FACSLyric™ System

Instructions For Use

 
 
 
 
 
 
 
 
 

23-21284-02
   
12/2020
Copyrights
No part of this publication may be reproduced, transmitted, transcribed, stored in retrieval systems, or
translated into any language or computer language, in any form or by any means: electronic,
mechanical, magnetic, optical, chemical, manual, or otherwise, without prior written permission from BD.

The information in this guide is subject to change without notice. BD reserves the right to change its
products and services at any time. Although this guide has been prepared with every precaution to
ensure accuracy, BD assumes no liability for any errors or omissions, nor for any damages resulting from
the application or use of this information. BD welcomes customer input on corrections and suggestions
for improvement.

Trademarks
BD, the BD Logo, Assurity Linc, FACS, FACSFlow, FACSLink, FACSLyric, FACSuite, and Trucount are
trademarks of Becton, Dickinson and Company or its affiliates. All other trademarks are the property of
their respective owners. © 2020 BD. All rights reserved.

Cy™ is a trademark of GE Healthcare. Cy™ dyes are subject to proprietary rights of GE Healthcare and
Carnegie Mellon University, and are made and sold under license from GE Healthcare only for research
and in vitro diagnostic use. Any other use requires a commercial sublicense from GE Healthcare, 800
Centennial Avenue, Piscataway, NJ 08855-1327, USA.

Laser safety information

Class 1 Laser Product.

Regulatory information
For In Vitro Diagnostic Use.

FCC information
WARNING: Changes or modifications to this unit not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.

NOTICE: This equipment has been tested and found to comply with the limits for a Class A digital
device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial environment. This
equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in
accordance with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference in which case
the user will be required to correct the interference at his or her own expense. Shielded cables must be
used with this unit to ensure compliance with the Class A FCC limits. This Class A digital apparatus
meets all requirements of the Canadian Interference-Causing Equipment Regulations. Cet appareil
numérique de la classe A respecte toutes les exigences du Réglement sur le matériel brouilleur du Canada.

EC information
The BD FACSLyric™ flow cytometer is for in vitro diagnostic use. The system is CE marked in compliance
with the European In Vitro Diagnostic Medical Device Directive 98/79/EC.

NOTICE: For a patient/user/third party in the European Union and in other countries with identical
regulatory regime: if, during the use of this device or as a result of its use, a serious incident has
occurred, please report it to BD and/or its authorized representative and to your national authority
managing health products.

Electromagnetic Compliance
The BD FACSLyric™ System complies with standard EN 61326-2-6:2013, Section 9.3 (emission and
immunity requirements). This equipment has been designed and tested to CISPR 11 Class A. In a
domestic environment it may cause radio interference, in which case, you may need to take measures to
mitigate the interference. The electromagnetic environment should be evaluated prior to operating the
device. Do not use this device in close proximity to sources of strong electromagnetic radiation (e.g.,
unshielded intentional radio frequency sources), as these can interfere with the proper operation.

History

Revision Date Change made

23-21284-00 2/2019 Initial release (in English only).

23-21284-01 4/2020 Updated from software version 1.3 to 1.4. IFU expanded

to cover both BD FACSuite™ and BD FACSuite™ Clinical
applications (instead of just BD FACSuite™).

23-21284-02 12/2020 Version updated to 1.5 including modified handling of

high-sensitivity fluidics mode, FCS file concatenation, and
updates to worklist and gating user interface.
 Contents
1  INTRODUCTION 11
About this guide 12
Symbols in this guide 14
Technical support 15
Intended use 16
Cybersecurity guidelines 16
Limitations 17

2  ABOUT THE SYSTEM 19

System overview 20
Cytometer overview 25
Optical components 29
Fluidics components 31
System options and upgrades 34
Software overview 36
About the Home page 39
Software components 42
Daily workflow 45

3  SYSTEM STARTUP AND SHUTDOWN 47

Performing system startup 48
Performing manual system shutdown 49
Performing automated system shutdown 51

4  DAILY SETUP AND QC 53

Daily setup and QC workflow 54
Running daily performance QC 54
About the Setup and QC workspace 57
About QC reports 59

5  EXPERIMENT BASICS 65
6      BD FACSLyric™ System Instructions For Use

About the experiment 66

Using the Manage Experiments tab 68
About tube properties 70
About experiment panels 72

6  DATA ACQUISITION IN AN EXPERIMENT 81

Data acquisition workflow 82
Creating and opening an experiment 83
Experiment building workflow 86
Creating and adding tubes 87
Creating plots and gates 88
Viewing and adjusting cytometer settings 93
Modifying the compensation matrix 95
Setting general tube properties and applying tube settings 97
Modification of tube properties for multiple tubes 99
Editing single-color reagent labels 101
Assigning and editing keywords 102
Setting acquisition stopping rules 104
Acquiring data in an experiment 105

7  DATA ANALYSIS IN AN EXPERIMENT 109

Data analysis workflow 110
Exporting and printing experiment worksheets and reports 111
Creating a user-defined assay from an experiment 112

8  EXPERIMENT SETTINGS 115

Creating tube settings 116
Creating default reference settings 117
Creating user-defined reference settings 120
Viewing tube and reference settings in the library 126
Saving modified reference settings 127

9  WORKLIST OVERVIEW 129

About the worklist 130
 Contents    7

Using the Manage Worklists tab 132

About the Worklist Entries table 134
About the Worklist Controls bar 140
About worklist entry controls 142
About Entry Details panel controls 145
About Worklist panels 147

10  DATA ACQUISITION IN A WORKLIST 153

Data acquisition overview 154
Creating a worklist 155
Running a worklist 157
Worklist run options 161
Re-acquiring entries in a worklist 164
Concatenating FCS files 165
Deleting Concatenated FCS files 170

11  DATA ANALYSIS IN A WORKLIST 173

Data analysis overview 174
Working with assay reports 175
Reviewing reports 176
Approving entries in a worklist 177
Working with audit trails 179
Using E-Signature 182
Running batch data analysis 183

12  BD IVD ASSAYS 185

Overview of BD IVD assays 186
Creating an assay worklist 187
About lab reports 188
About physician reports 191
About supplemental reports 193

13  BD FACS™ UNIVERSAL LOADER 197

BD FACS™ Universal Loader overview 198
8      BD FACSLyric™ System Instructions For Use

