Beckman Coulter COULTER EPICS XL User manual

COULTER®EPICS®XLTM Flow Cytometer
COULTER EPICS XL-MCLTM Flow Cytometer
SYSTEM IITM Software Getting Started
PN 4237238BA (October 2010)
Beckman Coulter, Inc.
250 S. Kraemer Blvd.
Brea, CA 92821
TM
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MED HIGH
FS
SS
AUX
FL4
FL3
FL1
FL2
®

WARNINGS AND PRECAUTIONS
READ ALL PRODUCT MANUALS AND CONSULT WITH BECKMAN COULTER-TRAINED PERSONNEL BEFORE ATTEMPTING
TO OPERATE INSTRUMENT. 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 YOUR BECKMAN COULTER REPRESENTATIVE.
BECKMAN COULTER, INC. 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.
HAZARDS AND OPERATIONAL PRECAUTIONS AND LIMITATIONS
WARNINGS, CAUTIONS, and IMPORTANTS alert you as follows:
WARNING - Can cause injury.
CAUTION - Can cause damage to the instrument.
IMPORTANT - Can cause misleading results.
WARNING Risk of operator injury if:
r All doors, covers and panels are not closed and secured in place prior to and during instrument operation.
r The integrity of safety interlocks and sensors is compromised.
r Instrument alarms and error messages are not acknowledged and acted upon.
r You contact moving parts.
r You mishandle broken parts.
r Doors, covers and panels are not opened, closed, removed and/or replaced with care.
r Improper tools are used for troubleshooting.
To avoid injury:
r Keep doors, covers and panels closed and secured in place while the instrument is in use.
r Take full advantage of the safety features of the instrument. Do not defeat safety interlocks and sensors.
r Acknowledge and act upon instrument alarms and error messages.
r Keep away from moving parts.
r Report any broken parts to your Beckman Coulter Representative.
r Open/remove and close/replace doors, covers and panels with care.
r Use the proper tools when troubleshooting.
CAUTION System integrity might be compromised and operational failures might occur if:
r This equipment is used in a manner other than specified. Operate the instrument as instructed in the Product Manuals.
r You introduce software that is not authorized by Beckman Coulter into your computer. Only operate your system’s
computer with software authorized by Beckman Coulter.
r You install software that is not an original copyrighted version. Only use software that is an original copyrighted
version to prevent virus contamination.
IMPORTANT If you purchased this product from anyone other than Beckman Coulter or an authorized Beckman Coulter
distributor, and, if 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.

iii
PN 4237238BA
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.
Issue BA, 10/10
SYSTEM II Software, Version 3.0.
Updates were made to the company corporate address.
Note: Changes that are part of the most recent revision are indicated in text by a bar in the
margin of the amended page.
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.

PN 4237238BA
iv
REVISION STATUS

PN 4237238BA v
CONTENTS
WARNINGS AND PRECAUTIONS
REVISION STATUS, iii
INTRODUCTION,xi
Description of Reporting Units, xiii
1 CONTROLS AND INDICATORS,11
Cytometer Ready and Laser On Indicators,12
Sample Flow Rate Indicators,13
Signal Amplitude Indicators,13
Operating Mode Buttons,14
Level Sense and Flow Indicators: XL-MCL Flow Cytometer,15
Level Sense and Flow Indicators: XL Flow Cytometer,15
Sample Stage Area,15
Computer,17
2 LEARNING THE BASICS,21
2.1 LEARNING THE BASIC OPERATING TECHNIQUES,21
2.2 USING THE SAMPLE STAGE,21
Test Tube and Sample Requirements,21
Putting a Tube on the Sample Stage,22
Removing a Tube from the Sample Stage,25
2.3 USING THE MCL (XL-MCL FLOW CYTOMETER ONLY),26
Carousels,26
Putting Sample Tubes in a Carousel,26
Putting a Carousel in the MCL,27
Removing a Carousel from the MCL,29
Bar-Code Labels, 210
Putting a Bar-Code Label on a Sample Tube, 210
2.4 USING THE MOUSE, 211
Selecting Screen Items, 211
Symbols for Selecting Menu Items, 211
Symbols for Selecting Screen Buttons, 212
2.5 MOVING BETWEEN SCREENS, 213
2.6 USING YOUR NETWORK WORKSTATION AND SERVER, 213
3 SOFTWARE OVERVIEW,31
3.1 APPLICATIONS MENU,31
Description of the Applications,31
Screen Features,31

