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Beckman Coulter COULTER EPICS XL Getting Started

Beckman Coulter COULTER EPICS XL Getting Started

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

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Summary of Contents for Beckman Coulter COULTER EPICS XL

  • Page 1 ® ® COULTER EPICS Flow Cytometer COULTER EPICS XL-MCL Flow Cytometer SYSTEM II Software Getting Started CYTOMETER READY LASER SAMPLE FLOW MED HIGH ® PN 4237238BA (October 2010) Beckman Coulter, Inc. 250 S. Kraemer Blvd. Brea, CA 92821...

  • Page 2: Warnings And Precautions

    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.

  • Page 3: Revision Status

    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.
  • Page 4 REVISION STATUS PN 4237238BA...

  • Page 5: Table Of Contents

    CONTENTS WARNINGS AND PRECAUTIONS REVISION STATUS, iii INTRODUCTION, xi Description of Reporting Units, xiii 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...
  • Page 6 CONTENTS 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...
  • Page 7 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...
  • Page 8 CONTENTS CHANGING THE CURSOR MODE, 54 ASSIGNING REGIONS, 54 Assigning Gates to Histograms, 56 Assigning a Region as a Gate, 57 Gating Equations, 59 Sequential Gating, 59 CELL-SEEKER (AUTOGATING) REGIONS, 510 Assigning Autogating Regions, 511 CELL-TRACKER REGIONS, 511 Assigning Cell-Tracker Regions, 512 PRISM EQUATION REGIONS, 513...
  • Page 9 CONTENTS CREATING A PANEL, 65 Selecting Protocols, 65 Making Assignments and Ordering Protocols, 66 Saving a Panel, 67 Adding Panels, 68 Adding Protocols, 69 THE OPERATING SYSTEM, 71 ® THE XL OR XL-MCL FLOW CYTOMETER AND THE MS-DOS OPERATING SYSTEM, 71 Restarting the Software from the MS-DOS Operating System, 71 ®...
  • Page 10 CONTENTS PN 4237238BA...

  • Page 11: Introduction

    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.
  • Page 12 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: Chapter 1, Controls and Indicators Describes the parts of the instrument used during normal operation and how you interact with them...

  • Page 13: Description Of Reporting

    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. ë...
  • Page 14 INTRODUCTION ICONS Press and release the left mouse Press and release the right mouse button. button. Move the mouse without Press and hold the left mouse pressing either button. button while moving the mouse. Press and hold the right Operational check. mouse button while moving the mouse.

  • Page 15: Controls And Cytometer Ready And Laser On

    CONTROLS AND INDICATORS XL AND XL-MCL FLOW CYTOMETRY SYSTEM COMPUTER WORKSTATION CYTOMETER CYTOMETER READY LASER SAMPLE FLOW MED HIGH ® OPTION POWER SUPPLY MODULE ® 7029077D PN 4237238BA...
  • Page 16 CONTROLS AND INDICATORS CYTOMETER INDICATOR PANELS CYTOMETER INDICATOR PANELS CYTOMETER READY LASER SAMPLE FLOW LOW MED HIGH CYTOMETER READY LASER SAMPLE FLOW MEDHIGH ® 7021001A Cytometer Ready and Laser On Indicators CYTOMETER READY Green means LASER Cytometer can be put in an operating mode.

  • Page 17: Sample Flow Rate

    CONTROLS AND INDICATORS CYTOMETER INDICATOR PANELS Sample Flow Rate Indicators CYTOMETER READY LASER SAMPLE FLOW HIGH 7021043A Green shows the sample flow rate. Signal Amplitude Indicators If this indicator is green, the signal is FORWARD SIDE assigned to AUX. SCATTER SCATTER AUXILIARY FLUORESCENCE 1, 2, 3,...

  • Page 18: Operating Mode

    CONTROLS AND INDICATORS CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER) CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER) SHEATH WASTE CLEANSE FLOW FULL CYTOMETER READY LASER SAMPLE FLOW MED HIGH ® 7021044A Operating Mode Buttons The XL-MCL flow cytometer is shown in this figure.