Sample carrier specifications 201

Placing carriers into the Loader 203
Defining sample carrier layouts 205
Cleaning the Loader 207

14  USER MANAGEMENT 209

Managing user accounts 210
Managing departments 211
Managing users 213
Setting operator permissions 216

15  PREFERENCES 217
Preferences overview 218
Setting administration preferences 219
Setting system preferences 220
Setting setup and QC preferences 222
Setting experiment preferences 225
Setting worklist preferences 226
Specifying assay properties 231

16  PERIODIC SETUP AND QC 235

Cytometer Setup and QC overview 236
Importing or adding a CS&T bead lot 238
QC tracking overview 239
Setting Levey-Jennings charts preferences 240

17  MAINTENANCE 245
Maintenance overview 246
Running the daily clean procedure 247
Refilling the sheath tank 248
Emptying the waste tank 250
Performing the monthly clean procedure 252
Replacing the sheath filters 256
Managing your database 259
 Contents    9

Archiving procedure for worklists 261

Archiving procedure for experiments (BD FACSuite™ application only) 262
Performing disk cleanup 263
Decommissioning the instrument 263

18  BD FACSLYRIC™ TECHNICAL SPECIFICATIONS 265

Technical specifications 266

INDEX 269
 1 
Introduction
This chapter includes the following topics:
 l About this guide (page 12)
 l Symbols in this guide (page 14)
 l Technical support (page 15)
 l Intended use (page 16)
 l Cybersecurity guidelines (page 16)
 l Limitations (page 17)
12      BD FACSLyric™ System Instructions For Use

About this guide

In this guide
This guide provides information for setting up and running the BD FACSLyric™ system.
The guide includes:
 l Introductory information about system hardware and components, a basic overview
of the software, and instructions about preparing the system for use.
 l Instructions for performing daily quality control, basic acquisition, and analysis of
flow data using the software.
 l Instructions for maintaining the system and information about the optional
BD FACS™ Universal Loader.
The software that controls the BD FACSLyric™ system features two applications:
 l The BD FACSuite™ Clinical application supporting BD IVD assays
 l The BD FACSuite™ application supporting BD IVD Single Color Reagents and user-
defined panels, which need to be verified and validated by the user
The following chapter applies to the BD FACSuite™ Clinical application for BD IVD
assays only:
 l Chapter 12: BD IVD assays (page 185)
The following chapters apply to the BD FACSuite™ application only:
 l Chapter 5: Experiment basics (page 65)
 l Chapter 6: Data acquisition in an experiment (page 81)
 l Chapter 7: Data analysis in an experiment (page 109)
 l Chapter 8: Experiment settings (page 115)
To provide a visual reminder of which application you are running, the color theme in
the graphical user interface (GUI) of the software is application-specific: green for the
BD FACSuite™ Clinical application and blue-gray for the BD FACSuite™ application.
Most of the content in this guide applies to both applications. For screenshot
examples that are applicable to both, this guide uses the blue-gray color theme from
the BD FACSuite™ application.
 Chapter 1  Introduction    13

Additional help
In the BD FACSuite™ and BD FACSuite™ Clinical applications, you can use the Help or
Reference menus to access additional information.

 l Click Help to view the product documentation, including this manual and the
BD FACSLyric™ System Safety and Limitations Guide. Help documents are provided
in PDF format, and you can set a system preference for which language is
displayed. Clicking About BD FACSuite™ or About BD FACSuite™ Clinical
(depending on the application) displays version information and the unique device
identifier (UDI) for the software.
 l Click Reference to open the BD FACSLyric™ Reference System in a separate
window. Internet access is not required to access this content.
The BD FACSLyric™ Reference System is a comprehensive collection of information
that includes all content from this guide and additional concepts, procedures, and
reference information about the cytometer and software.
You can use the table of contents, interactive links, or the search tool to locate topics
of interest. Search results are displayed in a familiar web search format to help you
find information quickly.
Use the print tools to print individual topics or to print entire sections as formatted
PDF files.

Training
BD recommends that operators complete device-specific training offered by the
manufacturer before using the system.
14      BD FACSLyric™ System Instructions For Use

Symbols in this guide

Introduction
The following table describes the symbols used in this guide.

Safety symbols

Symbol Meaning

Caution. Identifies a hazard or unsafe practice that could result in data loss,
material damage, minor injury, severe injury, or death.

Biological hazard

Electrical hazard

Laser hazard

Mechanical hazard, pinch points

 Chapter 1  Introduction    15

Technical support
Introduction
This topic describes how to get technical support.

Before contacting technical support

Try the following options for answering technical questions and solving problems:
 l Read the section of this guide specific to the operation you are performing.
 l Read topics about related information, which are listed in the More Information
section (at the bottom of each topic).
 l Search the troubleshooting topics in the BD FACSLyric™ Reference System for
solutions to problematical system behaviors.

When contacting technical support

If assistance is required, contact your local BD technical support representative or
supplier. Visit our website, bdbiosciences.com, for up-to-date contact information.
When contacting BD, have the following information available:
 l Product name, part number, and serial number
 l Software application and version number
 l Any error messages
 l Details of recent system performance
 l A system health report. See topics about generating one in the BD FACSLyric™
Reference System.
16      BD FACSLyric™ System Instructions For Use

Intended use
Intended use statement
The BD FACSLyric™ flow cytometer system is intended for use as an in vitro diagnostic
device for identification and enumeration of human cell subsets for flow cytometry.

Intended user statement

TheBD FACSLyric™ flow cytometer system is intended for laboratory professional use.

Cybersecurity guidelines
Introduction
For network-connected workstations, the recommendations below should be
considered.

BD FACSuite™/BD FACSuite™ Clinical application guidelines

 l In User Management Settings, configure the options for Lockout Attempts,
Password Expiration, and Password Expiration Warning to require users to regularly
change their passwords.
 l Use a complex password of at least 8 characters with the full set of alphanumeric
characters and special symbols.
 l All users should have their own User ID and IDs should not be shared.
 l Users should be given administrator privileges only if their duties require that level
of access (to create users, for example).
 l Software backups should be performed on a regular basis to secure storage external
to the workstation, and to allow a restore to be performed. The default backup
directory on the BD FACSLyric™ workstation for the BD FACSuite™ application is
C:\ProgramData\BD\FACSuite\BD Backup and for the BD FACSuite™ Clinical
application is C:\ProgramData\BD\FACSuite Clinical\BD Backup.
 l As software updates including security updates are made available, these updates
should be applied in a timely manner.
 l Install antivirus software per company IT policy and periodically scan hard drives.
 Chapter 1  Introduction    17

 l Do not enter sensitive patient information, such as patient name and social security
number, into keywords and other text fields in the software. Doing so could expose
this sensitive patient information to unintended use.