PN 4237238BA
vi
CONTENTS
3.2 ACQUISITION APPLICATION,32
Acquisition Setup Screen Menu,32
Acquisition Protocol Menu,33
Acquisition Screen Buttons,33
Histogram Display Buttons,33
File Buttons,33
Acquisition Buttons,34
Display and Region Buttons,34
Output Options Window,35
Cytometer Control Windows,35
Counters and Stops Window,35
Signal Window,36
Discriminators Window,36
Color Compensation Window,36
3.3 LISTMODE APPLICATION,37
Listmode Setup Menu,37
Listmode Screen Buttons,38
Histogram Display Buttons,38
Replay Options Buttons,38
Output and Region Buttons,38
3.4 MULTIGRAPH APPLICATION,39
Multigraph Screen Menu,39
Multigraph Screen Buttons, 310
Histogram Display Buttons, 310
Mode Buttons, 310
Save and Print Buttons, 310
3.5 REPORTS APPLICATION,311
Reports Screen Menu, 311
3.6 QC APPLICATION, 312
QC Screen Menu, 312
3.7 UTILITIES APPLICATION, 313
Utilities Screen Menu, 313
3.8 POP-UP WINDOWS, 314
3.9 FILE MENU, 316
3.10 USING THE KEYBOARD, 317
Utility Keys, 317
Histogram Display Keys, 317
Acquisition Keys, 317
Selecting Menu Items with the Cursor Keys, 318
Keyboard Shortcuts/Hot Keys, 318

PN 4237238BA vii
CONTENTS
3.11 RESPONDING TO PROMPTS AND MESSAGES,319
Prompts, 319
Clearing the Prompt from the Screen, 319
Using the Default Information, 319
Entering Information, 319
Editing the Default or the Information You Type, 319
Messages, 320
Acknowledging a Message, 320
3.12 ADJUSTING CYTOMETER SETTINGS, 320
Acquisition Cytosettings Screen, 321
4 CREATING PROTOCOLS,41
4.1 WHAT IS A PROTOCOL?,41
4.2 CREATING AND EDITING PROTOCOLS,41
4.3 SELECTING SIGNALS,42
Naming Signals,42
Erasing Signals,43
Selecting and Assigning AUX,44
Editing AUX Parameter,45
Selecting and Assigning Ratio Parameter,45
Selecting and Assigning TIME Parameter,47
Activating PRISM in Acquisition,48
Activating PRISM in Listmode,48
4.4 DEFINING HISTOGRAMS,49
Assigning Parameters and Titles to Histograms,49
Erasing Parameters and Histograms, 411
Specifying Histogram Options, 411
Histogram Resolution, 412
Positives Analysis, 412
4.5 SPECIFYING FUNCTION OPTIONS, 413
4.6 SAVING OR UPDATING A PROTOCOL, 414
Saving a Protocol,414
5 USING REGIONS,51
5.1 REGION TYPES,51
Acquisition Regions,51
Region List,51
One-Parameter Histogram Regions,52
Numeric and Linear Regions,52
Two-Parameter Histogram Regions,52
Numeric and Rectilinear Regions,52
Quad-stat Region,53
Amorphous Region,53