  • Page 19: Level Sense And Flow Indicators: Xl-Mcl Flow

    CONTROLS AND INDICATORS CYTOMETER CONTROL PANEL AND SAMPLE STAGE AREA (XL-MCL FLOW CYTOMETER) Level Sense and Flow Indicators: XL-MCL Flow Cytometer WASTE SHEATH CLEANSE FLOW FULL Red symbol means a Green symbol means reagent container needs sample is going through refilling or the waste the flow cell.
  • Page 20 CONTROLS AND INDICATORS MCL (MULTI-TUBE CAROUSEL LOADER) MCL (MULTI-TUBE CAROUSEL LOADER) Press to open the MCL. The door 7021069A opens automatically. WORKSTATION MONITOR MONITOR CONTROLS COMPUTER Use the KEYBOARD and MOUSE to communicate with the system. 7238191B PN 4237238BA...

  • Page 21: Computer

    CONTROLS AND INDICATORS POWER SUPPLY Computer Switch turns the XL or XL-MCL Locks the Cytometer on or off, not just the keyboard. computer. The Cytometer does not have a separate on/off switch. 7238192B POWER SUPPLY FILTER WATER TRAP TRAP FILTER FILTER WATER Refer to Special...
  • Page 22 CONTROLS AND INDICATORS PRINTER (OPTIONAL) PRINTER (OPTIONAL) This guide does not explain how to use the optional Printer. Operating instructions from the Printer manufacturer are included with the Printer. PN 4237238BA...

  • Page 23: Learning The Basics

    LEARNING THE BASICS LEARNING THE BASIC OPERATING TECHNIQUES Before reading the other chapters in this manual: Read about the Cytometer operating mode buttons in Heading 1.3, Cytometer Control Panel and Sample Stage Area. Read this chapter to become experienced with: Using the Sample Stage.

  • Page 24: Putting A Tube On The Sample

    LEARNING THE BASICS USING THE SAMPLE STAGE Putting a Tube on the Sample Stage Ensure that the Cytometer is in Run mode (the RUN button light is steady green). The Acquisition Run screen must be displayed and must show the message Insert sample tube.
  • Page 25 LEARNING THE BASICS USING THE SAMPLE STAGE 7238140A Insert the tube: Top-first Bottom-second. The Cytometer beeps quickly as a reminder to remove your hand from the Sample Stage before it rises. 7021009A The stage rises, positioning the tip of the sample probe near the bottom of the tube.
  • Page 26 LEARNING THE BASICS USING THE SAMPLE STAGE The FLOW indicator turns green when the tube is pressurized. CLEANSE FLOW Green symbol means sample is going through the flow cell. 7238145A Close the door. When data acquisition ends, the tube is depressurized, the FLOW indicator turns off and the Sample Stage lowers.

  • Page 27: Removing A Tube From The Sample

    LEARNING THE BASICS USING THE SAMPLE STAGE Removing a Tube from the Sample Stage Open the door. 7021046A Pull from the bottom of the tube and remove it from the Sample Stage. 7021012A Close the door. 7021047A PN 4237238BA...

  • Page 28: Using The Mcl

    LEARNING THE BASICS USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) Carousels The XL-MCL flow cytometer starter kit has: Two carousels, each with 32 tube positions. A sheet of bar-code labels, numbered 01 to 99, for you to use to identify the carousels.

  • Page 29: Putting A Carousel In The Removing A Carousel From The

    LEARNING THE BASICS USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) Putting a Carousel in the MCL Press the MCL door release. Pick up the carousel. 7021065A PN 4237238BA...
  • Page 30 LEARNING THE BASICS USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) Line up the carousel with its turntable, and then push down. The carousel is in home position when the handle points toward the back. 7021066A Close the MCL. 7021-067 PN 4237238BA...
  • Page 31 LEARNING THE BASICS USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) Removing a Carousel from the MCL Press the MCL door release. Remove the carousel. 7021068A Close the MCL. 7021072A PN 4237238BA...

  • Page 32: Bar-Code Labels

    LEARNING THE BASICS USING THE MCL (XL-MCL FLOW CYTOMETER ONLY) Bar-Code Labels You can put a bar-code label on each sample tube. Bar-code label specifications are in the Specifications Chapter in the Reference manual. IMPORTANT To prevent misidentified samples, affix the bar-code label as shown below so the MCL can read the label correctly.

  • Page 33: Using The Mouse

    LEARNING THE BASICS USING THE MOUSE USING THE MOUSE Selecting Screen Items The mouse is a pointing device you use MOUSE BUTTONS to select items on the screen. When you move the mouse, a graphic image called a cursor moves on the screen. The cursor changes depending on what is happening in the software.

