BD FACS Loader

Reference Manual

bdbiosciences.com
Part No. 643280 Rev. A
November 2007

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© 2007, Becton, Dickinson and Company. All rights reserved. No part of this publication may be reproduced,
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The information in this manual is subject to change without notice. BD Biosciences reserves the right to change its
products and services at any time to incorporate the latest technological developments. Although this manual has
been prepared with every precaution to ensure accuracy, BD Biosciences assumes no liability for any errors or
omissions, nor for any damages resulting from the application or use of this information. BD Biosciences welcomes
customer input on corrections and suggestions for improvement.
BD Worklist Manager and BD Loader Manager software © 2007, Becton, Dickinson and Company. This software is
the property of Becton, Dickinson and Company. Each sale of a stored unit of this software grants the purchaser a
nontransferable, nonexclusive, personal license. This software may not be duplicated, reproduced, or copied in any
form or by any means whatsoever, except as otherwise permitted by law.
This program was written with MacApp®, © Apple®, Inc. The MacApp software is proprietary to Apple, Inc. and is
licensed to BD Biosciences for distribution only for use in combination with this software. Apple, Inc. makes no
warranties whatsoever, either expressed or implied, regarding this product, including warranties with respect to its
merchantability or its fitness for any particular purpose.
BD, the BD logo, BD CellQuest, BD FACS, BD FACSCalibur, BD FACSComp, BD FACStation, BD Falcon,
BD Multiset, BD Multitest, BD Tritest, and BD Trucount are trademarks of Becton, Dickinson and Company.
Apple, Mac, Macintosh, Power Macintosh, and QuickTime are trademarks of Apple, Inc, registered in the US and
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associated.

History

Revision Date Change Made

11-10821-03 12/98 Updated for BD™ Worklist Manager software v3.3

349197 7/05 Revised for Mac OS X

344006 7/05 Changed title

643280 Rev. A 11/07 Revised for Intel processor details.

 Contents
About This Manual vii
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Technical Assistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

Chapter 1: Introduction 11
BD FACS Loader Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Tube Loader Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Rack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Keypad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Launching the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Quitting the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Chapter 2: Becoming Familiar with BD FACS Loader Software 23

Worklist Manager Application Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Loader Manager Status Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Computer-Controlled Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Manually Controlled Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

iii
 Worklist Manager Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Loader Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Columns Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Worklist Manager Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
File Naming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Printing and Saving Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Chapter 3: Getting Started 37

Preparing an Acquisition Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Defining a BD CellQuest Pro Experiment Document . . . . . . . . . . . . . . . 38
Defining a BD Multiset Schedule Document . . . . . . . . . . . . . . . . . . . . . . 42
Signing In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Setting Up the Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Accessing BD FACSComp Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Creating a Worklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Entering Sample Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Importing Sample Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Specifying the Starting Point for the Run . . . . . . . . . . . . . . . . . . . . . . . . 62
Assigning Racks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Chapter 4: Running Samples 67

Setting Up the Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Running Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Pausing Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
BD CellQuest Pro Options During Acquisition . . . . . . . . . . . . . . . . . . . . 74
BD Multiset Options During Acquisition . . . . . . . . . . . . . . . . . . . . . . . . 75
Rerunning a Full Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Viewing the Summary Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Chapter 5: Maintenance 81
Loader Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

iv BD FACS Loader Reference Manual

 Loader Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Accessing the Error Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Checking Tube Lifter Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Unscheduled Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Verifying Connection Ports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Replacing the Loader Seal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Replacing a Loader Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Cleaning the Tube Lifter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Modifying the Cytometer for Non-Loader Use . . . . . . . . . . . . . . . . . . . . . . . 95

Chapter 6: Troubleshooting 99
Loader Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
LoaderManager Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
WorklistManager Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

Appendix A: Technical Specifications 105

Replacement Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Index 107

Contents v
vi BD FACS Loader Reference Manual
 About This Manual
BD FACS Loader Reference Manual describes how to set up and use the
BD FACS™ Loader for automated sample introduction into a BD FACSCalibur™
flow cytometer. This manual is intended for laboratory personnel and flow
cytometry operators experienced in general flow cytometric applications. For
information on operating your instrument, refer to the instrument guide.

This reference manual assumes you have a working knowledge of

BD CellQuest™ Pro software, other BD clinical software, and the Mac® OS X
operating system. If you are not familiar with the Macintosh® computer, refer to
the documentation provided by Apple, Inc.

Before using BD™ Worklist Manager or BD™ Loader Manager software, review
the BD FACStation™ ReadMe file that was copied to your hard disk during
software installation. This file contains late-breaking information that is not
printed in this reference manual.

vii
Conventions
The following tables list conventions used in this guide.

Table 1 Hazard symbolsa

Symbol Meaning

Caution, hazard, or unsafe practice that could result in material damage,

data loss, minor or severe injury, or death

Electrical danger

Laser radiation

Biological risk

a. Although these symbols appear in color on the flow cytometer, they are in black and white throughout this
reference manual; their meaning remains unchanged.

Table 2 Text and keyboard conventions

Convention Use

; Tip Highlights features or hints that can save time and prevent difficulties

NOTICE Describes important features or instructions

Italics Italics are used to highlight book titles and new or unfamiliar terms on
their first appearance in the text.

> The arrow indicates a menu choice. For example, “choose

File > Print” means to choose Print from the File menu.

Command-X Keyboard shortcuts use the Command key (a) in combination with
another indicated keystroke. For example, Command-K means to hold
down the Command key while pressing the letter K.

viii BD FACS Loader Reference Manual

Limitations
• For In Vitro Diagnostic use.

• Samples containing BD Trucount™ beads should be vortexed immediately

before placing them on the instrument.

• BD Biosciences has not validated Loader mixing for volumes greater than
1 mL.

• Not all manufactured 12 x 75-mm test tubes have been checked for proper
functionality on the BD FACS Loader. BD Biosciences has validated only
disposable 12 x 75-mm BD Falcon™ capped polystyrene test tubes
(Catalog No. 352058).

• When you interrupt a Worklist, do not remove and replace racks until a
message instructs you to do so.

• If you need to reinstall any software you use with BD Worklist Manager
software, you must launch that software to enter registration information,
and then quit the application before launching Worklist Manager.

About This Manual ix

Technical Assistance
For technical questions or assistance in solving a problem:

• Read the section of the reference manual specific to the operation you are
performing.

• See Chapter 6, Troubleshooting.

If additional assistance is required, contact your local BD Biosciences technical

support representative or supplier.

When contacting BD Biosciences, have the following information available:

• product name, part number, and serial number

• any error messages

• details of recent instrument performance

For instrument support from within the US, call (877) 232-8995, prompt 2, 2.

For support from within Canada, call (888) 259-0187.

Customers outside the US and Canada, contact your local BD representative or

distributor.

x BD FACS Loader Reference Manual

 1

Introduction
The following topics are covered in this chapter:

• BD FACS Loader Overview on page 12

• Requirements on page 17

• Installing the Software on page 18

• Launching the Software on page 20

• Quitting the Software on page 21

11
BD FACS Loader Overview
The BD FACS Loader provides automated introduction of prepared samples to
BD FACSCalibur flow cytometers. The Loader is controlled by BD
Worklist Manager software which communicates with other BD software to
provide a total system of automated data collection and analysis.

Use BD software such as BD CellQuest Pro or BD Multiset software to set

acquisition criteria; use Worklist Manager software to input sample information
and specify data file storage. Load the racks, click Run Tests, and
Worklist Manager automatically runs the samples and provides status updates
during the run. When the Worklist is completed, you can print a Summary
Report that lists the files saved and status of each sample.

The BD FACS Loader consists of a sample tube loading device, remote keypad
control, and an electronics module. The Loader can be operated manually via the
keypad control, or automatically via Worklist Manager software.

12 BD FACS Loader Reference Manual

 FACSCalibur

Loader drawer

BECTON
DICKINS
ON

ON

OFF

keypad
UP
DOWN HIGH
RACK
LOW
LIFTER
MIXING

Figure 1-1 BD FACS Loader on a BD FACSCalibur flow cytometer

Tube Loader Components

The sample tube loading device is mounted directly on the flow cytometer. The
device consists of a drive system, tube lifter mechanism, rack spindle, and optical
sensors, all of which are attached to a sliding drawer.

Chapter 1: Introduction 13
 tube lifter
rack spindle

optical
sensors

drawer

Figure 1-2 Tube loader components

The tube lifter is a stainless steel rod that lifts the sample tube from the rack to
the sample injection port (SIP). The speed and distance of the lifter are optimized,
and should not be changed unless you are instructed to do so by BD Biosciences.

There are two optical sensors. One reads the rack ID to verify the rack installed is
correct. The other scans the rack to verify the tube locations match the associated
Rack Manifest. It also verifies a tube is in place before activating the tube lifter
and that a tube is returned to the rack when the tube lifter is lowered.

To operate the Loader, the cover must be in place on the Loader drawer. Tubes
will not be loaded if the cover is off, and currently running tubes will be unloaded
if the cover is removed during a run.

The only modifications necessary for the cytometer to work properly with the
Loader are removing the Bal seal and installing the tube guide and Loader seal on
the SIP. This helps to provide proper installation and pressurization of the tubes
during acquisition.

14 BD FACS Loader Reference Manual

Note that you can return the cytometer to its original state if you want to install
tubes manually on the cytometer without using the Loader. For instructions, see
Modifying the Cytometer for Non-Loader Use on page 95.

Rack
The Loader rack can accommodate up to forty 12 x 75-mm tubes in its labeled
tube locations. Each rack has a rack ID (1–16) printed on its top and on an
optically read label on the inner surface of the rack. The rack is positioned on the
rack spindle within the Loader drawer (Figure 1-2 on page 14), which slides in
and out for easy access.

Note that the Loader is compatible with both the traditional Loader racks (gray)
and the newer, greenish racks labeled “Sample-Prep Ready” (Figure 1-3).

ous p Re a d y
ck
Capr le-Preiences
el Ra
am BD Biosc
S

Figure 1-3 Loader rack

NOTICE Not all manufactured 12 x 75-mm test tubes have been checked for
proper functionality on the Loader. BD Biosciences has validated only disposable
12 x 75-mm BD Falcon capped polystyrene test tubes (Catalog No. 352058).

Keypad
The keypad (Figure 1-4) communicates with the Loader electronics module via a
SCSI cable. Use the keypad to turn the Loader power on and off, and to operate
the Loader manually. (The keypad keys are disabled during a Worklist run.)

Chapter 1: Introduction 15
 Each time the Loader is turned on and the cover is in place, the Loader performs
an initialization scan. The LED display on the keypad shows the status of the
Loader. After a successful scan, the Loader status reads Tube 01.

SCSI cable

BECTON
DICKINSON

LED display

ON

OFF
Rack buttons Lifter button
UP HIGH
DOWN LOW Mixing button
RACK LIFTER MIXING

Figure 1-4 Loader keypad

During manual operation, press the buttons on the keypad to perform the
following functions:

• Rack—advances the rack to another position

• Lifter—raises or lowers a tube

• Mixing—vibrates the rack to mix samples in the sample tubes

Press and release the button for a short (Low) mix; press and hold the
button for 2 seconds for a longer (High) mix.

16 BD FACS Loader Reference Manual

Requirements

Hardware
• BD FACSCalibur flow cytometer

• BD FACStation Macintosh® computer purchased through BD Biosciences

Other platforms might be supported; contact your BD Biosciences

representative for more information.

NOTICE If you have an external modem on your system, BD recommends

turning it off while running our software.

Software
See the Read Before You Install file on the BD FACStation CD for specific version
requirements.

• Mac® OS X

• BD Worklist Manager requires Mac OS X versions of the following

BD FACStation software applications. Refer to the Read Before You Install
file for version compatibility.