PN 4237238BA
viii
CONTENTS
5.2 CHANGING THE CURSOR MODE,54
5.3 ASSIGNING REGIONS,54
Assigning Gates to Histograms,56
Assigning a Region as a Gate,57
Gating Equations,59
Sequential Gating,59
5.4 CELL-SEEKER (AUTOGATING) REGIONS, 510
Assigning Autogating Regions, 511
5.5 CELL-TRACKER REGIONS, 511
Assigning Cell-Tracker Regions, 512
5.6 PRISM EQUATION REGIONS, 513
Assigning Prism Equations, 514
5.7 LISTMODE GATING, 514
Assigning Listmode Gates,515
Activating Listmode Gating,515
Assigning Negative Listmode Gates, 515
5.8 PRIME REGIONS, 516
Assigning Prime Regions,516
5.9 MAPPING REGIONS, 516
Assigning Mapping Regions, 517
5.10 CALIBRATION REGIONS, 518
5.11 QC REGIONS, 519
Assigning a QC Region, 519
5.12 LOT NUMBER REGIONS, 520
6 CREATING PANELS,61
6.1 WHAT IS A PANEL?,61
6.2 PANEL PROTOCOL ASSIGNMENTS,62
Primary Assignment,63
Control Assignment,63
Secondary Assignment,63
Next Assignment,63
Passing Cytometer Settings in a Panel,63
Passing Regions in a Panel,64
Passing Region Names in a Panel,64
Gating in a Panel,64
Cell-Seeker (Autogating) Regions in a Panel,64
Passing Other Regions in a Panel,64

PN 4237238BA ix
CONTENTS
6.3 CREATING A PANEL,65
Selecting Protocols,65
Making Assignments and Ordering Protocols,66
Saving a Panel,67
Adding Panels,68
Adding Protocols,69
7 THE OPERATING SYSTEM,71
7.1 THE XL OR XL-MCL FLOW CYTOMETER AND THE MS-DOS®OPERATING SYSTEM,71
Restarting the Software from the MS-DOS Operating System,71
7.2 THE XL OR XL-MCL FLOW CYTOMETER AND MICROSOFT®WINDOWSTM
SOFTWARE,72
INDEX,INDEX-1
TRADEMARKS

PN 4237238BA
x
CONTENTS

PN 4237238BA xi
INTRODUCTION
This introductory section contains the following topics:
r Using your COULTER EPICS XL and XL-MCL Flow Cytometer Manuals
r About this Manual
r Conventions
r 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 User's Comment Card in the Reference manual to give us your comments about the
manual and ways to improve it.

PN 4237238BA
xii
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:
s Chapter 1, Controls and Indicators
Describes the parts of the instrument used during normal operation and how you
interact with them
s Chapter 2, Learning the Basics
Contains instructions for basic operating techniques, loading samples, using the MCL,
and using the mouse.
s Chapter 3, Software Overview
Contains illustrations, descriptions for each software screen and instructions for using
the screen buttons and keyboard.
s Chapter 4, Creating Protocols
Contains instructions on creating, editing and saving protocols, defining histograms,
creating regions, assigning gates and adjusting cytometer settings.
s Chapter 5, Using Regions
Contains information on region types and instructions for creating, assigning and editing
regions.
s Chapter 6, Creating Panels
Contains information on what panels and worklists are and how to use them to process
batches of samples.
s 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®WindowsTM and XL and XL-MCL
software.
s Index
Use the Index to easily locate specific information in this manual.

PN 4237238BA xiii
INTRODUCTION
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.
ëindicates a key (such as Û).
ë+ëindicates that the two keys listed (such as Þ+Ê) 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.
ëëindicates to press and release the first key listed then press and release the next key
listed. For example, YÛ.
File tt Save Select the Save item on the File menu.
[OKAY] Use the mouse to click on the screen button labeled [OKAY].
Éthrough ÔSpecial function keys.
Description of Reporting Units
Unless otherwise stated, all parameter units are shown in the US unit format (cells/µL)
throughout the manuals.