  • Page 34: Symbols For Selecting Screen

    LEARNING THE BASICS USING THE MOUSE Press and release either mouse button once. The drop-down menu appears. Move the cursor down the menu. As the cursor passes items, some of them highlight with a colored background. Items that do not highlight cannot be selected now.

  • Page 35: Moving Between

    LEARNING THE BASICS MOVING BETWEEN SCREENS MOVING BETWEEN SCREENS At the second menu on every screen you can choose among the screens that are part of the current application. This menu is called either Setup Screen (in the Acquisition application), Setup (in the Listmode application), or Screen (in the other applications).
  • Page 36 LEARNING THE BASICS USING YOUR NETWORK WORKSTATION AND SERVER 2-14 PN 4237238BA...

  • Page 37: Software Overview

    SOFTWARE OVERVIEW APPLICATIONS MENU You control most of the functions of the XL and XL-MCL flow cytometer from a series of different software screens. The screens are grouped into applications and give you access to a group of logically related actions.

  • Page 38: Acquisition Application

    SOFTWARE OVERVIEW ACQUISITION APPLICATION ACQUISITION APPLICATION Acquisition Setup Screen Menu Panels Goes to Run screen to acquire data from a Goes to Panel screen to select, define, sample using a worklist, panel, or protocols. setup, and save panels. Run/Regions Worklist Goes to Run screen and activates Region Goes to the Worklist screen to define button to create, edit, erase, move, copy, or...

  • Page 39: Acquisition Protocol Menu

    SOFTWARE OVERVIEW ACQUISITION APPLICATION Acquisition Protocol Menu Select Save As Opens a protocol file. Saves a protocol file with a new name. Save PCX File Saves a protocol file with the current name. Saves the screen (or a portion of the screen) as a PCX graphics file.

  • Page 40: Acquisition Buttons

    SOFTWARE OVERVIEW ACQUISITION APPLICATION Acquisition Buttons Display and Region Buttons PN 4237238BA...

  • Page 41: Output Options Window

    SOFTWARE OVERVIEW ACQUISITION APPLICATION Output Options Window Cytometer Control Windows Counters and Stops Window PN 4237238BA...

  • Page 42: Signal Window

    SOFTWARE OVERVIEW ACQUISITION APPLICATION Signal Window Discriminators Window Color Compensation Window PN 4237238BA...

  • Page 43: Listmode Application

    SOFTWARE OVERVIEW LISTMODE APPLICATION LISTMODE APPLICATION Listmode Setup Menu Analysis Panels Goes to Analysis screen to display histograms. Goes to Panel screen to select, define, setup, and save panels. Regions List Queue Goes to Analysis screen and activates Region Goes to List Queue screen to put listmode button to create, edit, erase, move, copy, or files in a queue for batch analysis.

  • Page 44: Listmode Screen Buttons

    SOFTWARE OVERVIEW LISTMODE APPLICATION Listmode Screen Buttons Histogram Display Buttons Note: Click inside a histogram to display it at full size. Replay Options Buttons Output and Region Buttons PN 4237238BA...

  • Page 45: Multigraph Application

    SOFTWARE OVERVIEW MULTIGRAPH APPLICATION MULTIGRAPH APPLICATION Multigraph Screen Menu Gallery Hist Queue Goes to Gallery screen to display and analyze Goes to Hist Queue screen to select groups up to eight histograms at one time. of histograms for analysis and display. Single Overlay Hist Data Goes to Overlay screen to superimpose up to...

  • Page 46: Multigraph Screen Buttons

    SOFTWARE OVERVIEW MULTIGRAPH APPLICATION Multigraph Screen Buttons Histogram Display Buttons Mode Buttons Save and Print Buttons 3-10 PN 4237238BA...

  • Page 47: Reports Application

    SOFTWARE OVERVIEW REPORTS APPLICATION REPORTS APPLICATION Reports Screen Menu Data Entry Goes to Reports Data Entry screen to enter patient and specimen information and print reports. Template Goes to Reports Template Setup screen to define a template for your report layout. 3-11 PN 4237238BA...