- BD Loader Manager—for communication with the Loader electronics

module

- BD CellQuest Pro or BD Multiset (or both)—for acquisition and

analysis

- BD FACSComp™—for instrument quality control (optional;

instrument settings can also be generated using BD CellQuest Pro or
BD Multiset software)

Chapter 1: Introduction 17
Installing the Software
Note that BD Worklist Manager and Loader Manager software are already
installed on BD FACStation systems purchased from BD Biosciences. Use these
instructions if you need to reinstall or upgrade the software.

1 Turn on your computer.

2 Insert the BD FACStation software CD into the CD-ROM drive.

3 Double-click the CD icon that appears on the desktop.

A window appears showing the CD contents. The BD FACStation software
CD includes several BD applications and corresponding electronic
documentation. Review the BD FACStation ReadMe file for more
information.

4 Double-click the installer icon.

5 Enter your password, and click OK.

You must have Administrator access to install the BDPAC device driver and
the security module software, thus a password is required.

After you click OK, the BD FACStation splash screen appears.

6 Click Continue; review the information in the ReadMe file window.

Click Print to print a copy of the ReadMe file. Note that a copy of the file is
saved in the BD Applications folder after software installation.

7 Click Continue, and then Install to install all BD FACStation software

applications.

The Installer automatically loads BD Worklist Manager software,

BD Loader Manager software, and all support files to your hard disk. A
message appears when installation is complete.

8 Click Quit when you see a message reporting that installation was
successful; restart the computer.

18 BD FACS Loader Reference Manual

 The software installer creates a BD Applications folder and BD Files folder
on the hard disk. If another BD application was installed previously, these
folders already exist and the installer adds the new files to these folders. See
the following figure.

Note that BD Multiset software also installs an alias to its PanelReagentFile

in the ClinApps Info Folder in the BD Applications folder. This alias must
be present for BD Multiset software to work with Worklist Manager.

9 Review the ReadMe files for the applications you will be using.
A ReadMe file is installed in the corresponding folder for each
BD FACStation application. These files contain important information
about the new features, defect corrections, and known issues with the
software. Carefully review each applicable file.

Chapter 1: Introduction 19
Launching the Software
BD Worklist Manager software will not launch if other BD applications are
already running. In addition, other BD applications cannot be launched
independently while Worklist Manager is running.

Before you use Worklist Manager with BD CellQuest Pro, BD Multiset, or

BD FACSComp software, you must first launch that application once to register
the software, and then close the application before launching it with
Worklist Manager. This also applies if you have upgraded these applications.

Before launching BD Worklist Manager software, make sure the security module
included with your BD FACStation CD is plugged into a USB port on your
keyboard or computer. The security module is needed to launch
BD CellQuest Pro software.

Launch Worklist Manager in one of the following ways.

• Navigate to the Worklist Manager application icon in the Finder window

and double-click the icon.

; Tip After launching the application, press the Worklist Manager icon in
the Dock and choose Keep In Dock. You can then open the application by
clicking its icon in the Dock.

Worklist Manager icon

• Double-click the icon for a saved Worklist document or Summary Report.

Note that Loader Manager software is launched automatically when

Worklist Manager starts up. To launch Loader Manager separately, you must
first quit Worklist Manager before launching Loader Manager.

20 BD FACS Loader Reference Manual

 Registering the Software

The first time you launch Worklist Manager, a registration dialog appears.

Enter your name and the name of your institution, and click Save.

Quitting the Software

NOTICE You cannot quit BD Worklist Manager software while a Worklist is
being run.

To quit the software, choose Quit Worklist Manager from the Worklist Manager
menu, or hold down the Command key while you press the Q key (a-Q).

Chapter 1: Introduction 21
22 BD FACS Loader Reference Manual
 2

Becoming Familiar with

BD FACS Loader Software
The following topics are covered in this chapter:

• Worklist Manager Application Window on page 24

• Loader Manager Status Window on page 26

• Worklist Manager Preferences on page 28

• Worklist Manager Files on page 32

23
Worklist Manager Application Window
When Worklist Manager software is launched, it automatically launches Loader
Manager software and checks to see if the Loader is connected. The Worklist
Manager application window and the Loader Manager Status window appear on
the desktop.

The application window is described in this section. For information about the
Status window, see Loader Manager Status Window on page 26.

menu bar

icon bar

message box

content area

button panel

Figure 2-1 Application window displaying Sign In view

The application window contains the following elements:

• Menu bar—displays application menus with the commands you will need
to operate the software.

• Icon bar—contains a panel of icons that allow you to navigate through the
software. Each icon represents a different view; the icon for the current
view is highlighted. Click Accept in the button panel to advance to the next

24 BD FACS Loader Reference Manual

 view. For a description of each view, see the following section, Worklist
Manager Views.

• Message box—displays noneditable status messages and prompts to assist

you in operating the Loader system.

• Content area—displays a series of views that allow you to enter

information specific to the run.

• Button panel—contains buttons that allow you to control the software. The
pulsing button is the default button that moves you along in the program.
To select this button, click it or press the Return key.

Worklist Manager Views

A typical Worklist Manager run starts with the Sign In view and ends with the
Summary view. If you want to return to a previous view to modify information
already entered, click the appropriate icon to display the view.

Each view functions as follows:

• Sign In—Sign in to Worklist Manager software as the operator.

• Set Up—Define information specific to the test run.

• FACSComp—Launch and run BD FACSComp software.

• Worklist—Enter sample identification information.

• Summary—Lists the status of all samples run and files saved

You can save the information entered in the Sign In, Set Up, and Worklist views
as a Worklist document. See Worklist Manager Files on page 32.

Chapter 2: Becoming Familiar with BD FACS Loader Software 25

Loader Manager Status Window
When Worklist Manager software is launched, it automatically launches Loader
Manager software and checks to see if the Loader is connected. The Loader
Manager Status window appears, displaying connectivity status and whether the
Loader is controlled manually or by the computer.

The Status window can appear to the side or below the Worklist Manager
application window; to bring the window to the front, click the Loader Manager
icon in the Dock (Figure 2-2). For an overview of the two status modes, see
Computer-Controlled Mode or Manually Controlled Mode on page 27.

Loader Manager icon

Figure 2-2 Loader Manager Status window and icon in Dock

Note that Loader Manager can also be launched independently of Worklist

Manager software. The functionality of Loader Manager software depends on
how it is launched. If it is launched by Worklist Manager software, the only item
you can access is the Loader Status window. If it is launched independently, you
can access cleaning, maintenance, and diagnostic functions, as described in
Chapter 5.

26 BD FACS Loader Reference Manual

Computer-Controlled Mode
The Loader enters computer-controlled mode after Run Tests is clicked in the
Worklist view of Worklist Manager software. In this mode, all Loader functions
are controlled by the software.

Figure 2-3 Status during tube loading (left) or Loader run (right)

You cannot quit Loader Manager software or access maintenance and diagnostic
functions while in computer-controlled mode. You can only view the Loader
Status window, which indicates the rack and tube number of the tube being run.

Manually Controlled Mode

The Loader is in manually controlled mode when Worklist Manager software is
running but no Worklist is being run, or when Loader Manager software is
launched independently. In this mode, the Loader keypad keys are enabled.

Cleaning and maintenance and diagnostic functions are available only when
Loader Manager software is launched independent of Worklist Manager
software.

Chapter 2: Becoming Familiar with BD FACS Loader Software 27

Worklist Manager Preferences
You can change certain default settings and customize the program using
Worklist Manager preferences. When you save a Worklist document, any
preferences you set are saved with that document.

To access preferences, choose WorklistManager > Preferences.

The following preferences are available:

• Loader Preferences, described on this page

• Columns Preferences on page 30

Loader Preferences
Use Loader Preferences to connect the Loader to the computer and to define rack
IDs. Note that Worklist documents can be generated on computers not connected
to a Loader.

1 Choose WorklistManager > Preferences.

28 BD FACS Loader Reference Manual

2 Select the checkbox for Loader connected to workstation.

Deselecting this box allows you to generate a Worklist on a computer not

attached to the Loader. Loader Manager software is not launched when
Worklist Manager is launched if Preferences indicates the Loader is not
connected. In addition, the Assay Settings button in the Set Up view and the
Run Tests and Assign Racks buttons at the Worklist view are not available.

3 Define Allowable Rack IDs.

Enter the correct number for the Minimum and Maximum field to define
the racks available for assignment to a system; 1 is the default setting for
Minimum and 16 is the default setting for Maximum.

Consider the following when selecting rack ID ranges.

• Rack IDs that fall outside the entered range cannot be assigned in the
Assign Racks dialog.

• If you open a Worklist containing un-run entries with out-of-range

rack IDs, these entries will revert to being unassigned.

• If you open a Worklist with entries already run with racks that are out
of range, these entries will revert to being unassigned. You will not be
able to assign new rack IDs to these entries since they have been run.

• If you change the Rack ID preference after completing a Worklist, an

error dialog appears when you press Run Tests.

Chapter 2: Becoming Familiar with BD FACS Loader Software 29

 • If you try to install a rack with an out-of-range ID, an error dialog
appears with the message that an unassigned rack is on the Loader.

4 Click Save.

Columns Preferences
Up to three custom columns can be added to the right of the Case Number
column in the Worklist view. Any information entered into these columns is stored
in the text section of FCS data files. Do the following to add custom columns.

1 Choose WorklistManager > Preferences, and click the Columns icon.

2 Select the checkboxes to add up to three custom columns; enter column

titles, as needed.

Column titles can consist of up to 20 characters. The default names are

Column #1, Column #2, and Column #3.

You do not have to use these columns sequentially; select the first and the
third, if you want (Figure 2-4 on page 31).

30 BD FACS Loader Reference Manual

 Figure 2-4 Selecting columns out of order

3 Click Save.

Custom columns appear to the right of the Case Number column in the
Worklist view. Titles appear exactly as they were entered.

The preferences are saved by Worklist Manager software and apply to all
new Worklists.

Chapter 2: Becoming Familiar with BD FACS Loader Software 31

Worklist Manager Files
Worklist Manager can create two types of files. Note that Flow Cytometry
Standard (FCS) data files are saved by the appropriate application software, not
by BD Worklist Manager software.

Worklist Document Files

The Worklist document file contains all data entered at the Sign
In, Set Up, and Worklist views, as well as preferences. You can
save a Worklist document and open it later to view, to complete
processing, or to add more samples for processing. If you open a
partially run Worklist and continue to run it, the Summary
Report is updated to contain information for the entire run.
If you attempt to close the Worklist Manager application
window or quit the program before saving the Worklist
document, a dialog appears asking if you want to save the
Worklist document. Only one Worklist document can be open
on the desktop at a time.
This version of the software can read Worklist documents from
Worklist Manager version 3.3 or later.

Summary Report Files

A Summary Report file contains a list of the samples run, the

name of the data files saved, and the status of the run. When
you save a Summary Report file, the suffix .sum is appended to
the file name. Summary Reports are saved as a PDF file.
A Summary Report can be printed at the conclusion of each
run. You can open as many Summary Reports as computer
memory allows.

32 BD FACS Loader Reference Manual

File Naming
Worklist Manager files are named by their creation date, by default.

File Type Naming Convention Example

Worklist document file DDMMYY.wrk 150403.wrk

Summary Report file DDMMYY.sum 150403.sum

You can change the default file names (DDMMYY) for these files. To rename a
Worklist document, choose Save or Save As at any view and enter a new name in
the standard Save dialog. To rename a Summary Report, click the Location
button in the Set Up view. (See Setting Up the Assay on page 44.)

Output File Naming

When running a BD CellQuest Pro Experiment document or a BD Multiset

Schedule document, Worklist Manager can generate data files and export files.
Worklist Manager software can also generate up to three types of reports when
running a BD Multiset schedule document.

The default name for all files contains at least three parts:

(Prefix)(Entry Number).(Tube Number)

• The file name prefix is selected in the Set Up view. (See Setting Up the Assay
on page 44.)