Microsoft® Windows® OS guidelines

 l Password options for the Microsoft Windows operating system should be configured
as required to meet organizational IT standards, including password complexity,
password expiration, limits on attempts to guess users’ passwords, and password
reuse rules.
 l Administrative access to the Windows operating system should be given only to
users that require such access (to perform backups, for example).
 l Windows operating systems security updates should only be applied if they have
been reviewed and approved by BD Biosciences. Non-approved updates can affect
the correct functioning of the system.
 l Remote access to the workstation should only be enabled if it is required.
 l For more information about operating system configuration and additional tools,
see the document Information Security Guidelines, BD Biosciences Workstations,
available on bdbiosciences.com.

Limitations
Fluidics modes
The BD FACSLyric™ system has a high-sensitivity fluidics mode that should not be used
with BD IVD assays.

Sample carriers
The BD FACSLyric™ system with the BD FACS™ Universal Loader option has the
capability of using tube racks that can include 30 or 40 tubes. The Loader can also
handle plates, but plates should not be used with BD IVD assays. Always refer to the
reagent package insert for sample carrier requirements.

System requirements
You must have Microsoft Windows Administrator access to install the BD FACSuite™
and BD FACSuite™ Clinical applications.
18      BD FACSLyric™ System Instructions For Use

If you are installing the software on a standalone workstation, we recommend that

the computer meets the following minimum requirements:
 l Intel® Pentium® Quad Core processor.
 l Microsoft Windows 64-bit version.
 l 8 GB of RAM.
 l Hard drive with at least 50 GB of free space.
 l PDF-capable printer. The BD FACSuite™/BD FACSuite™ Clinical application renders
content to PDF before sending it to a directly connected or networked printer. Any
printer that supports PDF format can be used to print from the BD FACSuite™/BD
FACSuite™ Clinical application.
 l Google Chrome™ browser for proper display of the system documentation.
 l Software, such as Adobe® Acrobat® Reader®, for reading PDF files.
 2 
About the system
This chapter includes the following topics:
 l System overview (page 20)
 l Cytometer overview (page 25)
 l Optical components (page 29)
 l Fluidics components (page 31)
 l System options and upgrades (page 34)
 l Software overview (page 36)
 l About the Home page (page 39)
 l Software components (page 42)
 l Daily workflow (page 45)
20      BD FACSLyric™ System Instructions For Use

System overview
About the system
The BD FACSLyric™ system includes the BD FACSLyric™ cytometer, the optional
BD FACS™ Universal Loader (Loader), and workstation that runs the software. The
system also includes setup beads and reagents. All of these components combine to
create an integrated system designed for use in a wide variety of clinical applications.

No. Description

1 Waste tank

2 Sheath tank

3 BD FACSLyric™ cytometer

4 BD FACS™ Universal Loader (optional)

5 Workstation with BD FACSuite™ and BD FACSuite™ Clinical applications Note that the

workstation for newer BD FACSLyric™ systems is more compact than shown in the
illustration and, as a result, the monitor cannot be placed on top of it.

The BD FACSLyric™ flow cytometry system acquires and analyzes particles or cells in a
liquid suspension. Antibodies to specific cell proteins are labeled with a fluorescent dye
and incubated with the cell suspension. The suspension flows through the cytometer
and is interrogated by a laser which excites the fluorescent antibodies. The
fluorescence is captured and the resulting data is analyzed to reveal information
 Chapter 2  About the system    21

about the cells. Multiple antibodies, each labeled with a different dye, can be used in a
single tube to simultaneously identify different cell populations.

Principle of operation
The BD FACSLyric™ system, using flow cytometry, identifies and enumerates cell
subsets. Flow cytometry is a technology that simultaneously measures and then
analyzes multiple physical characteristics of single particles, usually cells, as they flow
in a fluid stream through a beam of light. The properties measured include a particle's
relative size, relative granularity or internal complexity, and relative fluorescence
intensity. An optical-to-electronic coupling system determines these characteristics by
recording how the cell or particle scatters incident laser light and emits fluorescence.
A fluorochrome is conjugated to an antibody and used to identify a particular cell type
based on the individual antigenic markers of the cell.

Fluorochrome-labeled
antibodies Antigenic surface marker

Analyze

Incubate

In a mixed population of cells, different fluorochromes can be used to distinguish

different cell populations. The staining pattern of each population, combined with
forward-scattered light (FSC) and side-scattered light (SSC) data, can be used to
identify which cell populations are present in the sample and to count their relative
percentages.
The stained sample is carried in a fluid stream through the laser beam. Any suspended
particle or cells from 0.2 to 150 micrometers in size is suitable for analysis. The design
of the flow chamber causes the sample core to be focused in the center of the sheath
fluid. Based on principles relating to laminar flow, the sample core remains separate
but coaxial within the sheath fluid. The flow of the sheath fluid accelerates the
particles and restricts them to the center of the sample core. This process is known as
hydrodynamic focusing.
22      BD FACSLyric™ System Instructions For Use

Low sample High sample

pressure pressure
(12 µL/min) Laser Laser
(60 µL/min)
beam beam

Sheath Sheath Sheath Sheath

fluid Sample fluid fluid Sample fluid

The fluidic system is vacuum-driven, which draws the sheath fluid and the sample into
the system rather than pushing it through using positive pressure. This approach
enables the fluid to be drawn from a nonpressurized sheath and sample vessels. This
method avoids potential issues surrounding the pressurization of sample tubes and
also avoids the use of complicated syringe drive mechanisms.
When the particles pass through the laser beam, they scatter laser light. The extent of
the scattering depends on the physical properties of each particle. The scattered light
is differentiated into two categories:
 l Forward-scattered light (FSC) provides a measure of cell size and shape. It is a
measurement of mostly diffracted light, which is detected just off the axis of the
incident laser beam in the forward direction. FSC is detected by a photodiode.
 l Side-scattered light (SSC) provides a measure of the complexity of the cytoplasm.
It is a measurement of refracted light that occurs at any interface within the cell
where there is a change in refractive index. SSC is collected at approximately 90
degrees to the laser beam by a collection lens, which is redirected by a beam
splitter to the appropriate detector.
 Chapter 2  About the system    23