  • Page 48: Qc Application

    SOFTWARE OVERVIEW QC APPLICATION QC APPLICATION QC Screen Menu 7238214B QC Template Compare Defines a QC template for a protocol. Goes to QC Compare screen to compare two QC files. Levey-Jennings Maintenance Displays QC data in Levey-Jennings graphs Goes to the QC Maintenance screen to according to the layout designed in the QC record and print system maintenance log.

  • Page 49: Utilities Application

    SOFTWARE OVERVIEW UTILITIES APPLICATION UTILITIES APPLICATION Utilities Screen Menu Configuration Changes the system configuration and startup options. Data Management Sets up file paths, and automatic archiving and deleting. 3-13 PN 4237238BA...

  • Page 50: Pop-Up Windows

    SOFTWARE OVERVIEW POP-UP WINDOWS POP-UP WINDOWS Many screens have buttons on the menu bar, which access pop-up windows. A pop-up window is a screen that is displayed on top of the current screen. The window does not completely cover the current screen, but you must close the window before you can use the current screen again.
  • Page 51 SOFTWARE OVERVIEW POP-UP WINDOWS 3-15 PN 4237238BA...

  • Page 52: File Menu

    SOFTWARE OVERVIEW FILE MENU FILE MENU The File menu is a generic menu that appears on most screens. From certain screens, specific items from the File menu are temporarily disabled. These disabled options appear gray and cannot be selected. Select Print Opens a pop-up window to select files.

  • Page 53: 3.10 Using The Keyboard

    SOFTWARE OVERVIEW USING THE KEYBOARD 3.10 USING THE KEYBOARD HISTOGRAM EXIT & PRINT DISPLAY ACQUISITION KEYBOARD KEYS FUNCTIONS FUNCTIONS TEMPLATE ESCAPE cancels what you did last. 7238193B Utility Keys Histogram Display Keys Shows the histogram Shows the histogram in contour format. in isometric format.

  • Page 54: Selecting Menu Items With The Cursor Keys

    SOFTWARE OVERVIEW USING THE KEYBOARD Selecting Menu Items with the Cursor Keys Press Ý+è to pull down the Applications menu or press and hold down è or é until the menu title you want is highlighted. Press Û. Press æ or ç until the item you want is highlighted. Press Û.

  • Page 55: 3.11 Responding To Prompts And Messages

    SOFTWARE OVERVIEW RESPONDING TO PROMPTS AND MESSAGES 3.11 RESPONDING TO PROMPTS AND MESSAGES Prompts When a prompt appears on the screen, the Current sample name Sample Name: software needs information from you. 7238119A The software uses the information displayed (called the default) unless you change it. Clearing the Prompt from the Screen Press È.

  • Page 56: Messages

    SOFTWARE OVERVIEW ADJUSTING CYTOMETER SETTINGS Messages When a message appears on the screen in a The sample pressure failed. green, amber, or red box something unexpected has happened. Green is for the PLEASE ACKNOWLEDGE least severe message; red, the most severe. The Special Procedures and 7021-110 Troubleshooting manual lists the error...

  • Page 57: Acquisition Cytosettings Screen

    SOFTWARE OVERVIEW ADJUSTING CYTOMETER SETTINGS Acquisition Cytosettings Screen 3-21 PN 4237238BA...
  • Page 58 SOFTWARE OVERVIEW ADJUSTING CYTOMETER SETTINGS 3-22 PN 4237238BA...

  • Page 59: Creating Protocols

    CREATING PROTOCOLS WHAT IS A PROTOCOL? A protocol tells the Cytometer what data to acquire. It specifies: The parameters to be used The type of analysis to be run The Cytometer settings The regions to use The statistics to report The histograms and regions to print The histogram definitions Other information.

  • Page 60: Selecting Signals

    CREATING PROTOCOLS SELECTING SIGNALS SELECTING SIGNALS You can select up to eight of the signals the system generates, including AUX, RATIO, and TIME and you can assign descriptive names to some signals. Setup Screen Protocols in the Signal Sources box, the signals you want, including any you need for RATIO or AUX.

  • Page 61: Erasing Signals

    CREATING PROTOCOLS SELECTING SIGNALS You are prompted for the new parameter name. Type a new name for the signal and press Û. The new name appears in the User Name column in the Parameters box. Erasing Signals If you decide not to use a selected signal: the highlighted signal you do not want in the Signal Sources box.