• The entry number corresponds to the Worklist line number, from 01 to 99.
(See Creating a Worklist on page 52.)

• The tube number is indicated by tube position in a panel and ranges from
001 to 040 (for BD CellQuest Pro documents) or 01 to 40 (for BD Multiset
documents) with 40 being the maximum number of tubes per panel.

Chapter 2: Becoming Familiar with BD FACS Loader Software 33

 To illustrate:

BD CellQuest Pro file BD Multiset file

JaneDoe03.002 JaneDoe03.02

indicates Jane Doe is the third entry in the Worklist, and this file is from the
second tube in the panel.

To prevent an original file from being overwritten, the helper application adds a
unique character to a file name under the following circumstances.

File-Naming Conflict During a Run

The application attempts up to five times to give the new file a unique name by
adding an uppercase letter (V through Z) after the tube position. Thus, the
following file names illustrate the first and second attempts to resolve a
conflicting file name. The Worklist is aborted if it attempts to rename a file more
than five times.

BD CellQuest Pro file BD Multiset file

JaneDoe03.002V JaneDoe03.02V

JaneDoe03.002W JaneDoe03.02W

For a conflict in naming a BD Multiset report, the application attempts up to ten

times to give the new file a unique name by adding an uppercase letter (Q
through Z) after the report name. To illustrate:

BD Multiset report

test03.labQ (1st attempt)

test03.labR (2nd attempt)

test03.labW (7th attempt)

34 BD FACS Loader Reference Manual

Naming a Rerun Tube

You can rerun a tube up to five times. The application adds a lowercase letter,
(a through e) to each subsequent file, placing the appropriate letter after the entry
number to indicate a full-entry rerun or after the tube number to indicate a
single-tube rerun.

The following illustrates the first and second reruns for a BD CellQuest Pro file
(CQP) named test01.003 and a BD Multiset file (MS) named test 01.03.

Full-Entry Rerun Single-Tube Rerun

test01a.003 (CQP) Í1st rerunÎ test01.003a (CQP)

test01a.03 (MS) test01.03a (MS)

test01b.003 (CQP) Í2nd rerunÎ test01.003b (CQP)

test01b.03 (MS) test01.03b (MS)

For more information, see Rerunning a Full Entry on page 78.

Printing and Saving Files

Saving a Worklist Document

A Worklist document is stored in the computer’s

temporary memory until you save it to disk. You can
save a Worklist document at any time by choosing Save
or Save As from the File menu. If you do not save the
Worklist before clicking Run Tests, a dialog appears
prompting you to do so.

Note that only one Worklist can be open at a time. To

open a saved Worklist, close the application window,
and then choose Open Worklist from the File menu.
The saved Worklist document opens at the Sign In view.

Chapter 2: Becoming Familiar with BD FACS Loader Software 35

 Saving a Summary Report

You can set up the software to save a Summary Report automatically at the
conclusion of a run by selecting the appropriate checkbox in the Set Up view. (See
Setting Up the Assay on page 44.) You can also save a Summary Report by
choosing Save Report from the File menu while at the Summary Report view.

To open a saved report, choose Open Report from the File menu. Reports can be
viewed using Adobe® Acrobat® software or the Preview application included
with your Macintosh computer.

Printing a Summary Report

You can print a Summary Report within Worklist Manager software by choosing
Print from the File menu at the Summary view. Page and Print Setup options can
also be accessed from the File menu.

Alternatively, you can open and print a saved report using the Print command in
the PDF viewer application.

NOTICE Options set in the Page Setup and Print Setup dialogs within Worklist
Manager software apply only to the Summary Report and Rack Manifest
printouts. Print options for BD Multiset reports are specified within BD Multiset
software.

36 BD FACS Loader Reference Manual

 3

Getting Started
The following topics are covered in this chapter:

• Preparing an Acquisition Document on page 38

• Signing In on page 43

• Setting Up the Assay on page 44

• Accessing BD FACSComp Software on page 50

• Creating a Worklist on page 52

• Assigning Racks on page 63

37
Preparing an Acquisition Document
BD Worklist Manager software requires access to an application-specific
document defined with the conditions for acquisition. When you click Run Tests
at the Worklist view, Worklist Manager launches the appropriate acquisition
software, using the defined document, for use with the Loader.

This section describes the following:

• Defining a BD CellQuest Pro Experiment Document on this page

• Defining a BD Multiset Schedule Document on page 42

Defining a BD CellQuest Pro Experiment Document

A BD CellQuest Pro Experiment document launched by Worklist Manager must
contain the conditions for acquisition (acquisition and storage settings), and have
a panel defined and selected.

Do the following to set up an acquisition Experiment document in

BD CellQuest Pro software.

1 Open an existing Experiment document or create a new one.

2 Format all dot plots to Acquisition-to-Analysis plots.

; Tip Select all plots in the document, and then choose Acquisition ->
Analysis from the Plot Type pop-up menu in the Inspector.

3 Choose Acquire > Acquisition & Storage.

4 Enter the acquisition criteria in the Acquisition & Storage window; click
OK when you are finished.

• Set Collection Criteria to Event Count or Time.

• Enter values for stopping acquisition.

38 BD FACS Loader Reference Manual

; Tip For walkaway operation, choose Event Count or Time for the
Collection Criteria, and enter a time of less than 600 seconds (10 min.) for
the stopping time. If you choose Event Count only or enter a time of more
than 10 minutes, you run the risk of Worklist Manager timing out if the
specified number of events is not collected during the entered time, or after
after 10 minutes. During a timeout, no data is saved, and you might not
have a sufficient amount of sample left to rerun.

5 Load a defined panel using the Acquisition Browser.

Chapter 3: Getting Started 39

 6 Edit the Acquisition Tube List in the Browser, if required (Figure 3-1).
To change a tube name or parameter label, select the tube icon in the
Browser and make changes in the Inspector. To change the acquisition
order, drag a tube icon up or down on the list.

Figure 3-1 Acquisition Tube List

Do not add or delete tubes from the Acquisition Tube List in the Browser. If
you want to add or remove tubes, edit the panel rather than the Acquisition
Tube List. Changes made to the Acquisition Tube List are not recognized by
Worklist Manager, and can negatively impact acquisition.

7 Specify tube-specific settings, if required.

Each tube in the panel can have different acquisition settings, such as the
number and type of events acquired and the type of parameters saved. In
addition, different instrument settings can be associated with different
tubes in the panel.

To add tube-specific settings, click on the pop-up control in the Browser,

add the required settings, and use the Inspector to customize the settings.

Refer to the BD CellQuest Pro Software Reference Manual for

instructions.

40 BD FACS Loader Reference Manual

8 Associate Acquisition plots in the Experiment document with tubes in the
panel, if required.

After creating plots, you can set up one or more plots to display data only
for a specific tube. Any plots that have been associated with tubes remain
empty until data is acquired for the corresponding tube.

Refer to the BD CellQuest Pro Software Reference Manual for more

information and instructions.

; Tip If you are using this feature, deselect the checkbox to Print CellQuest
Plots in the Assay Settings dialog (Figure 3-4 on page 49), accessed in the
Worklist Manager Set Up view. When the checkbox is selected, the
document prints after each sample is run, and only the final printout
contains a complete set of data.

9 Save the defined Experiment document in the CellQuest Experiments

Folder in the WorklistManager Folder.

NOTICE If you copy a Worklist document that uses BD CellQuest Pro

software to another computer, you must also copy the Experiment
document(s) and instrument settings file(s) used by that Worklist document
into the appropriate folders on the other computer.

Chapter 3: Getting Started 41

 Defining a BD Multiset Schedule Document
During BD Multiset software installation, a default Schedule document is
installed in the MultiSET Folder in the BD Applications folder. To run
BD Multiset software with the Loader, use this default Schedule document or
define your own.

A BD Multiset Schedule document launched by Worklist Manager must contain

acquisition conditions, such as those specified in BD Multiset preferences, and
the amount of time for viewing reports.

NOTICE Worklist Manager allows you to view BD Multiset reports for up to

5 seconds. All other options specified in the MultiSET Set Up view (ie, Until
“Next” Button Pressed, or a choice of >5 seconds) default to 5 seconds.

If you choose to define your own Schedule document, you must

• customize the Preferences, such as setting the export file delimiter, report
printing, minimum and maximum number of events, and the conditions
under which Worklist Manager will stop.

NOTICE Worklist Manager cannot acquire data for more than 5 minutes
(300 seconds). If you select time as a stopping criteria, Total Time entries of
more than 300 seconds will revert to 300 when the Schedule is run.

• verify or enter new lot IDs in the Tools > Lot IDs dialog.

Always make sure that the software lists the correct Absolute Count Bead
lot ID and bead count when obtaining absolute counts using BD Trucount
tubes. If you change lots, remember to input the new lot ID and bead count
into the software. To obtain accurate results, it is critical that the correct
Lot ID and Beads/Pellet are entered.
Absolute count bead lot information is saved with BD Multiset Schedule
documents. All files within the Schedule document must be acquired with
the same lot of BD Trucount tubes. When running Worklist Manager with
BD Multiset software, do not mix lots of BD Trucount tubes in the same
Schedule document.

• save the Schedule document in your choice of location.

42 BD FACS Loader Reference Manual

Signing In
The Sign In view appears when you start Worklist Manager software.

1 Enter names for the Operator, Institution, and Lab Director.

Enter up to 42 characters in each field. The operator name is always
required. Use the tab key to move from one field to the next, or click in
each field and begin typing. The information at the Sign In view is saved for
subsequent sessions.

2 Click Accept to continue to the Set Up view.

Chapter 3: Getting Started 43

Setting Up the Assay
At the Set Up view, specify settings for the assay you are running. Choose the
prefix you want to attach to saved files, the sample label for the Summary
Reports, and the storage locations for application-specific files and reports you
want to save.

1 Select a File Name Prefix.

If you select Sample Name, Sample ID, or Case Number for the prefix, you
must enter this information in the appropriate column at the Worklist view.
See Entering Sample Information on page 54. If you select Custom prefix,
click in the text box and enter your own file name prefix (up to 22 characters).

2 Select a Summary Report Sample Label.

These are also read from the Worklist view.

44 BD FACS Loader Reference Manual

3 Select the Worklist Summary Report checkbox if you want to save this file.
Click the Location button to change the default name or storage location.
See Worklist Manager Files on page 32 for details on the Summary Report
file.

4 Choose the Assay Type from the pop-up menu under Automatic Savings
Options.

The files you can save for the assay are listed under the pop-up menu with
their checkboxes checked. Note that data files must be saved when you
acquire samples using BD CellQuest Pro software with the Loader.

current
file path

Figure 3-2 Automatic saving options

The current file path appears below each available file type. The default
location for data files is a dated folder (DDMMYY) located in the
application’s Files folder in the BD Files folder. If a file or folder no longer
exists or is owned by another user, Worklist Manager displays INVALID
LOCATION as the current file path.

Chapter 3: Getting Started 45

 5 Click each available Location button to change the file storage location, if
necessary.

• For BD CellQuest Pro software, you can change the storage location
for data files and export files. For an export file, Worklist Manager
tells BD CellQuest Pro software when it is launched to export or
append statistics into either the default folder location or into the new
folder location you choose. BD CellQuest Pro software names the file
for you by appending the word stats to the name of the Experiment
document. Each Experiment document opened by BD CellQuest Pro
software will export or append statistics to the same export file.

If statistics cannot be appended to an existing export file because the

statistics selections in the document have changed, BD CellQuest Pro
software creates a new export file in the same folder. If a file naming
conflict occurs for the export file, Worklist Manager specifies the
conflict in its Summary Report. See File-Naming Conflict During a Run
on page 34.

