL1 FL2

FL3 FL4

®

C 7021001A

Cytometer Ready and Laser On Indicators

Green means laser is on.

CYTOMETER

READY

FS

LASER

ON

SS AUX

SAMPLE FLOW LOW MED HIGH

FL1 FL2 FL3 FL4

Green means Cytometer can be put in an operating mode.

7021031A

2

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CYTOMETER INDICATOR PANELS

Sample Flow Rate Indicators CYTOMETER

READY

FS

LASER

ON

SS AUX

LOW

MED

FL1 FL2 FL3 HIGH FL4

CONTROLS AND 1 INDICATORS

SAMPLE FLOW

7021043A

Green shows the sample flow rate.

Signal Amplitude Indicators If this indicator is green, the signal is assigned to AUX.

FORWARD SIDE SCATTER SCATTER

FS

AUXILIARY FLUORESCENCE 1, 2, 3, AND 4 (OPTIONAL)

SS AUX

FL1 FL2 FL3 FL4

7021042A

CYTOMETER LASER

READY

FS

ON

SS AUX

FL1

SAMPLE FLOW

FL2 FL3

LOW MED HIGH

FL4

The indicators show the intensity of signals that particles generate during sample analysis.

Low, off-scale signals are yellow.

On-scale signals are green.

High, off-scale signals are red. 7021030A

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CONTROLS AND INDICATORS

CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER)

AND INDICATORS 1 CONTROLS

1.3

SHEATH LOW

WASTE FULL

CLEANSE LOW

FLOW

CYTOMETER READY

FS SS

LASER

ON

SAMPLE FLOW LOW MED HIGH

AUX

FL1

FL2

FL3 FL4

®

C 7021044A

Operating Mode Buttons The XL-MCL flow cytometer is shown in this figure. The information also applies to the XL flow cytometer except there is no AUTO button. You must have the Acquisition Run screen displayed to use these buttons. Press to use the Run mode. Press again for Idle mode. The indicator color shows the Cytometer operating mode: Glowing (solid) green

Run mode. Cytometer is waiting for you to insert a sample tube.

Flashing green

Idle mode.

Glowing (solid) orange

Run mode during sample cycle.

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4

FLOW

XL-MCL flow cytometer only (Shown). Press to use the optional Automatic mode. Press again to use the Manual mode. Glowing (solid) green indicator means the Cytometer is in the Auto mode and a carousel is in the MCL.

Press to flush the flow cell with sheath fluid. Data acquisition pauses until the prime cycle is done. During the 10-second cycle, indicator is green. Press to flush the flow cell with cleaning agent. During the 60-second cycle, indicator is green. There must not be a tube on the sample stage.

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CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL)

Level Sense and Flow Indicators: XL-MCL Flow Cytometer WASTE FULL

SHEATH LOW

CLEANSE LOW

CONTROLS AND 1 INDICATORS

Red symbol means a reagent container needs refilling or the waste container needs emptying.

FLOW

Green symbol means sample is going through the flow cell. 7021032A

Level Sense and Flow Indicators: XL Flow Cytometer

Red means a reagent container needs refilling or the waste container needs emptying.

LEVEL SENSE SHEATH LOW WASTE FULL CLEANSE LOW FLOW

RUN PRIME

CLEANSE

7021201A

Sample Stage Area

DOOR HANDLE

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7021037A

5

CONTROLS AND INDICATORS

MCL (MULTI-TUBE CAROUSEL LOADER)

AND INDICATORS 1 CONTROLS

1.4

Press to open the MCL. The door opens automatically.

7021069A

1.5

WORKSTATION MONITOR

MONITOR CONTROLS

COMPUTER Use the KEYBOARD and MOUSE to communicate with the system.

7238191B

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WORKSTATION

Computer Switch turns the XL or XL-MCL Cytometer on or off, not just the computer. The Cytometer does not have a separate on/off switch.

CONTROLS AND 1 INDICATORS

Locks the keyboard.

7238192B

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