  • Page 62: Selecting And Assigning Aux

    CREATING PROTOCOLS SELECTING SIGNALS Selecting and Assigning AUX The AUX signal can only use Lin or Peak signals as its source. AUX cannot use a Log signal. Setup Screen Protocols next to SIG: the X next to the signal you want to use for AUX, from the Signal Sources box.

  • Page 63: Editing Aux Parameter

    CREATING PROTOCOLS SELECTING SIGNALS The AUX parameter and its signal name are now displayed in the Parameters box. Editing AUX Parameter If you want to change the AUX parameter assignment: the signal name next to SIG:. It highlights. the X next to the new signal you want to assign to AUX.
  • Page 64 CREATING PROTOCOLS SELECTING SIGNALS the X next to the signal to use as the numerator. The signal name displays next to NUM:. next to DEN: You can use any of the parameters already selected, including AUX, for NUM and DEN. the X next to the signal to use as the denominator.

  • Page 65: Selecting And Assigning Time Parameter

    CREATING PROTOCOLS SELECTING SIGNALS the X next to Ratio. The X is highlighted and Ratio is displayed in the Parameters box. Selecting and Assigning TIME Parameter The stop time, in seconds, is entered in the Functions box on the Protocol screen. Setup Screen Protocols the X next to Time in the Signal...

  • Page 66: Activating Prism In Acquisition

    CREATING PROTOCOLS SELECTING SIGNALS Activating PRISM in Acquisition Protocol Select the protocol you want to use. [Okay]. Setup Screen Protocols the X next to Prism. File Save File Save As to save the protocol. Setup Screen Assign the prism equations as explained in Heading 5.6, Prism Equation Regions.

  • Page 67: Defining Histograms

    CREATING PROTOCOLS DEFINING HISTOGRAMS DEFINING HISTOGRAMS In any protocol, you can have up to eight histograms. For each of those histograms, you can specify different regions, gates, stop counts, and other settings. Assigning Parameters and Titles to Histograms Applications Acquisition Setup Screen Protocols Click here...
  • Page 68 CREATING PROTOCOLS DEFINING HISTOGRAMS Click here to assign the desired Y-axis parameter, if any, Y-axis parameter in the Parameters box Signal column. the Y-axis of the histogram you want to assign the parameter to. 7238129A Click here to edit title. on the top outside border of the histogram to enter a Title, if desired.

  • Page 69: Erasing Parameters And Histograms

    CREATING PROTOCOLS DEFINING HISTOGRAMS Erasing Parameters and Histograms Applications Acquisition Setup Screen Protocols Erase Hist/Param in the Parameters box. The parameter names on the histograms you want to erase. Note: When you click inside the histogram or erase all the parameter names on a histogram, the histogram is erased.

  • Page 70: Histogram Resolution

    CREATING PROTOCOLS DEFINING HISTOGRAMS Histogram Resolution Two-parameter histograms can be displayed in 64 x 64, 128 x 128, or 256 x 256 resolution. Histogram resolution affects region statistics because region boundaries are different at different histogram resolutions. The affected statistics can be normalized by toggling [Normalize]on (green) in the Statistics pop-up window from the Protocol screen.

  • Page 71: Specifying Function Options

    CREATING PROTOCOLS SPECIFYING FUNCTION OPTIONS SPECIFYING FUNCTION OPTIONS The Functions box is in the lower right of the Acquisition Protocol screen. Select an option to change it to the desired setting; the defaults are shown here. Note: Use the statistics selection pop-up box to select which statistics to display. 4-13 PN 4237238BA...

  • Page 72: Saving Or Updating Aprotocol

    CREATING PROTOCOLS SAVING OR UPDATING A PROTOCOL SAVING OR UPDATING A PROTOCOL At any point in the creation of a protocol, you can save what you have done so far. As a safeguard, you should: Save a protocol whenever you make any changes to it. Archive your protocols on a weekly basis.

  • Page 73: Using Regions

    USING REGIONS REGION TYPES Create regions by selecting the Region button at the bottom of the Acquisition Run and Listmode Analysis screens. Use the Region Definition box to specify their type. Acquisition Regions Region List PN 4237238BA...

  • Page 74: One-Parameter Histogram Regions

    USING REGIONS REGION TYPES One-Parameter Histogram Regions Numeric and Linear Regions Two-Parameter Histogram Regions Numeric and Rectilinear Regions PN 4237238BA...

  • Page 75: Quad-Stat Region

    USING REGIONS REGION TYPES Quad-stat Region Amorphous Region PN 4237238BA...