• For BD Multiset software, you can change the storage location for data
files, report files, and export files. For export files, when you change
the storage location, you can choose to append data to an existing file
or create a new file.

To specify the name and storage location for a new export file, click
New File and enter a name in the dialog that appears. The file path
displays the new name when you return to the Set Up view.

By default, Summary Reports and export files are named according to

the date they are generated (see File Naming on page 33). If you change

46 BD FACS Loader Reference Manual

 the name for either file type, the Use Date Generated File Name
checkbox is deselected when you return to the Set Up view.

checkbox deselected

To return to naming files by date, select the checkbox.

The default location for a Schedule document template is the MultiSET

folder in the BD Applications folder. Click the Location button to
choose another Schedule document.

NOTICE Make sure you have sufficient storage space for all files to be
generated. If the data storage disk becomes full during acquisition, the
Worklist stops.

6 Click Assay Settings to access the Assay Settings dialog (Figure 3-3).

application icon

slider control

Figure 3-3 Assay Settings dialog

Chapter 3: Getting Started 47

 Use this dialog to associate instrument settings with a panel, customize mix
settings, and to specify whether to print plots in BD CellQuest Pro software.

Note that for BD CellQuest Pro software, the dialog lists panels from all
Experiment documents stored in the Worklist Manager > CellQuest
Experiments folder. Panel names are followed by the Experiment document
name in which they are defined (Panel name : Experiment document name).

panel name : Experiment document name

For BD Multiset software, the dialog lists all panels defined in the software.

To set up assay settings, do the following.

• Select an application icon.

• To link an instrument settings file with each panel, click the Instrument
Settings pop-up control and choose a file from the menu that appears.
The menu lists all Instrument Settings files that are stored in the
BD Files > Instrument Settings Files folder. BD FACSComp Calib files
should be available. The No File option allows you to clear the panel/
instrument settings association.

pop-up menu

• Change the Acquisition Start Delay by clicking the arrows or using the
slider control (Figure 3-3 on page 47). Acquisition Start Delay occurs
after the tube is lifted and properly pressurized. It allows the flow rate
to stabilize before events are saved.

48 BD FACS Loader Reference Manual

 • Customize mix setting(s) by clicking the arrows or using the slider
control.

For BD CellQuest Pro software, mix settings are specific to each panel.
Choose mix settings after you select a panel (Experiment document)
from the Panel list. Every time you run that panel, these mix settings
are used. Default mix settings are suggested settings for
immunophenotyping.

For BD Multiset software, mix settings are common to all panels.

Click Default Settings to reset mix settings to those recommended by

BD for each assay.

Figure 3-4 Default mix settings for BD CellQuest Pro (left) and BD Multiset (right)
software

• To print the BD CellQuest Pro Experiment document after each

acquisition, select the Print CELLQuest Plots checkbox. This turns on
printing for all panels in the Worklist. This feature is most useful if
your Experiment document has acquisition-to-analysis plots defined
and displays the statistics necessary for your analysis. If only
acquisition plots are defined, the statistics printed reflect the last events
acquired, not the entire data file.

; Tip If you have tube-specific plots in your Experiment document, note that
only the final printout will contain a complete set of data. To save paper,
deselect the checkbox and print the analysis only after all tubes have been
acquired.

Chapter 3: Getting Started 49

 7 Click Save to return to the Set Up view.

8 Click Accept to proceed to the FACSComp view.

Accessing BD FACSComp Software

You can launch BD FACSComp software from the FACSComp view. The
FACSComp view appears when you click Accept at the Set Up view.

BD Biosciences recommends that you run BD FACSComp software for

instrument setup and quality control before running samples. The FACSComp
view displays the current date and time as well as the pass or fail status for the
four types of instrument settings files saved in the BD Files > Instrument Settings
Files folder.

If you already ran BD FACSComp software to set up your instrument for this
Worklist run, click Skip FACSComp to proceed to the Worklist view.

50 BD FACS Loader Reference Manual

To run BD FACSComp software, click Launch FACSComp to proceed with
instrument setup specific to the application you are running. Refer to the
BD FACSComp Software Reference Manual for instructions. When the setup
software is complete, manually quit BD FACSComp software; the FACSComp
view reappears with the updated settings displayed.

The button panel now offers the following choices; click Continue to advance to
the Worklist view.

Chapter 3: Getting Started 51

Creating a Worklist
The Worklist view is displayed after you click the Skip FACSComp or Continue
button at the FACSComp view.

At the Worklist view, you can enter sample information for up to 99 samples and
associate each sample with a different panel. The Assay and Panel Name fields
contain pop-up menus where you choose the type of assay and panel. For more
information, see Entering Sample Information on page 54.

Alternatively, you can import sample information from a tab-delimited file, or

from a worklist created using BD FACS™ Sample Prep Assistant (SPA) software.
See Importing Sample Information on page 56 for instructions.

Use buttons in the button panel to assign a fixed panel and to assign (or release)
racks for the Loader. If you are running more than one assay type, use the Sort by
Assay button to group samples by assay.

52 BD FACS Loader Reference Manual

The status icons to the left of the entry numbers indicate whether or not all
necessary sample information has been entered. These icons also provide the
status for each entry.

The status icons include:

Information not entered for this entry. If no information is entered

for a sample, this entry is removed from the list, and the entries that
follow move up.

File Name Prefix choice made at Set Up view (Sample Name,

Sample ID, or Case Number) not entered, or Assay and Panel Name
not yet defined

File Name Prefix choice made at Set Up view (Sample Name,

Sample ID, or Case Number) entered, and Assay and Panel Name
entered; ready for rack assignment

Information completed and tube location and rack ID defined;

ready to run

Sample acquired

Error encountered during acquisition

Currently running test

To resize columns in the Worklist view, drag column borders to the right or left.
BD CellQuest Pro software does not use the last four columns (Param #1,
Param #2, Param #3, and Param #4), so you can make these columns as narrow
as possible. For BD Multiset software, however, you might need the first three
columns to enter application-specific information such as white blood count
(WBC), % Lymphs, or Absolute Lymphs.

NOTICE BD Multiset–specific information entered in any of these columns

(Param #1, Param #2, and Param #3) must match the analysis parameters set in

Chapter 3: Getting Started 53

 the Schedule document in order to be used when Worklist Manager launches
BD Multiset software.

Up to three custom columns can be added to the right of the Case Number
column. Use these columns to enter additional information that will be stored in
the text section of FCS data files. To add custom columns, see Columns
Preferences on page 30.

Entering Sample Information

For all applications, you must enter information in at least one of the first three
columns—Sample Name, Sample ID, or Case Number—depending on the File
Name Prefix and Summary Report Sample Label you specified in the Set Up view.
See Setting Up the Assay on page 44.

; Tip To scan sample information directly from a barcode label, use the
BD™ barcode scanner (Catalog No. 345037). Contact your local BD sales
representative for more information.

1 Click the Sample Name field and enter the name (up to 42 characters).
Press the Tab key to move from field to field. Press Shift-Tab to move
backwards. To move up or down, press the corresponding arrow key. If the
information in this field is used as a file prefix, you can type up to 22
characters.

2 Repeat for Sample ID and Case Number, if necessary.

Remember to enter information in the first three columns based on the File
Name Prefix and Summary Report Sample Label specified in the Set Up
view. Note that the Assign Racks button is not available until the label type
specified in the Set Up view is entered in the Worklist view.

3 Assign an assay and panel for each sample, or assign a fixed assay or fixed
panel to all samples.

• To assign individual samples, click in the Assay and Panel Name

columns to activate a drop-down menu. Choose options from the
available choices.

54 BD FACS Loader Reference Manual

 • To assign all samples, click the Fixed Assay/Panel button in the button
panel and make appropriate choices in the dialog that appears
(Figure 3-5).

Figure 3-5 Assigning a fixed assay or panel to all samples

Use the Select Mode radio buttons to assign a fixed assay, fixed panel, or
both. Select Flexible to continue making assignments one sample at a time.

Make appropriate selections from the Assay and Panel drop-down menus,
and click OK. The Worklist view appears with your choices in place.

NOTICE After assigning fixed assays or panels, you can still change
settings for individual sample entries in the Assay or Panel Name fields in
the Worklist view.

4 View the information in the Instrument Settings column.

The Instrument Settings column displays the instrument settings file
associated with the chosen panel. To change the associated file, go back to
the Set Up view and click the Assay Settings button. See step 6 on page 47.

Chapter 3: Getting Started 55

 5 Click Sort by Assay at the Worklist view if you are running multiple assays.
Worklist Manager groups all of the same assays together on the Worklist.
This button is active when you complete all sample information.

BD Biosciences recommends that you always group like assays together

when you are running multiple assays in the same Worklist. Since Worklist
Manager can open only one application at a time, each application’s
Summary Report file is renamed with every new run. In addition, launching
and closing a Worklist of ungrouped applications and waiting for Loader
Manager to perform a Short Clean between each different assay are time-
consuming and not recommended.

6 Proceed to Assigning Racks on page 63.

Importing Sample Information

Sample information from a tab-delimited file, such as one generated by an LIS
system, can be read into the correct columns at the Worklist view. Alternatively,
you can import sample information from a Worklist created in BD FACS SPA
software. For details on import file criteria, see Tab-Delimited File Criteria on
page 60 or SPA Worklist Criteria on page 61.

Do the following to import a Worklist.

1 Choose File > Import Worklist (Command-I).

Note that sample information can only be imported into a new, blank
Worklist; you cannot add imported information to a Worklist that is
already started. In addition, the File > Import Worklist command is enabled
only at the Worklist view.

2 Locate and select a file to import in the dialog that appears; click Open
(Figure 3-6 on page 57).

Alternatively, double-click the file icon.

If the imported file is an XML file, Worklist Manager imports it as a SPA

Worklist; otherwise, the file is imported as an tab-delimited file.

56 BD FACS Loader Reference Manual

 Figure 3-6 Selecting a file to import

3 If prompted, choose a Rack ID, and click OK.

If an imported XML file does not contain information for the
<CarouselID> tag, Worklist Manager prompts you to choose one. Choose
an option from the drop-down menu.

The specified ID and tube number are automatically written to the

Location field in the Worklist view.

Chapter 3: Getting Started 57

 For details on import file criteria, see SPA Worklist Criteria on page 61.

4 Review the import errors, if applicable.

A dialog appears if errors occurred during the import. Note that invalid
data is not imported.

If needed, return to the SPA Worklist and correct invalid entries, save the
Worklist, and re-import it.

Valid data is automatically input into the appropriate columns in the

Worklist view, starting at the first available entry (indicated by a •).

5 Review the imported information at the Worklist view; edit missing or

incorrect entries, if needed.

For SPA Worklists, if the imported Worklist does not have a

<SampleName> field and you specify Sample Name for the File Name
Prefix at the Set Up view, Worklist Manager copies the Sample ID to the
Sample Name column.

58 BD FACS Loader Reference Manual

 BD Tritest™ and BD Multitest™ panels are automatically mapped to
MultiSET; user-defined panels are automatically mapped to CellQuest. If
no <AssayName> field is present, the assay name is mapped to MultiSET.

6 (Optional) To view information about an imported SPA Worklist, click the

SPA Info button at the Worklist view.

All of the keywords in the SPA <Globals> section are displayed in the SPA
Info dialog. These keywords are written to the FCS file header when the
acquisition software is run.

7 After importing a tab-delimited file, proceed with Assigning Racks on

page 63; after importing a SPA Worklist, proceed with Setting Up the
Loader on page 68.

An imported SPA Worklist already has Rack IDs assigned; you cannot enter
them in Worklist Manager software.

Chapter 3: Getting Started 59

 Tab-Delimited File Criteria

Information in an imported tab-delimited file (worklist.txt) must meet the

following criteria in order to be successfully imported.