Pictorial representation of FSC and SSC:

Side scatter detector

Light source Forward scatter detector

Correlated measurements of FSC and SSC can allow for differentiation of cell types in
a heterogeneous population.
Photodetectors convert the light signals to electronic signals that in turn are converted
into digital channel numbers for display on a data plot. BD currently used two types of
photodetectors:
 l Photodiodes, used to detect FSC signals
 l Photomultiplier tubes (PMTs), used to detect fluorescence and SSC signals
Once the light signals (photons) strike one side of the PMT or the photodiode, they are
converted into a proportional number of electrons, which results in a voltage pulse.
The pulse reaches maximum amplitude when the particle is in the center of the beam,
which corresponds to where the maximum amount of scatter or fluorescence occurs.
As the particle leaves the beam, the pulse amplitude drops back to the baseline.
An analog-to-digital converter (ADC) converts the voltage pulse to a digital channel
number. This number is then transferred to the computer and displayed in an
appropriate position on a data plot and stored by the computer system.

BD FACSLyric™ cytometer
The BD FACSLyric™ cytometer is a compact flow cytometer. Several hardware options
and upgrades can be used to customize the system for different applications.
Three laser configurations provide the ability to analyze up to 12 colors (14
parameters). A unique heptagon detector array ensures that the correct filters and
mirrors are installed.
The vacuum-driven fluidics, along with a uniquely designed flow cell and sample
injection tube, provide reliability and good signal resolution. The BD FACSuite™
24      BD FACSLyric™ System Instructions For Use

application includes high, medium, and low flow rates. In addition, a special high-
sensitivity fluidics mode makes it easier to detect dimly stained particles. In the BD
FACSuite™ Clinical application, flow rate is fixed by the BD IVD assay and cannot be
changed.
Note: High-sensitivity fluidics mode should not be used with BD IVD applications.

BD FACS™ Universal Loader

The Loader is an optional automated loading system that delivers samples to the
BD FACSLyric™ cytometer for acquisition. It is designed for walkaway operation.
The Loader offers various settings to resuspend and mix samples. It can draw from 12
x 75-mm tubes in 30- and 40-tube racks. The Loader can also handle multiple types of
microtiter plates, including deep-well plates. Plates should not be used for BD IVD
assays. A barcode reader verifies the ID on tube racks, plates, and individual tubes in
30- tube racks. A built-in imaging system provides safety checks, such as verifying the
correct rack type and tube layout, and ensuring that tubes and plates were loaded
correctly.

Workstation
The system is shipped with a workstation that includes a monitor, keyboard, and
mouse. The workstation runs the BD FACSuite™/BD FACSuite™ Clinical application
and other software, which controls the cytometer. The workstation comes equipped
with the following software:
 l Microsoft® Windows® 10  operating system, 64-bit compatible   
 l BD FACSuite™ version 1.5 or later, comprising the BD FACSuite™ application and
the BD FACSuite™ Clinical application
The workstation requires a security key that plugs into a USB port to run the software.

Sheath and waste tanks

Several tank sizes are available depending on the sample throughput and needs of
individual laboratories. The standard 5-L capacity sheath and waste tanks are located
to the left side of the cytometer in a dock that can be disconnected from the
cytometer. Optional 10-L extended-use tanks are also available. Level sensors alert you
when fluid levels are low (sheath) or high (waste). Additionally, for high-volume labs, a
BD FACSFlow™ cubitainer can be used to supply sheath fluid.
 Chapter 2  About the system    25

Beads, reagents, and assays

BD® CS&T Beads are used to check the cytometer performance and automatically
make adjustments, ensuring consistent values from day to day.
Note: Ensure that you use the BD® CS&T Beads designed specifically for your
BD FACSLyric™ IVD system.
BD® FC Beads are used to set up reference settings, which are valid for 60 days.

BD IVD assays are available as separate modules that can be used with BD IVD kits.
Worksheets with plots and gates are already set up for acquisition and analysis.
In the BD FACSuite™ application, user-defined assays can be used as a starting point
for creating customized experiments and reports.

More information
 l Cytometer overview (page 25)
 l System options and upgrades (page 34)
 l Software overview (page 36)

Cytometer overview
Main components
The locations of the main components of the cytometer, including the status
indicators, are shown in the following figures.
26      BD FACSLyric™ System Instructions For Use

Cytometer front view

No. Description

1 Cytometer status indicator

2 Acquisition status indicator

3 Fluidics status indicator

4 Sample injection tube (SIT) door

5 Manual tube port

6 Heptagon detector arrays, behind front door

7 Access door for sheath filter on left side of cytometer

 Chapter 2  About the system    27

Cytometer right-side view

No. Description

1 Cytometer power button

2 Connector panel

3 Ethernet connector for workstation

4 AC power circuit breaker

5 Captive screw for front door

6 Grip area for front door

28      BD FACSLyric™ System Instructions For Use

Status indicators
When the system is started, indicators display different conditions to show the
system’s status. The functions of the status indicators are described in the following
table.

Indicator Condition Status

Cytometer status Green Ready for operation

Solid amber Fault condition

Blinking amber Warming up

Red System inoperable

Cytometer power button Amber Power is off to all major subsystems

Green Power is on

Blinking green Shutdown process has started

Acquisition status Off Not previewing or acquiring sample

Blinking blue Previewing or acquiring sample

Fluidics status Off Ready

Blinking amber  l Sheath fluid low

 l Waste tank almost full

Red  l Sheath fluid empty

 l Waste tank full
 l Waste tank disconnected
 Chapter 2  About the system    29

Cytometer configurations
The BD FACSLyric™ system is available in the following configurations.

Lasers Number of colors

2 lasers (blue, red) 4 color (3-1)

2 lasers (blue, red) 6 color (4-2)

3 lasers (blue, red, violet) 8 color (4-2-2)

3 lasers (blue, red, violet) 10 color (4-3-3)

3 lasers (blue, red, violet) 12 color (4-3-5)

More information
 l Optical components (page 29)
 l Fluidics components (page 31)
 l System options and upgrades (page 34)
 l See Laser and detector configurations in the BD FACSLyric™ Reference System.