  • Page 76: Changing The Cursor Mode

    USING REGIONS CHANGING THE CURSOR MODE CHANGING THE CURSOR MODE When you are working with regions, the cursor is in one of five modes: Edit Create Redraw Copy , and Erase . The cursor mode affects what happens to screen items you select.
  • Page 77 USING REGIONS ASSIGNING REGIONS Region Type Description Cell-Seeker Must be amorphous regions. (Autogating) Cell-Tracker Must be linear, rectilinear, or amorphous regions. Listgate Must be linear or rectilinear regions. Must contain "LISTGATE" in the region name. Negative listmode gates must contain "LISTGATENOT" or "LISTGATE-" in the region name.

  • Page 78: Assigning Gates To Histograms

    USING REGIONS ASSIGNING REGIONS Assigning Gates to Histograms The "gating" process consists of: Creating regions appropriate for the types of analyses you are doing. Assigning the regions as gates so that other histograms include data from only those regions. The software lets you create up to 24 regions in a protocol.

  • Page 79: Assigning A Region As A Gate

    USING REGIONS ASSIGNING REGIONS Assigning a Region as a Gate Setup Screen Run/Regions [4 Hists] or [8 Hists] so that you are displaying more than one histogram at a time. [Region] Edit until it changes to Create the region in the region list you want to use as a gate.
  • Page 80 USING REGIONS ASSIGNING REGIONS To remove an assigned gate: the cursor mode to change it to Erase on the region in the Regions Definition box you do not want to use as a gate. the histogram number that has the gate you want to remove.

  • Page 81: Gating Equations

    USING REGIONS ASSIGNING REGIONS Gating Equations To gate a histogram using the — sign, or to edit an existing histogram equation: [Region]. The histogram number above the histogram you want to gate. Type the gate equation and press Û. Sequential Gating IMPORTANT For a sequentially gated histogram, gating may not work as intended resulting in possible incorrect analysis results, if you do not include all the gate regions in the gate equation.

  • Page 82: Cell-Seeker (Autogating) Regions

    USING REGIONS CELL-SEEKER (AUTOGATING) REGIONS CELL-SEEKER (AUTOGATING) REGIONS Any amorphous region with a name that begins with AUTO is a Cell-Seeker region. After 10 seconds of acquisition or 10,000 events have been acquired (whichever comes first): The original region is replaced by an elliptical region that encloses the cell population. The data acquired is replayed in the new region.

  • Page 83: Assigning Autogating Regions

    USING REGIONS CELL-TRACKER REGIONS Autogating works differently under certain circumstances: Panel The primary and secondary protocols are used for Autogating; the autogated region is passed on. You can edit that region in the control protocol; the edited region is passed on. Stop-on-volume Autogating occurs after data acquisition is complete.

  • Page 84: Assigning Cell-Tracker Regions

    USING REGIONS CELL-TRACKER REGIONS Assigning Cell-Tracker Regions [Region]. [Edit] until it changes to [Create]. [4 Hists] to change to [8 Hists], if necessary. on the region in the region box you want to assign to a color. one of the four available colors in the Cell-Tracker box that you want to use.

  • Page 85: Prism Equation Regions

    USING REGIONS PRISM EQUATION REGIONS PRISM EQUATION REGIONS Each Prism parameter requires a divider value to separate the negative from the positive population. You set the prism dividers by assigning linear or quad-stat regions to a prism equation. The prism equation can have up to four regions.

  • Page 86: Assigning Prism Equations

    USING REGIONS LISTMODE GATING Assigning Prism Equations Assign regions to the prism equation to display the Prism parameter as a histogram. Up to four parameters can be used in the prism equation. Only one region per histogram can be used. If a parameter occurs more than once in the prism equation, only the lower alphabet region ID letter is used.

  • Page 87: Assigning Listmode Gates

    USING REGIONS LISTMODE GATING Assigning Listmode Gates Run some of the sample. Draw a rectilinear or linear region around the population you want to include in the listmode file (all events outside the region are excluded). Name the region. The name LISTGATE (all caps) must be included in the name.

  • Page 88: Prime Regions

    USING REGIONS PRIME REGIONS PRIME REGIONS Prime regions are used to initiate an autoprime if the peak of a histogram does not accumulate in the region within 10 seconds after beginning acquisition, or every second thereafter, or 10,000 events are acquired (whichever comes first). Only linear or rectilinear regions can be assigned as Prime regions.