• Each line in the file must correspond to an entry or sample in the Worklist
view and must contain the following values in this exact order:

Sample Name

Sample ID

Case Number

Custom Column #1

Custom Column #2

Custom Column #3

Assay

Panel Name

Param #1

Param #2

Param #3

Param #4

All values in a line must be separated by a tab, and each line must be
terminated with a return. If there is no data for a required value, periods (.)
can be used as placeholders; for example:

DKilian 4432 321 . . . CellQuest IMK Lymph . . . .

• The assay name must match one of the names in the Assay menu at the
Worklist view.

• The panel name must exactly match one of the choices in the Panel Name
menu at the Worklist view. Note that panel names are case sensitive, and
spaces in the panel names must match. BD CellQuest Pro panel names must

60 BD FACS Loader Reference Manual

 include the Experiment document name, separated by a colon
(Panel name : Experiment document name).

• For BD Multiset assays, values to be entered in the Param #1, #2, and #3
columns must be the correct type and within the expected numeric range.

SPA Worklist Criteria

SPA Worklists are written as XML files (worklist.xml) that consist of one major
section, <Worklist>, containing a <Globals> section and one or more <Sample>
sections. The following XML tags can be imported into Worklist Manager.

Section Tag Comments

<Globals> <CarouselID> If missing, Worklist Manager prompts for

a Rack ID during import.

<UniqueCarouselID> If present, Worklist Manager prompts for a

unique ID during the run.

All other <Globals> tags are displayed in the SPA Info dialog and are
written to the FCS file header when the acquisition software is run.

<Sample> <SampleID> Sample identifier that can be used as a file

name prefix

<PanelName> The name must exactly match one of the

choices in the Panel Name menu at the
Worklist view. BD CellQuest Pro panel
names must include the Experiment
document name, separated by a colon
(Panel name : Experiment document name).

<CarouselStartPosition> Tube location on the rack.

<Status> <Status> is missing until the Worklist is

run. Samples with Status = Incomplete
cannot be imported.

Chapter 3: Getting Started 61

 Section Tag Comments

<Sample> <SampleName>a Sample identifier that can be used as a file

(continued) name prefixb

<CaseNumber>a Sample identifier that can be used as a file

name prefix

<AssayName>a CellQuest or MultiSET

a. Not exported in BD FACS SPA software version 1.0, but can be imported into Worklist Manager software
b. If <SampleName> is missing, and you specify Sample Name for the File Name Prefix at the Set Up view,
Worklist Manager copies the Sample ID to the Sample Name column.

Specifying the Starting Point for the Run

The arrow icon to the right of the sample entry number indicates the starting
point for the run. You can specify a different starting point by dragging the icon
to any fully defined entry not yet run, although BD Biosciences recommends that
you leave the starting arrow next to the first entry in the Worklist.

arrow icon

During the run, the arrow icon moves down to point to the sample currently
being run.

If the arrow is pointing to a partially defined entry or a previously run entry,

Worklist Manager automatically skips to the next entry not yet run and starts
acquisition. If acquisition starts in the middle of the Worklist, it cycles to the
beginning after it reaches the end of the Worklist and tries to run entries that have
not yet been run. If you click Run Tests after all entries are run, the Summary
Report appears and the end-of-run cleaning begins if it hasn’t already been done.

62 BD FACS Loader Reference Manual

Assigning Racks
After defining sample information, you are ready to assign each tube to a specific
rack location. Before proceeding, make sure you understand these rules for
assigning racks.

• Tube positions are assigned to samples according to their order in the

Worklist view, starting with Position 1.

• Tube positions are filled in unbroken sequence.

• All the tubes from a sample’s panel must reside on one rack; they cannot be
split between two racks.

• Cleaning tubes are always located in Position 39 (bleach) and 40 (DI water)
on a rack. Cleaning tubes are required on the last rack and can be required
on other racks if you are running multiple assays. Cleaning is automatically
performed between assays and at the end of the Worklist. If 39 or 40 tubes
are assigned on the last rack, the cleaning tubes can be put on in Position
39 or 40 on any unassigned rack.

Follow these steps to assign racks.

1 Click the Assign Rack button in the Worklist view.

The Assign Rack dialog appears, displaying the suggested tube positions on
the rack map for the first sample. A rack break is represented by a
horizontal line, and indicates the start of a new rack (Figure 3-7).

Chapter 3: Getting Started 63

 rack break

Figure 3-7 Rack map for assigning racks

2 Select samples in the Sample list to view the tube and reagent assignments
for each tube in the panel.

The appropriate number of tubes in the rack map are numbered and
colored red, and the tube numbers and corresponding reagents are
displayed in a scrollable list. By default, tubes from different assays are
assigned to different racks, as the following table illustrates.

Entry Number Assay Rack

1 CellQuest 1

2 MultiSETa 2

3 MultiSETa 2
a. like assays

3 Make any necessary changes in the rack map by inserting or deleting rack
breaks.

You can remove a rack break only when there is sufficient space on the
previous rack to contain all tubes from the next sample’s panel.

64 BD FACS Loader Reference Manual

 • To insert a rack break, select a sample in the Sample list; then click
Insert Break. The rack break is inserted above the selected sample.

• To delete a rack break, select the line in the Sample list; then click
Delete Break. Make sure you start at the top of the list.

After inserting or deleting rack breaks, the Sample list is automatically

adjusted.

Different panels in BD CellQuest Pro software can be associated with

different mix settings. BD Biosciences recommends that you consider mix
settings when you group samples from different BD CellQuest Pro panels
on the same rack.

4 Assign a Rack ID.

Choose an unused rack ID from the Rack ID pop-up menu. Rack IDs are
printed on top of each rack and on a label inside the rack which can be read
optically by the Loader.

After choosing a rack ID, the Sample list displays the chosen number. Once
a sample entry is assigned to a rack, entries in the Location, Assay, and
Panel Name columns cannot be changed, and rack breaks cannot be
inserted or deleted.

5 Select a printing option to print the Rack Manifest Report.

Click Print Rack to print a report for the current rack; click Print All Racks
to print reports for all assigned racks. The Rack Manifest report lists
sample information, reagent names, and tube locations for each sample,
and cleaning tube information and locations. The report also contains a
rack map showing the corresponding sample entry numbers for each tube.
Cleaning racks print only if you choose Print All Racks.

Having a printout of rack assignments makes loading the samples into the
rack easier. You cannot view this report on the screen; it must be printed to
be seen.

Chapter 3: Getting Started 65

 ; Tip After you exit the Assign Rack dialog, you can print the Rack Manifest
Report by choosing File > Print Assigned Racks. Cleaning racks do not print.

6 Click OK when you are satisfied with the rack assignments.

The Location column in the Worklist view shows the rack IDs and starting
tube positions for each sample.

7 To edit rack assignments, click Release Rack.

Use the Release Rack dialog to edit entries after racks have been assigned
or to reassign racks.

Select the racks to release by selecting their checkboxes or by clicking Select

All; then click Release. If you release a rack with samples that haven’t been
run, be sure to print a new Rack Manifest and verify that the samples are
loaded into the rack according to the new tube positions.

66 BD FACS Loader Reference Manual

 4

Running Samples
Once you define all sample and rack information and save the Worklist
document, you are ready to acquire samples.

The following topics are covered in this chapter:

• Setting Up the Loader on page 68

• Running Samples on page 70

• Rerunning a Full Entry on page 78

• Viewing the Summary Report on page 79

67
Setting Up the Loader
Follow these steps to set up the Loader rack(s) and install the first rack on the
cytometer. If you are running samples that were prepared on a BD FACS Sample
Prep Assistant (SPA), skip to step 3 on page 69. Then proceed to Running
Samples on page 70.

1 Remove the Loader rack from the instrument, if needed.

Slide the Loader cover forward and pull out the Loader drawer. Place your
thumb on the center spindle, and press down with your thumb while gently
pulling up on the rack handle with two fingers, as shown in Figure 4-1.

Figure 4-1 Removing a rack

2 Vortex the sample tubes and place them in the rack(s) according to the
Rack Manifest.

If the Rack Manifest indicates cleaning tubes are required on that rack,
load a tube containing 3 mL of 10% bleach in Position 39 and a tube
containing 3 mL of deionized water in Position 40.

If the last rack is full of sample tubes, use another rack for cleaning. The
cleaning rack does not need to be assigned. Worklist Manager prompts you

68 BD FACS Loader Reference Manual

 to install a rack with bleach and water tubes at the completion of sample
acquisition.

Make sure the actual tube loading sequence matches what is printed on the
Rack Manifest.
If loaded racks sit for an extended period of time before you run the
samples on the Loader, you must vortex the tubes again before proceeding.

3 Install the first rack to be acquired on the Loader.

Position the spindle hole in the rack handle over the center spindle of the
Loader drawer. Rotate the rack until the alignment guide pin fits into the
small alignment hole at the top of the rack. Press down firmly to seat the
rack.

spindle hole rack handle

alignment hole
ous p Re a d y
ck
Capr le-Preiences
el Ra
am BD Biosc

Figure 4-2 Installing the Loader rack

4 Close the Loader drawer completely, and install the Loader cover.
The Loader scans and positions the rack at tube Position 1.

To operate the Loader, the cover must be in place on the Loader drawer.
Tubes will not be loaded if the cover is off, and currently running tubes will
be unloaded if the cover is removed during a run.

Chapter 4: Running Samples 69

Running Samples
After you click Run Tests at the Worklist view, Worklist Manager runs the
samples listed in the Worklist. If a Worklist contains both BD CellQuest Pro and
BD Multiset assays, a short cleaning cycle (approximately 3 minutes) is
performed as each completed application closes. When the Worklist is complete,
a long cleaning cycle (approximately 12 minutes) is performed. When the final
cleaning cycle is complete, the Summary Report appears in the Summary view.

For application-specific options during acquisition, see BD CellQuest Pro

Options During Acquisition on page 74 or BD Multiset Options During
Acquisition on page 75.

1 Place the flow cytometer in RUN mode and choose the appropriate flow
rate.

; Tip Before proceeding with step 2, make sure the paper tray for the printer
you are using has a sufficient supply of paper. If the printer runs out of paper
in the middle of a run, the run will stop.

2 Click Run Tests at the Worklist view.

If you have not yet saved the Worklist document, a dialog appears,
instructing you to do so.

The following initialization steps are performed:

• The Loader checks the Rack ID.

• Tube locations are checked against the Rack Manifest.

• The acquisition software is launched.

A number of things happen as the acquisition software is launched.

• The application-specific document for the first sample is opened.

• Instrument settings are downloaded to the cytometer, if a file was

linked to the sample’s panel in Assay Settings.

70 BD FACS Loader Reference Manual

 • The start-of-rack mix occurs.

• Sample acquisition begins.

NOTICE If a Loader error occurs during a run, a dialog appears with

options to Retry, Continue, or Stop Run. Click Retry to recheck the status;
click Continue to complete acquisition of that tube without fixing the error
condition. Errors are noted on the Summary Report.

If a file-naming conflict occurs during the run, the application modifies the
file name by adding an uppercase letter after the tube number. See File-
Naming Conflict During a Run on page 34 for more information. The
Worklist is aborted if the conflict cannot be resolved.

3 If prompted, enter or scan the unique carousel ID from the imported SPA
Worklist (Figure 4-3), and click Continue.

The following dialog appears if you defined a unique carousel ID in the

SPA worklist.

Figure 4-3 Entering a unique Carousel ID

4 Install the next rack, if prompted.

After acquisition is complete for the first sample or panel, acquisition of the
next sample or panel begins. If the next sample or panel uses different
instrument settings, the new settings are automatically downloaded to the
cytometer. If the next sample or panel uses a different acquisition

Chapter 4: Running Samples 71

 document, the first acquisition document is closed, and the next one is
opened.

Worklist Manager software automatically launches and closes acquisition

software to run their respective panels.