Optical components
Location of optical components
The optical compartment is located on the front of the cytometer, behind the front
door. The heptagon arrays for each laser are accessible when the door is open. The
following figure shows the locations of the optical components.
30      BD FACSLyric™ System Instructions For Use

No. Description

1 Front door in open position

2 Red laser (640 nm)

3 Blue laser (488 nm)

4 Violet laser (405 nm)

5 Heptagon detectors, one for each laser

Heptagon detector arrays

The heptagon detector arrays contain the filters, mirrors, and photomultiplier tubes
(PMTs) for each laser. There is a separate heptagon for each laser.

Filter holders
For all channels, there is a removable filter holder. The filter holder has an ID chip that
identifies the holder to the system so the software can confirm that the correct filter
holder is in place.
The following figure shows a heptagon and a filter holder.
 Chapter 2  About the system    31

No. Description

1 Heptagon

2 Handle

3 Filter holder

4 ID chip

Location of lasers
The system lasers and beam-steering optical components are located at the top of the
cytometer, under the top cover. There is no user access to the laser area.

More information
 l Fluidics components (page 31)
 l System options and upgrades (page 34)

Fluidics components
Manual tube port
The manual tube port is located on the right front of the cytometer. A circular LED
indicator at the base of the port turns green when the system is ready to accept a
tube.
The following figure shows the manual tube port.
32      BD FACSLyric™ System Instructions For Use

No. Description

1 Manual tube port

2 LED status indicator

3 Tube loaded on port

The following table describes the conditions and status of the LED status indicator.

Condition Status

Solid green Ready to accept a tube

Blinking green Error, SIT moving down without a tube present

Solid amber SIT flush in progress, do not load a tube

Off Tube is loaded

Sample injection tube (SIT)

The sample injection tube (SIT) aspirates sample from a tube or a well and delivers it
to the flow cell.

Qualified tubes
Only the following tubes have been qualified for use on the manual tube port on the
cytometer. When using 5-mL tubes, for optimal performance in reducing carryover, fill
to 0.5 mL or less, so the wash probe does not make contact with the sample.
Note: Only qualified 5 ml tubes should be used with BD IVD assays. Other sizes of
tubes should not be used.
 Chapter 2  About the system    33

Tube type Maximum volume

Falcon® 5-mL (12 x 75-mm) polystyrene 2 mL

Falcon 5-mL (12 x 75-mm) polypropylene 2 mL

BD Trucount™ 5-mL (12 x 75-mm) 2 mL

Falcon 15-mL (when used with adapter) 14 mL

Falcon 50-mL (when used with adapter) 45 mL

Eppendorf® 2-mL (when used with adapter) 1.5 mL

Tube adapters
You can use 15-mL, 50-mL, and Eppendorf 2-mL tubes by installing a tube adapter. The
15-mL and 50-mL adapters screw onto the tops of the tubes. The Eppendorf adapter
slides onto the tube from the side.

No. Description

1 50-mL adapter

2 15-mL adapter

3 Eppendorf 2-mL adapter

Sheath filter
The sheath filter is located on the left side of the cytometer behind the access door.
The sheath filter should be changed every three months.
34      BD FACSLyric™ System Instructions For Use

More information
 l Replacing the sheath filters (page 256)
 l System options and upgrades (page 34)

System options and upgrades

Introduction
The BD FACSLyric™ system options and available upgrades are listed and described in
the following table.
 Chapter 2  About the system    35

Category Option Description

System BD FACS™ The Loader is an optional automated loading system that

hardware Universal mixes samples and delivers tube racks and plates to the
Loader BD FACSLyric™ system for acquisition.

Note: Plates See BD FACS™ Universal Loader overview (page 198).

should not be
used with BD
IVD assays.

Handheld The handheld barcode reader plugs into the USB port on the
barcode system computer workstation and reads most current barcode
reader standards.

See the topic about the barcode reader in the BD FACSLyric™

Reference System.

Optics Laser Upgrade a 2-laser to a 3-laser system. The number of colors

upgrades on a 2-laser system can be upgraded from a 4-color system to
a 6-color system. For a 3-laser system, upgrades are available
up to 12 colors from any lower-color configuration.

Fluidics Large fluidics The optional large volume sheath and waste tanks do not have
tanks (10-L a dock and are normally stored on the floor.
capacity)

Cubitainer Sheath fluid can also be supplied from a BD FACSFlow™

cubitainer by using an optional adapter.

Applications FCAP Array™ FCAP Array™ software facilitates the data analysis of bead
software assays. These assays can detect the presence of, or determine
concentrations for, multiple analytes (for example, proteins
Note: This and peptides) in a sample.
software
should not be
used with BD
clinical
applications.
36      BD FACSLyric™ System Instructions For Use

Category Option Description

Remote BD Assurity BD Assurity Linc™ software is a highly secure remote systems

diagnostics Linc™ management service that connects BD instruments and BD
software technical support personnel. Using the BD Assurity Linc Agent,
BD support personnel can securely access your workstation
(with your approval) through an enterprise server and diagnose
problems remotely.

See the topic about BD Assurity Linc™ software in the

BD FACSLyric™ Reference System.

Laboratory BD FACSLink™ BD FACSLink™ software provides an interface solution to LIS

Information software systems.
Systems
(LIS) BD FACS™ BD FACS™ Workflow Manager software is a data
Workflow management system that also provides an interface solution
Manager to LIS systems (available in Europe only).

Software overview
Introduction
This topic provides an overview of the basic features and functionality of the BD
FACSuite™ and BD FACSuite™ Clinical applications that control the BD FACSLyric™
cytometer and the optional BD FACS™ Universal Loader.
The software is used to operate the instrument, acquire samples, and analyze the
data. Quality control performance, tracking, and reporting are streamlined and
automated. Routine tasks such as startup and shutdown can be programmed to occur
automatically.

Setup and QC
The software provides comprehensive tools to run QC and to set up the cytometer on
a daily basis to maintain precise and reproducible results and ensure consistent
performance.
The setup and QC procedures use BD® CS&T Beads to measure and adjust cytometer
PMT voltages. This ensures that target values for the cytometer and the assays and
experiments are maintained.
 Chapter 2  About the system    37

As part of the QC tracking function, Levey-Jennings charts are generated daily. Use
these charts to track and set acceptance criteria for various performance parameters.
QC reports are generated to help document and track the system performance over
time.