  • Page 89: Assigning Mapping Regions

    USING REGIONS MAPPING REGIONS Assigning Mapping Regions Create a rectilinear or amorphous region on the histogram where you want a mapping region. To assign a mapping region to a rectilinear or an amorphous region, use [ ] (square brackets) around the ID letter of the rectilinear or amorphous region for the name of the mapping region.

  • Page 90: 5.10 Calibration Regions

    USING REGIONS CALIBRATION REGIONS 5.10 CALIBRATION REGIONS If a region in a histogram contains a population of a known concentration, name the region CAL to use it as a calibration region. There can be only one CAL region in each protocol or panel.

  • Page 91: 5.11 Qc Regions

    USING REGIONS QC REGIONS 5.11 QC REGIONS A QC region in a _Q protocol contributes its full statistics to the QC data (*.QCC) file for viewing in the Levey-Jennings graphs or QC data table. You define which statistics appear when you define the QC template for the _Q protocol. QC regions: Must contain QC in their file names.

  • Page 92: 5.12 Lot Number Regions

    USING REGIONS LOT NUMBER REGIONS 5.12 LOT NUMBER REGIONS Lot number regions are made as a means of identifying the lot number of the control materials and reagents used for Autostandardization panel. The lot number (from the region name) is written to the QC data file (*.QCS or *.QCC) for the related protocol and can be viewed in the QC template, the Levey-Jennings graphs, and the QC data table.

  • Page 93: Creating Panels

    CREATING PANELS WHAT IS A PANEL? A panel is a group of linked protocols that you can save under a name you choose. When you create a panel: You list the protocols in a certain order. Each protocol corresponds to a sample tube. You specify assignments of protocols as Secondary (S), Control (C), or Next (N).

  • Page 94: Panel Protocol Assignments

    CREATING PANELS PANEL PROTOCOL ASSIGNMENTS PANEL PROTOCOL ASSIGNMENTS The chart below shows how protocols function within a panel when they are assigned as either a primary, secondary, or control protocol. Function Primary Secondary Control Test First tube in a panel Gets Cytometer settings and regions from the protocol or from the Cytometer settings baseline file (*.QCS) for protocols with the same prefix as the Autostandardization panels.

  • Page 95: Primary Assignment

    CREATING PANELS PANEL PROTOCOL ASSIGNMENTS Primary Assignment The software automatically assigns Primary as the first tube in a panel. When you create a panel, the Primary tube must also be Next because Next denotes the first tube to be run. Cytosettings, regions, and region names are passed from the primary protocol to the protocols that follow it.

  • Page 96: Passing Regions In A Panel

    CREATING PANELS PANEL PROTOCOL ASSIGNMENTS Changes made to the Cytometer settings in the other protocols in the panel are used and saved only to those specific protocols (with [Save Cyto] turned on); they are not passed on. The software can also pass the Cytometer settings from the QC data (*.QCS) file. For protocols that have the same prefix used in the Auto Setup panels, for example 3CL 45-FITC/4-RD1/3-PC5, the Cytometer settings are accessed from the *.QCS data file (3CL.QCS in this example) stored on the hard drive.

  • Page 97: Creating Apanel

    CREATING PANELS CREATING A PANEL CREATING A PANEL Selecting Protocols Display the Acquisition Protocol screen. Applications Acquisition Setup Screen Protocols Clear the Protocol Select window: File Select [Clear All]. The protocols you want in the panel. [Okay]. PN 4237238BA...

  • Page 98: Making Assignments And Ordering Protocols

    CREATING PANELS CREATING A PANEL Making Assignments and Ordering Protocols After selecting protocols, display the Acquisition Panel screen. Setup Screen Panels The screen lists the protocols, in alphabetic order, with all of them highlighted. The first protocol is flagged as N (Next) and P (Primary).

  • Page 99: Saving A Panel

    CREATING PANELS CREATING A PANEL Make the secondary protocol assignments. [Secondary]. the protocol or protocols you want to flag as Secondary (S). The letter S appears next to each protocol selected. [Secondary]. Check that the protocol assignments and order are what you want. To delete a protocol from a panel, change the cursor mode to Erase and then select the protocol to be deleted.