5 When the final cleaning cycle is complete, review the Summary Report.
See Viewing the Summary Report on page 79. To print the Summary
Report, choose File > Print.

6 Remove the Loader cover, pull out the Loader drawer, and remove the rack.

7 Install a tube of distilled water on the SIP and place the support arm
underneath the tube.

8 Put the cytometer in Standby mode.

9 Quit Worklist Manager software.

Pausing Acquisition

To interrupt the Loader when you are running BD Multiset software,

always stop the run within BD Multiset software; do not interrupt the run
from Worklist Manager software. See Interrupting BD Multiset Software
on page 75. In addition, it is not good practice to interrupt a run by
removing the Loader cover.

To stop the Loader run when you are using BD CellQuest Pro software, do the
following.

1 Click Stop at the Worklist view.

2 When the countdown dialog appears, click Yes.

3 Click the Worklist Manager background view to activate it, and click Stop.

72 BD FACS Loader Reference Manual

 Alternately, activate Worklist Manager by clicking the application icon in
the Dock.

4 A 15-second countdown dialog appears; click Yes to stop acquisition of this

tube.

Choose from the following options.

• Rerun—reruns the current tube

• Next Tube—skips to the next tube on the Worklist

• Next Sample—advances the Loader to the first tube of the next sample
(if available), leaving the previous sample incomplete

• Stop Run—advances to the Summary Report view

NOTICE If you abort a run, the Long Clean is not performed

automatically. To clean after an aborted run, use the Cleaning option in
LoaderManager’s Maintenance and Diagnostics window. See Loader
Shutdown on page 82 for details.

The Worklist status icons indicate which samples have or have not been
run. See Creating a Worklist on page 52 for a description of the icons.

Chapter 4: Running Samples 73

 BD CellQuest Pro Options During Acquisition
You can use BD CellQuest Pro software controls during acquisition with the
Loader. Acquisition will proceed, uninterrupted, unless you click any of the
following Acquisition controls:

• Pause—suspends acquisition. The Loader keeps the sample running, but

data collection is suspended.

• Resume—continues collecting events, adding events to those already acquired

• Restart—begins collecting events, discarding the events already acquired

• Save—stops collecting events, saving the events already acquired to the

data file

• Abort—stops acquisition of the current tube only (discards the events

already acquired for this tube but does not abort the entire Worklist)

To make instrument setting adjustments during acquisition, click Pause, click

Abort, and then select the Setup checkbox in the Acquisition Control window.
After you make the needed adjustments, deselect the Setup checkbox, and then
click Acquire to continue with automated acquisition.

Be sure to enter Setup mode before changing instrument settings. If you

change instrument settings while not in Setup mode, the data file will
contain data acquired using the old and the new instrument settings.

Worklist Manager aborts acquisition of a tube and stops the Worklist run if
acquisition is not completed within 10 minutes. However, if you are acquiring a
BD CellQuest Pro document with a collection criteria based on time, the
BD CellQuest Pro–specified time overrules Worklist Manager.

NOTICE Any changes made to an Experiment document during a Worklist run

remain in effect only while the document is open. Changes are not saved when
the document is closed automatically by Worklist Manager software.

74 BD FACS Loader Reference Manual

BD Multiset Options During Acquisition
When Worklist Manager launches BD Multiset software, you will have access
only to the Acquisition, Analysis, Lab Report, and Physician Report views. You
will not be able to stop and view a Summary Report at the Summary view. This
report is created only when Worklist Manager quits the application.

The following information in a Schedule document can change when that

document is run with Worklist Manager, but these changes are not saved.

• Data Source becomes From Cytometer.

• View Reports defaults to 5 seconds unless a value of 2 or 0 was saved in the

Schedule document.

• Panel preference becomes Run Any Panel.

• All sample information is eliminated.

Interrupting BD Multiset Software

To interrupt the Loader when you are running BD Multiset software,

always stop the run within BD Multiset software; do not interrupt the run
from Worklist Manager software. In addition, it is not good practice to
interrupt a run by removing the Loader cover.

There are two places where you can interrupt BD Multiset software: at the
Acquisition view or the Lab Report view. To make instrument setting
adjustments, pause at the Acquisition view; to perform manual gating, pause at
the Lab Report view.

Chapter 4: Running Samples 75

 1 Within BD Multiset software, click Pause at the Acquisition view, if
necessary.

When you click Run Tests at the Worklist view, BD Multiset software
launches and events appear in plots at the Acquisition view. Acquisition
begins after a defined countdown. You can pause acquisition while the
countdown dialog is present.

2 Choose from the following options at the Acquisition view.

• To make instrument adjustments, choose Det/Amps, Threshold, or
Compensation from the Cytometer menu. Adjust the settings using the
appropriate software controls. Refer to the BD Multiset Software
Reference Manual for more information.

Instrument settings adjustments apply only to the current tube; they are not
saved with the Schedule document.

• To continue acquisition, click Acquire.

3 Within BD Multiset software, click Pause at the Lab Report view, if

necessary.

If you specified to view reports for 2 or 5 seconds in the BD Multiset Set Up

view, the Lab Report remains on display for the specified time and a
countdown dialog appears. You can pause at the Lab Report view while the
countdown dialog is present.

76 BD FACS Loader Reference Manual

4 Choose from the following options at the Lab Report view.

• To perform manual gating, click Manual Gate. You can make

adjustments to the expert gate or the attractors and change the
parameters displayed for the tube just analyzed. Refer to the
BD Multiset Software Reference Manual for more information..

The Manual Gate button is enabled only when the data source is From
Cytometer: Acquisition with Analysis. Changes to the attractors or the
display apply only to the current tube; they are not saved with the Schedule
document.

• To rerun the tube just acquired on the cytometer, click Rerun. You can
save the original data or you can overwrite it. Note that you can
choose to rerun an individual tube only at the Lab Report view; to
rerun all tubes in a panel, see Rerunning a Full Entry on page 78.

• To proceed with acquisition and analysis for the next tube, click
Continue. If this was the last tube in the panel, BD Multiset software
closes and Worklist Manager displays the Summary Report view.

• To skip to the next tube or the next sample, click Skip. Note that you
cannot skip tubes when running control panels.

• To stop the run, click Stop. A verification dialog appears asking if you
want to quit. If you click Yes, BD Multiset software quits and the
Worklist Manager Summary Report view appears..

Choose Stop only if you want to quit the clinical application. If you abort a
run, the Long Clean is not performed automatically. To clean after an
aborted run, use the Cleaning option in LoaderManager’s Maintenance and
Diagnostics window. See Loader Shutdown on page 82 for details.

Chapter 4: Running Samples 77

Rerunning a Full Entry
You can perform up to five full-entry (entire panel) reruns either at the
completion of a Worklist or if a Worklist is completely stopped. You must initiate
a full-entry rerun from the Worklist view.

See Naming a Rerun Tube on page 35 for information on file naming

conventions.

1 Click the Status icon of the sample you want to rerun at the Worklist view.
Status icons indicate the state of the run. See Creating a Worklist on
page 52 for a description of the various Status icons.

The Sample Run Status window appears, listing the status of all tubes in
the selected tube’s panel.

2 Click Rerun to rerun the entire panel.

Note that you cannot choose to rerun individual tubes. To cancel the rerun
and return to the Worklist view, click OK.

78 BD FACS Loader Reference Manual

Viewing the Summary Report
A Summary Report appears in the Summary view at the completion of every run.
The Summary Report lists all sample and reagent information, the rack location,
the data files saved, and the status of the run.

You can save and print the Summary Report by choosing the appropriate
commands from the File menu. If you clicked the Summary Report checkbox at
the Set Up view, the report is automatically saved when the Worklist is completed
or stopped.

At the Summary view you can quit the program or choose to run more samples
by clicking the Worklist icon.

Chapter 4: Running Samples 79

 If an error occurred during the run, an error message appears on the Summary
Report. There are four types of error messages; refer to the indicated
documentation for assistance in troubleshooting errors.

• For file-saving errors, see WorklistManager Troubleshooting on page 104

or refer to your acquisition software manual.

• For Loader errors, see Loader Troubleshooting on page 100.

• For cytometer errors, refer to your instrument manual.

• For multiple errors, refer to the appropriate documentation.

80 BD FACS Loader Reference Manual

 5

Maintenance
The following topics are covered in this chapter:

• Loader Shutdown on page 82

• Loader Diagnostics on page 84

• Unscheduled Maintenance on page 86

• Modifying the Cytometer for Non-Loader Use on page 95

81
Loader Shutdown
This section describes how to perform a Long Clean using Loader Manager
software, and how to shut down the Loader. Note that a Long Clean is
performed automatically at the end of each Worklist run. Run the cleaning
procedure manually if you stop a Worklist before it is complete, or for additional,
optional cleaning after the procedure has been run automatically.

1 Quit Worklist Manager software, if it is open.

2 Launch Loader Manager software.

The Loader Status window appears.

3 Click the Maintenance button, or press Command-M.

The Maintenance and Diagnostics dialog appears.

82 BD FACS Loader Reference Manual

 4 Verify the Long Clean option is selected; click Run.
The Long Clean procedure runs bleach and distilled water through the
cytometer for approximately 12 minutes.

A message appears, prompting you to install bleach and rinse tubes.

5 Set up a Loader rack with cleaning tubes; install the rack on the Loader.
Install a tube containing 3 mL of 10% bleach in position 39 and a tube
containing 3 mL of DI water in position 40.

6 Click Run.
A cleaning status dialog appears.

7 When the cleaning cycle is complete, remove the Loader cover and rack.

8 Install a tube of distilled water on the SIP.

9 Put the cytometer in Standby mode.

10 Quit Loader Manager software.

11 Vent the sheath tank and turn off the cytometer.

12 Switch off the Loader power on the keypad.

13 Push in the Loader drawer; leave the Loader rack and cover off.

Chapter 5: Maintenance 83
Loader Diagnostics
Diagnostic features in Loader Manager software allow you to access an error log,
check the calibration of the Loader’s tube lifter, and set or change the connection
port. Note that these features are available only when you launch Loader
Manager software independent of Worklist Manager software.

• To view the error log, see Accessing the Error Log on this page.

• To check the tube lifter calibration, see Checking Tube Lifter Calibration
on page 85.

Accessing the Error Log

The Error Log lists the last 100 hardware errors logged by the system. You can
print the log for use in Loader diagnostics or troubleshooting.

1 Quit Worklist Manager software, if needed, and launch Loader Manager.

2 Click the Maintenance button in the Loader Status window.

3 Click the Error Log button in the Maintenance and Diagnostics window.
The Loader Error Log dialog appears (Figure 5-1 on page 85), listing the
date, time, and description of the last 100 hardware errors.

84 BD FACS Loader Reference Manual

 Figure 5-1 Loader Error Log dialog

4 Click Print to print the log, if needed.

5 Click Done to return to the Maintenance and Diagnostics window.

6 Click Done to return to the Loader Status window.

Checking Tube Lifter Calibration

Tube lifter parameters are used to adjust the tube lifter to ensure proper sealing
with the SIP. You might be asked to communicate these settings to
BD Biosciences personnel if you call for troubleshooting assistance.

1 Quit Worklist Manager software, if needed, and launch Loader Manager

software.

2 Click the Maintenance button in the Loader Status window.

Chapter 5: Maintenance 85
 3 Click Check Lifter Parameters in the Maintenance and Diagnostics
window, and click Run.

The Check Lifter Parameters dialog appears (Figure 5-2).

Figure 5-2 Check Lifter Parameters dialog

4 Click Print to print a record of the stored lifter parameters, if needed.

5 Click Done to return to the Maintenance and Diagnostics window.

Unscheduled Maintenance
Perform the following maintenance procedures when indicated by an error
message or you observe a decline in instrument performance.

• For communication problems between the Loader and the cytometer, see
Verifying Connection Ports on page 87.