BD IVD assays
In the BD FACSuite™ Clinical application, you can measure and analyze samples using
BD IVD assays. Assays are run as entries in a worklist, which provides batch acquisition
and analysis.
BD IVD assays are predefined to target specific cell populations. The data displays
during preview and acquisition, and the plots with algorithm gates on the lab report
are designed for specific results. The gates can be adjusted, but the gating hierarchy
and other report elements cannot be changed.
The e-signature function can be enabled; the audit trail function is automatically
enabled. When enabled, the e-signature function requires that one or more authorized
persons sign the report. Up to three e-signatures can be configured. The audit trail
tracks changes to entries and keeps a log.

Experiments and assays

In the BD FACSuite™ application, you can measure and analyze samples using either
assays or experiments. Both formats organize and specify the conditions for
acquisition and analysis for tubes.
Use assays when you want to run a specific protocol or analysis on samples repeatedly.
Assays are run as entries in a worklist, which provides batch acquisition and analysis.
Use experiments to test studies and different samples, and to develop protocols.
Experiments are exploratory and highly customizable. You can define the properties of
each tube and create custom tube settings and apply them to other tubes. You can
refine an experiment and then save it as an assay to set the test protocols.
While assay protocols are predefined to target specific data (markers, populations,
fluorochromes, etc) and look for specific results, you can modify plots, gates, and other
worksheet or report elements for an assay. Worklists and assays provide administrative
control capabilities such as e-signature and audit trails.
In experiments, data can be displayed in a worksheet or report using any combination
of plots or histograms. In the application, worksheets and reports are live data portals
and continuously display current data. You can acquire data and then analyze it by
gating populations of interest, displaying statistics, and adding expressions. You can
38      BD FACSLyric™ System Instructions For Use

create custom, formatted reports that include the details you want to analyze and
present in a final lab report.

Worklist
The worklist is a set of tasks to be performed. It organizes the tasks and their
associated tubes, status, and other information into entries. Each task in an entry
includes an assay or fluidics (cleaning or maintenance) procedure.
Using the worklist, you can acquire tubes in entries, display acquisition data, perform
analysis on the acquired data, and export data automatically based on your
preferences.
With the BD FACS™ Universal Loader option, you can load tube racks or plates and run
worklists in a more automated manner.

Library
The library stores and manages shared resources and assay properties. Resources
include assays, beads, reagents, keywords, labels, and tube settings. You can import,
add, edit, and delete some resources.
Resources are used as elements in experiments, worklists, and in setup and QC. For
example, you can assign a tube setting to an experiment, or a keyword to an entry in a
worklist.

Rearranging and restoring the workspace

You can rearrange the workspace to fit your specific workflow and application needs.
You can also restore the default layout in all workspaces:
 l Setup and QC workspace
 l Experiment workspace
 l Worklist workspace
 l Library workspace
To restore a workspace layout, select View > Restore Default Layout. If the
workspace is already using the default layout, the command will be grayed out and
disabled.
 Chapter 2  About the system    39

About the Home page

Introduction
The Home page is the default starting page. This page includes the following sections:
 l Quick Start At the top of the Home page, displays shortcuts for the most commonly
used workflows or operations.
 l System Status In the center of the Home page, displays the current status and
serial numbers of the system for the fluidics, lasers, BD FACSLink™ status (if
applicable), all system components, and the connection status. It also displays all
installed options.
 l BD Assays In the lower section of the Home page, displays the list of currently
installed BD assays.
BD FACSuite™ application Home page:
40      BD FACSLyric™ System Instructions For Use

BD FACSuite™ Clinical application Home page:

Quick Start shortcuts

The following table describes the available Quick Start shortcuts.
 Chapter 2  About the system    41

Shortcut Task Description

Setup & QC Opens the Setup & QC workspace and displays the
Setup & QC tab.

Setup & QC Opens the Setup & QC workspace and displays the QC
Report Report tab.
 
QC Tracking Opens the Setup & QC workspace and displays the QC
Tracking tab.

Acquire Data in Opens the Experiment workspace and displays a new

Experiment experiment.

Acquire Data in Opens the Worklists workspace and displays a new

Worklist worklist.

Analyze Data in Opens the Experiment workspace and displays the

Experiment Experiment Management tab.

Analyze Data in Opens the Worklists workspace and displays the

Worklist Worklists Management tab.

Manage Library Opens the Library workspace and displays the

categories of library resources.

Manage Users (Administrators only) Opens the User Management

dialog and displays the list of users.
42      BD FACSLyric™ System Instructions For Use

Software components
Window components
The software windows consist of the following components.
 Chapter 2  About the system    43

No. Description Function

1 Title bar Displays the software product name and the standard window controls
(minimize, maximize, close).

2 Menu bar See the next section.

3 Message Located at the top of the window (below the Menu bar), displays system
bar messages.

4 Workspaces Contain the panels, fields, tables, and tools required for a specific
function. Individual workspaces are provided for setup and QC,
experiments, worklists, and the library.

5 Navigation Located at the left side of the window. Click the navigation bar icons to
bar open the different workspaces.

6 Panels Contain the tools, fields, and options for performing specific, detailed
functions required for a workspace. You can maximize, minimize, or
reposition most panels on the screen.

7 Status bar Located at the bottom of the window, displays the current cytometer
connection status, fluidics status, and an acquisition progress bar. Also
includes status of the BD FACSLink™ connection, if installed.

Menu bar
The menu bar displays the following software menus.
44      BD FACSLyric™ System Instructions For Use

Menu Description

File This menu includes specific tools and items for the current window or workspace.
Choices include importing, exporting, printing, saving, and managing specific
workspaces (for example, opening a worklist).

Edit This menu includes Cut, Copy, Paste, Delete, Undo, Redo, and other editing tools.

View This menu includes display control items.

Tools This menu includes user management, preferences, administration, tracking,

and setup items.

Cytometer This menu includes cytometer cleaning, instrument information, and control
items.

Help This menu includes documentation in PDF format and basic software
information.

Reference This menu includes the BD FACSLyric™ Reference System. Use the Reference
System to view and search for information on using the system.

User profile This menu item opens the My Profile dialog. Use this dialog to manage your
(username) login password and user profile information.