PN 4237238BA
xiv
INTRODUCTION
ICONS
Press and release the left mouse
button.
Press and release the right mouse button.
Move the mouse without
pressing either button.
Press and hold the left mouse
button while moving the mouse.
Press and hold the right
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.

PN 4237238BA 1-1
1
1CONTROLS AND INDICATORS
1.1 XL AND XL-MCL FLOW CYTOMETRY SYSTEM
®
TM
7029077D
TM
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MED HIGH
FS
SS
AUX
FL4
FL3
FL1
FL2
®
CYTOMETER
COMPUTER
WORKSTATION
MCL
OPTION
POWER
SUPPLY
MODULE

PN 4237238BA
1-2
CONTROLS AND INDICATORS
CYTOMETER INDICATOR PANELS
1.2 CYTOMETER INDICATOR PANELS
Cytometer Ready and Laser On Indicators
7021001A
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MEDHIGH
FS
SS
AUX
FL4
FL3
FL1
FL2
®
C
CYTOMETER
LASER
READY
ON
FS
SS
AUX
SAMPLE FLOW
LOW MED HIGH FL4
FL3
FL1
FL2
7021031A
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MED HIGH
FS
SS
AUX
FL4
FL1
FL2
FL3
Green means
Cytometer can
be put in an
operating mode
.
Green means
laser is on.

PN 4237238BA 1-3
CONTROLS AND INDICATORS
CYTOMETER INDICATOR PANELS 1
Sample Flow Rate Indicators
Signal Amplitude Indicators
7021043
A
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MED HIGH
FS
SS
AUX
FL4
FL1
FL2
FL3
Green shows the
sample flow rate.
7021042
A
FS
SS
AUX
FL4
FL1
FL2
FL3
If this indicator
is green, the
signal is
assigned to AUX. FORWARD
SCATTER SIDE SCATTER
AUXILIARY
FLUORESCENCE 1, 2, 3,
AND 4 (OPTIONAL)
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MED HIGH
FS
SS
AUX
FL4
FL1
FL2
FL3
7021030A
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.

PN 4237238BA
1-4
CONTROLS AND INDICATORS
CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER)
1.3 CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW
CYTOMETER)
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.
FLOW
CLEANSE
LOW
WASTE
FULL
SHEATH
LOW
7021044A
CYTOMETER
LASER
SAMPLE FLOW
LOW
READY
ON
MEDHIGH
FS
SS
AUX
FL4
FL3
FL1
FL2
®
C
7238136B
FLOW
Press to use the Run mode.
Press again for Idle mode.
The indicator color shows the
Cytometer operating mode:
Flashing
green
Idle mode.
Run mode
during
sample cycle.
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.
Glowing
(solid) green
Glowing
(solid) orange
Run mode.
Cytometer is
waiting for
you to insert
a sample tube.

PN 4237238BA 1-5
CONTROLS AND INDICATORS
CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER) 1
Level Sense and Flow Indicators: XL-MCL Flow Cytometer
Level Sense and Flow Indicators: XL Flow Cytometer
Sample Stage Area
7021032A
Red symbol means a
reagent container needs
refilling or the waste
container needs emptying.
CLEANSE
LOW
WASTE
FULL
SHEATH
LOW FLOW
Green symbol means
sample is going through
the flow cell.
7021201A
CLEANSE
PRIME
RUN
LEVEL
SENSE
FLOW
SHEATH
LOW
WASTE
FULL
CLEANSE
LOW
Red means a reagent
container needs refilling
or the waste container
needs emptying.
DOOR HANDLE 7021037A

PN 4237238BA
1-6
CONTROLS AND INDICATORS
MCL (MULTI-TUBE CAROUSEL LOADER)
1.4 MCL (MULTI-TUBE CAROUSEL LOADER)
1.5 WORKSTATION
7021069A
Press to open
the MCL. The door
opens automaticall
y
.
Use the KEYBOARD and
MOUSE to communicate
with the system.
MONITOR
COMPUTER
MONITOR
CONTROLS
7238191
B