• For tube pressurization issues, see Replacing the Loader Seal on page 88.
(Change the seal only after you have tried all other troubleshooting
solutions listed in Test tube not pressurizing on page 101.)

86 BD FACS Loader Reference Manual

 • To replace the fuse in the electronics module, see Replacing a Loader Fuse
on page 90.

• To correct a repeated vertical timeout error, see Cleaning the Tube Lifter on
page 93.

Verifying Connection Ports

The Loader electronics module connects to the computer via a Keyspan USB-to-
serial adapter. If you are experiencing communication problems between the
Loader and the cytometer, verify that the cables are securely connected, and the
correct port is selected in Loader Manager Preferences.

1 Check the cable connections between the Loader electronics module and
the adapter (Figure 5-3).

The cable attaches to the serial port in the electronics module, and to port 2
on the adapter.

NOTICE For Mac OS X computers, the cable should be attached only to

adapter port 2 (on the curved side of the adapter).

to computer
electronics module

adapter

to adapter to Loader

Figure 5-3 Cable connections between the Loader and the computer

2 Check the cable connections between the adapter and the computer.

; Tip For reliable performance, always plug the adapter directly into a USB
port on the computer; do not use a USB hub.

Chapter 5: Maintenance 87
 3 Quit Worklist Manager software, if needed, and launch Loader Manager
software.

4 Choose LoaderManager > Preferences.

The Serial Port Selection dialog appears.

5 Verify that Print Port (2) is selected; click Save.

If you continue to have connectivity problems after you have checked all
cable connections, contact your BD Biosciences service representative.

Replacing the Loader Seal

The Loader seal can become worn over time and need replacement. If you have
trouble sealing tubes when using the Loader, you might need to replace this seal.
Before replacing the seal, be sure to check other possible causes of sealing
problems in Test tube not pressurizing on page 101.

Any instrument surface that comes in contact with biological

specimens can transmit potentially fatal disease. Use universal
precautions when handling instrument hardware. Wear suitable
protective clothing and gloves.

1 Turn off the instrument main power.

2 Remove the tube guide retainer and attached tube guide.

88 BD FACS Loader Reference Manual

 Turn the tube guide and tube guide retainer counterclockwise, as shown in
Figure 5-4 on page 89.

tube guide retainer

tube guide

tube stop

Figure 5-4 Removing the tube guide retainer

3 Remove the outer droplet sleeve from the sample injection tube by turning
the SIP retainer counterclockwise (Figure 5-5).

Loader seal
SIP retainer

outer droplet sleeve

Figure 5-5 SIP components

Chapter 5: Maintenance 89
 ; Tip Hold the sleeve as you turn the retainer. The outer sleeve might fall
out as you loosen the retainer.

4 Remove the flat, red or white Loader seal.

5 Install the new seal.

NOTICE The Loader accessory kit includes three versions of the seal—a
thick, medium, and thin version. Install the next-thickest version,
compared to the seal that is currently installed. Make sure it is flush against
the sample injection tube.

For reordering information, see Replacement Parts on page 106.

6 Replace the outer droplet sleeve and tighten the SIP retainer.

7 Replace the tube guide retainer and the tube guide.

8 Test the new seal by loading a tube with the Lifter key on the Loader
keypad.

Replacing a Loader Fuse

There are two fuses located inside the fuse drawer on the back-left corner of the
electronics module. Change a fuse only if you are instructed to do so in the
troubleshooting section of this reference manual or by a BD Biosciences service
representative. .

Protect against the risk of fire by replacing fuses only with those of
the specified type and rating. To prevent shock injury or damage to
the instrument, turn off the power and unplug the Loader power cord
before attempting to change the fuse.

1 Turn off the power to the Loader and the cytometer.

2 Unplug the Loader power cord from the wall outlet.

90 BD FACS Loader Reference Manual

3 Remove the access panel from below the instrument sheath and waste
compartment.

This panel is easily removed by snapping it from the instrument frame.

4 Access the fuse drawer. Remove all the cables from the electronics module
and slide the module out from under the cytometer.

5 Place a small screwdriver into the slot at the left of the fuse drawer and pry
to pop out the drawer (Figure 5-6).

power switch
AC power plug
fuse drawer

Figure 5-6 Back corner of the electronics module

Chapter 5: Maintenance 91
 6 Pull out the fuse drawer, remove the fuses, and examine them (Figure 5-7).
If the filament is broken or if you see any discoloration of the glass, discard
the fuse.

Figure 5-7 Removing fuses

7 Replace any damaged fuses with new fuses from your spares kit.
For reordering information, see Replacement Parts on page 106.

8 Slide the fuse drawer into the electronics module.

The clip should be to the left. Push gently on the drawer until it snaps into
place.

9 Reconnect all Loader cables, if required.

Figure 5-8 illustrates the proper cable connections.

cytometer

Loader motors Loader communication USB adapter keypad

Figure 5-8 Cable connections on the electronics module

92 BD FACS Loader Reference Manual

10 Plug the AC power cord into the wall outlet, and turn on the Loader power
from the keypad control.

11 Replace the access panel on the cytometer.

Cleaning the Tube Lifter

The Loader tube lifter might need cleaning if a vertical timeout error is reported
by Loader Manager software. Use the Single Commands dialog to load a single
tube so you can access the tube lifter.

1 Place an empty test tube in position 1 on a Loader rack, and install the rack
on the Loader.

2 Push in the Loader drawer and replace the cover.

3 Confirm that all software applications are closed.

Use the Dock to make sure that all BD applications are closed.

4 Launch Loader Manager software, and click the Maintenance button.

5 Click Single Commands in the Maintenance and Diagnostics window, and

click Run.

The Single Commands dialog appears, where you can select individual
commands and send them to the Loader.

Chapter 5: Maintenance 93
 6 Select the Park lifter command in the left column, and click Send.
Ensure the tube number is 1 in the Enter the tube number to load field.

7 Once the lifter is raised, switch off the Loader power on the keypad.

8 Remove the Loader cover.

9 Hold the test tube in place with one hand, while you pull out the Loader
drawer with the other hand.

10 Remove the Loader rack and the test tube, and place the test tube in the
rack.

11 Use a gauze pad and deionized water to wipe the tube lifter shaft and base.

12 Push in the Loader drawer and replace the cover.

13 Switch on the Loader power.

The lifter will automatically lower.

14 Select the Reset controller command in the Single Commands dialog, and
click Send.

15 Install a rack with a tube in position 1 and check the tube lifting and
sealing.

For other troubleshooting suggestions, see Vertical Timeout Error on

page 103.

94 BD FACS Loader Reference Manual

Modifying the Cytometer for Non-Loader Use
When your Loader is installed, a BD Biosciences service representative removes
the Bal seal in the cytometer and installs a Loader seal and a tube guide. This
configuration creates the proper seal and pressurization for Loader use. If you
want to acquire samples without using the Loader, you must remove the tube
guide and replace the Bal seal.

Any instrument surface that comes in contact with biological

specimens can transmit potentially fatal disease. Use universal
precautions when handling instrument hardware. Wear suitable
protective clothing and gloves.

1 Turn off the instrument main power.

2 Remove the tube guide retainer and attached tube guide.

Turn the tube guide and tube guide retainer counterclockwise, as shown in
Figure 5-9.

tube guide retainer

tube guide

Figure 5-9 Removing the tube guide

Chapter 5: Maintenance 95
 3 Remove the outer droplet sleeve from the sample injection tube by turning
the SIP retainer counterclockwise.

Loader seal
SIP retainer

outer droplet sleeve

; Tip Hold the sleeve as you turn the retainer. The outer sleeve might fall
out as you loosen the retainer.

4 Remove the flat, red or white Loader seal.

5 Install the black, rubber O-ring in place of the Loader seal.

To order a replacement, see Replacement Parts on page 106.

6 Install the Bal seal spring-side up just above the threads for the SIP retainer.

7 Reinstall the SIP retainer and outer droplet sleeve over the sample injection
tube.

Gently push the Bal seal in place to seat it. If the seal does not remain in
position when you let go of it, hold it with one hand while you reinstall the
retainer. The seal will seat as you screw on the retainer.

Tighten the SIP retainer just enough to hold it in place, then slide the outer
sleeve over the sample injection tube and into the opening of the retainer.
Continue tightening the retainer.

96 BD FACS Loader Reference Manual

8 Install a sample tube on the SIP to ensure that the outer sleeve has been
properly installed.

If the sleeve hits the bottom of the tube, loosen the retainer slightly and
push the sleeve up as far as it will go. Tighten the retainer.

9 Adjust the tube stop so it fits snugly under the bottom of an installed test
tube.

tube stop

Chapter 5: Maintenance 97
98 BD FACS Loader Reference Manual
 6

Troubleshooting
The tips in this section are provided to help you troubleshoot issues that might
arise when using the BD FACS Loader. For additional troubleshooting
information, refer to your instrument manual.

If additional assistance is required, contact your local BD Biosciences technical

support representative. See Technical Assistance on page x.

Troubleshooting suggestions in this chapter are grouped under the following

headings:

• Loader Troubleshooting on page 100

• LoaderManager Troubleshooting on page 103

• WorklistManager Troubleshooting on page 104

99
Loader Troubleshooting
Observation Possible Causes Recommended Solutions

No LED display on Loader power not turned on Switch on the Loader power on
Loader keypad the keypad.

Loader power cord not Switch off the power, plug in the
plugged in Loader power cord, and switch
the power back on.

Main power switched off on 1 Turn off the power on the

Loader electronics module keypad.
2 Remove the front access panel
from the cytometer.
3 Reach to the back left corner of
the electronics module and
press the switch to the right
(while looking from the front).
4 Turn on the Loader keypad
power.
If the LED display appears,
reattach the access panel; if the
LED display does not appear,
see the next cause.

Loader electronics module Replace the fuse. See Replacing a

fuse blown Loader Fuse on page 90.

Incorrect rack spin Rack not engaged with Rotate the rack on the spindle
alignment pin on drawer until the alignment guide pin
engages with the alignment hole in
the rack, and press down. See
Figure 4-2 on page 69. If the
problem persists, contact
BD Biosciences for assistance.

100 BD FACS Loader Reference Manual

Loader Troubleshooting (continued)
Observation Possible Causes Recommended Solutions

Test tube not Fluidic control switch not in Turn fluidic control switch to
pressurizing RUN RUN.

Test tube cracked Replace test tube.

Sheath tank not pressurized Make sure the vent valve is closed
and the sheath reservoir cap is
securely on.

SIP outer droplet sleeve not Loosen the SIP retainer, push the
properly installed sleeve up until it seats properly,
and then tighten.

Tube Lifter Parameters not Check the lifter parameters in

correctly set LoaderManager software. See
Checking Tube Lifter Calibration
on page 85. Compare these values
to the ones provided by your
service representative. If they do
not match, contact BD Biosciences
for assistance.

Difference between Loader See Modifying the Cytometer for

sealing and manual sealing Non-Loader Use on page 95 for
(Bal seal) instructions on reinstalling the Bal
seal. Manually check test tube
sealing. If tube still does not seal,
the problem is with the cytometer
and not the Loader. Refer to the
appropriate instrument guide for
additional troubleshooting
information.

Worn Loader seal Replace the seal as described in

Replacing the Loader Seal on page 88.
NOTICE This should be done only
after checking all other
troubleshooting solutions.

Chapter 6: Troubleshooting 101

Loader Troubleshooting (continued)
Observation Possible Causes Recommended Solutions

Communication problem Loader power not on Switch on the Loader power on the
between Loader and keypad.
computer
Quit the software and relaunch.

Loose or damaged cable Shut down the computer and switch

connecting Loader to off the Loader power. Check the
computer cable connections between the
computer and the Keyspan adapter.
Remove the access cover from the
cytometer, and check the connection
between the adapter and the
electronics module. See Verifying
Connection Ports on page 87.