Preferences This menu item opens the Preferences dialog. Use this dialog to set preferences.

Log Out This menu item logs the current user out of the software.

More information
 l Software overview (page 36)
 Chapter 2  About the system    45

Daily workflow
The following diagram shows the typical daily workflow for the BD FACSLyric™ system
when using the BD FACSuite™ application.
Experiment

Acquire data Analyze data

Start up Perform Shut down

the system Setup & QC the system

Acquire data Analyze data

Worklist

The following diagram shows the typical daily workflow when using the BD
FACSuite™ Clinical application for BD IVD assays.

Start up Perform Shut down

Acquire data Analyze data
the system Setup & QC the system

More information
 l System startup and shutdown (page 47)
 l Daily setup and QC (page 53)
 l Data acquisition in an experiment (page 81)
 l Data analysis in an experiment (page 109)
 l About the worklist (page 130)
 l Maintenance (page 245)
This page intentionally left blank
 3 
System startup and shutdown
This chapter includes the following topics:
 l Performing system startup (page 48)
 l Performing manual system shutdown (page 49)
 l Performing automated system shutdown (page 51)
48      BD FACSLyric™ System Instructions For Use

Performing system startup

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Introduction
This topic describes how to perform the normal system startup procedure. You can also
set up a pre-programmed time and day to start the system automatically.
See information about setting cytometer schedule preferences in the Setting system
preferences (page 220).

Required materials
The following list describes the required materials for daily operation of the system.
 l BD FACSFlow™ sheath fluid
 l Bleach (for the waste tank)
 l Deionized (DI) water
 l BD® CS&T Beads

Procedure
To start up the system:
 1. Turn on the power to the system by pressing the Power button.
The Power button turns green when system power is on.
 2. Wait 20 minutes for the system to warm up before starting any acquisition work.
 3. Log in to the software.
 a. Double-click the BD FACSuite™ icon or BD FACSuite™ Clinical icon to start the
application.
 b. Enter a username and password.
 c. Acknowledge you read and understood the statement on the login screen and
select the checkbox.
 d. Click OK.
 Chapter 3  System startup and shutdown    49

 4. Verify that the software is connected to the cytometer by looking for the green
Connected status icon in the lower-left corner of the workspace.
 5. Check the fluid levels.
 a. Check the sheath tank to ensure that there is enough sheath fluid to perform
your work.
 b. Check the waste tank to ensure there is adequate capacity.
 6. Verify that the fluidics system is ready by looking for the green Fluidics status icon
in the lower-right corner of the workspace.

More information
 l Refilling the sheath tank (page 248)
 l Emptying the waste tank (page 250)
 l Setting system preferences (page 220)

Performing manual system shutdown

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Introduction
This topic describes the manual system shutdown procedure. Use this procedure to
manually perform the daily cleaning and shutdown of the system.
Alternatively, you can program the system to shut down automatically. See
Performing automated system shutdown (page 51).

Required materials
 l 1 tube containing 2 mL of 10% bleach solution
 l 1 tube containing approximately 3 mL of DI water
 l Disposable towels or wipes
50      BD FACSLyric™ System Instructions For Use

Procedure
To manually shut down the system:
 1. From the menu bar, select Cytometer > Daily Clean.
The Daily Clean dialog opens.
 2. Place a tube containing 2 mL of 10% bleach solution on the manual tube port, then
click Continue.
 3. When prompted, place a tube containing approximately 3 mL of DI water on the
manual tube port, then click Continue.
The dialog closes after the tube is unloaded from the manual tube port.
 4. Load a tube containing 2 mL of DI water on the manual tube port.
Always leave a tube of DI water on the manual tube port whenever the system is
not in use.
 5. Clean external surfaces.
 a. Wipe down the external surfaces of the cytometer and work area.
 b. Dispose of the used cleaning materials in biohazard containers.
 6. From the menu bar, select Cytometer > Shutdown.
The Cytometer Shutdown dialog opens.
 7. Click Yes.
The Power button blinks green for a few seconds, then power to the system turns
off and the Power button turns amber.
 8. Log out of the software.
 a. From the right side of the menu bar, click the Log Out button.
 b. In the confirmation dialog, click Yes.

More information
 l Performing system startup (page 48)
 l Performing automated system shutdown (page 51)
 Chapter 3  System startup and shutdown    51

Performing automated system shutdown

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Introduction
This topic describes how to automate the process for shutting down the system by
adding cleaning and shutdown entries to a worklist and then running that worklist
using the Loader.
You can also set a preference to shut down the system after a specified length of idle
time. See information about setting cytometer schedule preferences in the
BD FACSLyric™ Reference System.
The following figure shows a sample worklist with cleaning and shutdown entries
added.

Procedure
To run an automated shutdown using a worklist:
 1. Prepare a tube containing 2 mL of 10% bleach solution and a tube containing
approximately 3 mL of DI water.
 2. Place the tubes in a 30- or 40-tube rack. Do not use a plate.
 3. Create a worklist with a Daily Clean and Shutdown as the last tasks.
 4. Run the worklist.
52      BD FACSLyric™ System Instructions For Use

When the worklist is finished, the system power turns off.

 5. Place a tube of DI water on the manual tube port.
A tube containing 2 mL of DI water should be loaded on the manual tube port
whenever the system is not in use.

More information
 l For details about creating cleaning and shutdown entries in a worklist, see topics on
adding fluidics cleaning or shutdown to a worklist in the BD FACSLyric™ Reference
System.
 4
Daily setup and QC
This chapter includes the following topics:
 l Daily setup and QC workflow (page 54)
 l Running daily performance QC (page 54)
 l About the Setup and QC workspace (page 57)
 l About QC reports (page 59)
54      BD FACSLyric™ System Instructions For Use

Daily setup and QC workflow

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Daily setup and QC tasks

Perform the daily performance QC task each day before you acquire and analyze data
using experiments or worklists.

More information
 l Running daily performance QC (page 54)
 l About the Setup and QC workspace (page 57)
 l About QC reports (page 59)

Running daily performance QC

Introduction
This topic describes how to run daily performance QC.
A typical performance QC should take approximately 5 to 10 minutes if the
BD® CS&T Beads have already been prepared.
As a part of performance QC, Lyse/Wash and Lyse/No-Wash tube settings are updated
through assay and tube settings setup. All assays using these tube settings are
therefore updated, and reports can be generated. For more information on these
settings, see the BD FACSLyric™ Reference System.