  • Page 100: Adding Panels

    CREATING PANELS CREATING A PANEL Adding Panels To add panels together to make a larger panel to analyze one specimen: [Panel]. the first panel you want to use. [Okay]. Setup Screen Panels [ADD Panel]. the panel you want to add. [Okay].

  • Page 101: Adding Protocols

    CREATING PANELS CREATING A PANEL Adding Protocols To add a protocol to an existing panel: [Panel]. the first panel you want to use. [Okay]. Setup Screen Panels [ADD Protocol]. the protocol you want to add. [Okay]. Repeat steps 5 through 7 to add other protocols.
  • Page 102 CREATING PANELS CREATING A PANEL 6-10 PN 4237238BA...

  • Page 103: The Operating System

    THE OPERATING SYSTEM ® THE XL OR XL-MCL FLOW CYTOMETER AND THE MS-DOS OPERATING SYSTEM 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.

  • Page 104: The Xl Or Xl-Mcl Flow Cytometer And Microsoft Software

    THE OPERATING SYSTEM ® THE XL OR XL-MCL FLOW CYTOMETER AND MICROSOFT WINDOWS SOFTWARE ® THE XL OR XL-MCL FLOW CYTOMETER AND MICROSOFT WINDOWS SOFTWARE The XL and XL-MCL flow cytometer SYSTEM II software is not compatible with Microsoft Windows software but can coexist with Windows 95 on a FlowCentre Multimedia Workstation.
  • Page 105 INDEX replay options, 28 sample stage area, 4 Acquisition screen, how to select, 19 application, software overview, 22 buttons, controls and indicators, 24 keys, 37 Protocol menu, 23 calibration, 71 Region screen, 57 regions, 71 Run screen, acquisition buttons, 24 carousel, sample Run screen, Cytometer buttons, 24 home position, 15...
  • Page 106 INDEX cursor in panels, 76 keys, 38 Listmode, 68 mode, 60 listmode gating (listgate), 68 working with the mouse, 18 negative Listmode, 69 Cytometer sequential, 64 buttons, on the Acquisition Run screen, Getting Started manual conventions used, xiii control panel, 4 introduction to your manuals, xi control window, 25 using the manuals, xi...
  • Page 107 INDEX use the sample stage, 9 lot number use the software, 21 regions, 72 icons used in the manual, xiv making assignments, 78 Important manuals for your instrument definition, ii conventions used, xiii indicator panels, Cytometer, 2 how to use, xi indicators introduction to your manuals, xi and controls, 1...
  • Page 108 INDEX output options printing buttons, 23, 28 Functions box, 55 function, 25 prism parameter illustration, 25 activating in Acquisition, 50 activating in Listmode, 50 setting regions, 67 prompts, 39 panels protocols adding protocols, 81 adding to a panel, 81 adding together, 80 control protocol, 75 autogated regions, 76 control, in panels, 75...
  • Page 109 INDEX lot number, 72 sheath low indicator mapping, 70 location, 5 one-parameter histograms, 58 shortcut prime, 69 changing screens, 38 prism equation, 67 signal amplitude indicators, 3 QC, 71 Signal window select to print, 55 functions, 26 two-parameter histograms, 58 illustration, 26 types of, 57, 60 signals...
  • Page 110 INDEX Warning definition, ii waste full indicator location, 5 what is a panel, 73 a protocol, 43 window Cytometer control, 25 pop-up, 34 Protocol Select, 34 Windows software compatibility with XL software, 84 restarting the XL software, 84 Workstation controls, 6 indicators, 6 network, using, 20 XL/XL-MCL system...
  • Page 111 TRADEMARKS "CC" logo, Cell-Seeker, Cell-Stat, Cell-Tracker, COULTER, CYTO-COMP , EPICS, FlowCentre, Flow-Count, SYSTEM II, reticONE, Retic-STAT, tetraONE, XL, and XL-MCL are trademarks of Coulter International Corp. All other trademarks, service marks, products, or services are trademarks or registered trademarks of their respective holders. PN 4237238BA...
  • Page 112 COULTER EPICS XL and XL-MCL Flow Cytometer Documentation Use and Function • Installation • Operation Principles • Reference Specifications/Characteristics • Precautions and Hazards • Log Sheets • Predefined PN 4235298 Panels, Protocols, and QC Templates • Glossary • Index (Black binding) Cleaning Procedures •...

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