Wrong communication port Choose LoaderManager >

selected in LoaderManager Preferences. Check that the selected
software port corresponds to the adapter port
the cable is plugged into. If it is not,
change the Preference, save, quit the
software, and relaunch. See
Verifying Connection Ports on
page 87.

Tube stuck message Firmware not clearing error Remove the Loader cover, even if the
displayed repeatedly message tube does not appear to be stuck.
Put the tube back into the rack. Re-
install the cover and click Retry.

102 BD FACS Loader Reference Manual

LoaderManager Troubleshooting
Observation Possible Causes Recommended Solutions

Vertical Timeout Error Test tube not completely Make sure the Loader drawer is
raised completely shut. Also, make sure
the test tube is free of unnecessary
labels or tape.

Tube lifter hitting rack during Make sure the rack is properly
ascent engaged with the alignment guide
pin. If the problem persists,
contact BD Biosciences for
assistance.

Spillage causing tube lifter to Clean the tube lifter. See Cleaning
bind the Tube Lifter on page 93.

Invalid rack ID Rack not spinning properly Rotate the rack on the spindle
until the alignment guide pin
engages with the alignment hole in
the rack, and press down. See
Figure 4-2 on page 69. If the
problem persists, contact
BD Biosciences for assistance.

Incorrect rack loaded Use the rack ID assigned in

WorklistManager software, and
load the tubes according to the
Rack Manifest.

Invalid tube sequence Incomplete scan resulting Remove and re-install the Loader
from an interrupt cover.

Wrong tubes installed Check the Rack Manifest Report

for proper tube locations; make
sure cleaning tubes are in place, if
required.

Chapter 6: Troubleshooting 103

WorklistManager Troubleshooting
Observation Possible Causes Recommended Solutions

BD CellQuest Pro Experiment document(s) not Place Experiment document(s) for

Experiment document(s) located in correct folder use with WorklistManager
not appearing in Panel software in the CellQuest
pop-up menu in Assay Experiments Folder in the
Settings dialog at WorklistManager Folder.
Worklist view
Panel not selected in Open document in
Experiment document(s) BD CellQuest Pro software and
load the panel in the Acquisition
Browser. See Defining a
BD CellQuest Pro Experiment
Document on page 38.

Instrument settings files Instrument settings not Place instrument settings files in
not appearing in located in correct folder the Instrument Settings Files
Instrument Settings pop- folder in the BD Files folder.
up menu in Assay
Settings dialog

MultiSET not listed in PanelReagentFile alias Re-install BD Multiset software.

the Assay pop-up menus missing from ClinApps Info
at Set Up view, Worklist Folder
view, or Assay Settings
dialog

BD CellQuest Pro Time not included in Redefine the Experiment

timeout during Collection Criteria document with Collection Criteria
acquisition, and event set to Event Count or Time. See
count not achieved Defining a BD CellQuest Pro
within 10-minute time Experiment Document on
limit page 38.

BD Multiset timeout Poor sample preparation; ie, Prepare new sample and re-
during acquisition sample too dilute acquire.

Unusual side scatter in Inappropriate mix settings at Use the default assay mix settings.
BD Multiset results Assay Settings dialog (Set Up
view)

104 BD FACS Loader Reference Manual

 Appendix A

Technical Specifications
Installation Requirements

Power: 120 VAC ±10%, 60 Hz ±5%

100 VAC ±10%, 60 Hz ±5%
200/240 VAC ±10%, 50 Hz ±5%

Size: width—91 cm (36 in)

depth—61 cm (24 in)
height—18 cm (7 in)

Weight: 34 kg (75 lb)

Temperature: 16–29°C (60–85°F)

Recommended work space:

BD FACStation + BD FACSCalibur + Loader 71"L x 39"D x 52"H

Total weight:
BD FACStation + BD FACSCalibur + Loader 175 kg (385 lb)

105
Replacement Parts
The BD FACS Loader comes equipped with four racks and an accessory kit,
containing spare and replacement parts. Use the following part numbers to order
additional racks or replacement parts. These part numbers are current at the time
of publication; contact your local BD representative or distributor for up-to-date
ordering information. See the title page of this reference manual or refer to our
website, www.bdbiosciences.com, for worldwide contact information.

Product Description Part Number

Carousel kit, racks 1–4 332727

Carousel kit, racks 5–8 332728

Carousel kit, racks 9–12 332729

Carousel kit, racks 13–16 332730

BD Falcon 12 x 75-mm tubes 343675

(bag of 125)

Tube guide 19-66208-00

Tube guide retainer 19-66206-00

Spare fuses (four each):

• 2.5 A, 250 V (US) • 343565
• 3.15 A, 250 V (Asia) • 38-30049-00
• 1.25 A, 250 V (Europe) • 38-30050-00

Loader seal (three each):

• thick (0.188 cm thick) • 19-66379-03
• medium (0.125 cm thick) • 19-66379-01
• thin (0.093 cm thick) • 19-66379-02

Black, rubber O-ring 88-20040-00

Bal seal 88-20085-00

Keyspan USB adapter 344299

106 BD FACS Loader Reference Manual

 Index
A BD CellQuest Pro See CellQuest Pro.
BD FACSComp See FACSComp.
acquisition BD Multiset See Multiset.
controls, CellQuest Pro 74 breaks, rack 64
documents 38 button panel 25
Multiset options 75
pausing 72, 75
start delay 48 C
starting 70 cables, Loader 87, 92
timeout 104 carousel ID, SPA 71
tube order 62 CellQuest Pro
adding custom columns 30 acquisition options 74
adjusting automatic printing option 49
column width 53 Experiment document 38
instrument settings 74, 76 file naming 33
arrow, starting 62 missing Experiment document 102,
assay settings 47 104
assays timeout 104
assigning to samples 54 choosing assays 45
saving options 45 cleaning
sorting 56 cycles 70, 82
assigning tube lifter 93
assays 54 tubes 68, 83
rack IDs 65 columns
racks 63 preferences 30
assistance, technical x resizing 53
communication error 87, 102
B compatibility, Worklist Manager 17
components, Loader 12
Bal seal, reinstalling 95 computer requirements 17
barcode scanner 54 computer-controlled mode 27
BD Applications folder 19 cover, Loader 69

107
custom columns 30 file-naming conventions
cytometer, modifying for non-Loader all assays 33
use 95 reruns 35
run conflict 34, 71
D Worklist Manager files 33
files
data files 32, 45 export 46
default Schedule document 42 importing Worklists 56
defining instrument settings 50
acquisition documents 38 naming conflict 34, 71
rack ID range 28 naming conventions 33
Worklists 52, 54 naming rerun tubes 35
diagnostics, Loader Manager 84 saving 35, 45
Disabled status 15 storage locations 45, 46
Summary Report 32
E tab-delimited 60
Worklist Manager 32
editing XML import requirements 61
racks 66 fixed assays/panels 54
Schedule document 42 folders
electronics module, Loader 87, 91 BD Applications 19
entering sample information 54 CellQuest Experiments 41
errors invalid location 45
log 84 fuses, replacing 90
SPA import 58
Summary Report messages 80
vertical timeout 93, 103 H
Experiment documents hardware
defining 38 components 12
missing 102, 104 requirements 17
saving 41
export files 46
I
F icon bar 24
See also Workist Manager views.
FACSComp import errors, SPA 58
launching 50 importing
skipping 50 tab-delimited files 60
view 25, 50 Worklists 56
FCS data files 32, 45 XML files 61
file name prefix 44

108 BD FACS Loader Reference Manual

installing Loader
Bal seal 95 about 12
Loader cover 69 cables 87, 92
Loader racks 69 communication problems 102
software 18 components 12
instrument settings connection port 87
adjusting during acquisition 74, 76 cover, installing 69
files 50 drawer 13
linking to panels 48, 55 electronics module 87, 91
not available 104 fuses, replacing 90
invalid keypad 15
location 45 limitations ix
rack ID 103 preferences 28
tube sequence 103 rack 15
seal, replacing 88
K setting up 68
shutting down 82
keypad spares kit 106
about 15 status 26
no display on 100 troubleshooting 100
Loader Manager
L about 26
diagnostics 84
launching installing 18
FACSComp software 50 launching 20, 24
software 20, 24 maintenance 82
limitations, hardware and software ix preferences 88
troubleshooting 103
log, error 84

M
manual operation 16, 27
menu bar 24
message box 25
mixing
manual operation 16
settings 48

Index 109
Multiset R
abnormal side scatter 104
acquisition options 75 rack breaks 64
file naming 33 rack IDs
pausing acquisition 75 about 14
reports 45 allowable range 28
Schedule document 42 assigning 65
timeout 104 invalid 103
unable to choose assay 104 SPA 57
Rack Manifest 65
racks
N about 15
naming conventions, file 33 advancing manually 16
assigning 63
incorrect spin 100
O
installing 69
optical sensors 14 releasing 66
removing 68
P setting up 68
registering software 21
panels releasing racks 66
assigning 54 removing
linking settings 48 racks 68
parameters, tube lifter 85 tube guide 95
pausing acquisition 72, 75 reordering parts 106
preferences replacing
columns 30 Loader fuses 90
Loader 28 Loader seal 88
Loader Manager 88 reports, saving 45
pressurization failure 101 requirements
printing hardware 17
lifter parameters 86 installation 105
options, CellQuest Pro 49 software 17
Rack Manifest report 65 rerunning tubes 35, 73, 77, 78
Summary Reports 36, 79 reruns, full-entry 78
running
Q FACSComp 50
samples 70
quitting software 21 single commands 93

110 BD FACS Loader Reference Manual

S software
about 12
sample information installing 18
entering 54 launching 20, 24
importing 56 quitting 21
Sample Prep Assistant (SPA) registering 21
global information 59 requirements 17
importing Worklists 56 software requirements 17
rack IDs 57 Sort by Assay 56
unique carousel ID 71 SPA See Sample Prep Assistant (SPA).
Worklist criteria 61 spinning problems, rack 100
saving starting
Experiment documents 41 arrow 62
files 45 software 20, 24
Summary Reports 36, 45, 79 status
Worklist documents 35 Disabled 15
scanner, barcode 54 icons, Worklist view 53
Schedule documents 42 Loader 26
security module 20 Summary Reports
serial port selection 88 about 32
Set Up view 25, 44 error messages 80
setting up printing 36, 79
Experiment documents 38 saving 36, 45, 79
Loader racks 68 Summary view 25, 79
Schedule documents 42
Worklist settings 44
settings T
assay 47 technical assistance x
instrument 48, 55 timeout, acquisition 104
mix 48
shutdown, Loader 82
Sign In view 25, 43
single commands, running 93
skipping FACSComp 50

Index 111
troubleshooting views
CellQuest Pro timeout 104 FACSComp 50
communication error 87, 102 Set Up 44
invalid rack ID 103 Sign In 43
invalid tube sequence 103 Summary 79
Multiset timeout 104 Worklist 52
no keypad display 100
rack spin 100 W
side scatter display 104
tube pressurization 101 Worklist Manager
tube stuck message 102 about 12
vertical timeout error 93, 103 application window 24
Trucount bead lot IDs 42 compatibility 17
tube guide, removing 95 file naming 33
tube lifter files 32
about 13 installing 18
cleaning 93 launching 20, 24
parameters 85 preferences 28
tubes troubleshooting 104
cleaning 68, 83 views 25
compatible 15 Worklist view 25, 52
installing in rack 68 status icons 53
invalid sequence 103 Worklists
lifting manually 16 assigning assays/panels 54
not pressurizing 88 defining 52, 54
pressurization problems 101 document file 32
rerunning 35, 73, 77, 78 importing 56
stuck 102 offline setup 29

U X
unique carousel ID 71 XML files, importing 61

V
vertical timeout error 93, 103

112 BD FACS Loader Reference Manual