Procedure
To run daily performance QC:
 1. Prepare a tube with BD® CS&T Beads according to the directions in the
instructions for use or technical data sheet for the beads.
 2. On the navigation bar, click Setup & QC.
 Chapter 4  Daily setup and QC    55

The Setup & QC workspace opens.

 3. In the Setup & QC Options panel, verify that Performance QC is selected.

 4. Verify that the correct CS&T bead lot ID is selected.

 5. Click Select next to the Assay Setup Reports field.
The panel opens similar to the following:

 6. In the Report column, select the assays for which a report is desired.
The reports reflect the results of assay and tube settings setup.
 7. In the Setup & QC Options panel, click Start.
The Load Tube dialog opens.
 8. Load the tube of BD® CS&T Beads onto the manual tube port.
56      BD FACSLyric™ System Instructions For Use

The system detects the tube and prompts for confirmation of its contents.
 9. Click Continue to initiate the setup tasks.
The details for the application-supported fluidics modes are displayed in the Setup
Tasks panel. A checkmark indicates that a step in the task has been completed.
Setup Tasks dialog for the BD FACSuite™ application including High Sensitivity
Fluidics mode:

Note: High Sensitivity Fluidics Mode is only available in the BD FACSuite™

application and is disabled by default. An administrator can change this setting if
required.
When all tasks are complete, the system displays a dialog to unload the tube.
 10. Unload the tube from the manual port.
A dialog opens and indicates whether the task completed successfully.
Caution! If the setup tasks did not pass, we recommend that you do not proceed.
Instead, see topics on failed setup tasks in the Troubleshooting section of the
BD FACSLyric™ Reference System.

 11. Click Yes to view the performance QC report or click No to close the dialog.
 Chapter 4  Daily setup and QC    57

More information
 l About the Setup and QC workspace (page 57)
 l Importing or adding a CS&T bead lot (page 238)
 l Setting setup and QC preferences (page 222)

About the Setup and QC workspace

Introduction
The Setup and QC workspace includes multiple tabs that you use to perform different
setup and quality control tasks, view reports, and track QC over time. You can also view
or modify the cytometer optical configuration.
To open the Setup and QC workspace, click Setup & QC on the navigation bar.

Setup & QC tab

The Setup and QC tab includes the following panels:
 l Setup & QC Options Use this panel to select setup and QC tasks, select CS&T bead
lots, select assay setup reports to be generated, and start or abort setup and QC
operations.

 l Cytometer This panel displays the current cytometer configuration and the current
cytometer status. The status area displays the system status (including information
for a tube loaded on the manual tube port), fluidics, and lasers. This panel also
indicates when you need to run system cleaning protocols.
58      BD FACSLyric™ System Instructions For Use

 l Setup Tasks This panel displays real-time status of setup and QC task steps. Green
checkmarks indicate completed steps.

QC Reports tab
In the QC Reports tab, the Reports panel lists all of the reports that are generated
when you perform a characterization, performance, or laser setup QC task, or a bead
lot transfer. Separate reports for each fluidics mode (normal and high sensitivity1) are
generated for each setup and QC task.
Reports contain details about the system, detector settings, lasers, setup bead lots,
and cytometer settings, as well as warnings, errors, and notifications. Click a report in
the table to view, print, or export the report.

QC Tracking tab
Use the QC Tracking tab to view performance values in Levey-Jennings charts and to
set the alarm ranges and scales. Levey-Jennings charts are used to track the
instrument performance over time.

Assay Setup Reports tab

In the Assay Setup Reports tab, the Assay Setup Reports table lists all of the reports
that are generated when you perform assay and tube settings setup.
Reports contain details about the assay-specific instrument settings, cytometer
configuration, setup bead lot, and user, as well as warnings or errors. Click a report in
the table to view, print, or export the report.

1In the BD FACSuite™ application, high-sensitivity mode is an option that can be set by the
administrator under Tools > Setup and QC Preferences.
 Chapter 4  Daily setup and QC    59

Configurations tab (BD FACSuite™ application)

Use the Configuration tab to view the current cytometer configuration and the details
for each laser and detector.

You can assign fluorochromes to detectors, and view, print, and export configuration
reports.

More information
 l Running daily performance QC (page 54)
 l About QC reports (page 59)

About QC reports
Introduction
This topic describes the content of the QC reports. You can access these reports in the
Setup & QC workspace, in the QC Reports tab.

QC report content
QC reports contain information about the system, detector settings, lasers, setup bead
lots, cytometer settings, and warnings, errors, and notifications relevant to the task.
They are generated after characterization QC, performance QC, laser setup, and bead
lot transfers.
60      BD FACSLyric™ System Instructions For Use

Each time a procedure is completed, a report is generated for each supported fluidics
mode. The status is listed in the Reports panel as either Passed or Failed. Items that
have passed might have an icon indicating that there are warnings or notifications,
despite the Passed status.

System information
The top section displays the cytometer type, name, configuration, serial number,
options, last characterization and QC date, and user and institution identity.

Summary
This section displays pass/fail status. Pass status is indicated by the word PASSED. Fail
status is indicated by the word FAILED.

Warnings
Warnings are displayed when the current values have increased by 50% since
characterization QC. Red text indicates out-of-range or expired values.
If the status is failed, there is also an Errors section in the report.

Section or field Description

Parameter Laser power and/or laser current

Value Current value of the parameter

Range Expected value range for the parameter

Message Reason for the warning

Notifications
Notifications are displayed for the following reasons:
 l Indicated values are outside of Levey-Jennings alarm ranges. Review Levey-
Jennings plots to see if the instrument performance is changing over time.
 l No value: values that could not be calculated because the baseline does not have
the corresponding measurement.
 Chapter 4  Daily setup and QC    61

Detector settings for performance QC Report

This table displays information that is displayed in the performance QC reports.

Section Field Description

Detector Name Name for the detector

Mirror Name of the mirror used with the detector

Filter Description of wavelengths transmitted

Position Location of the filter holder with mirror

PMTV at Actual Measured PMT voltage

LW Settings
Delta Delta from characterization QC value

Bright Bead Median at Median fluorescence intensity (MFI) value of the specific beads
LW Settings at LW settings

Median at MFI value of the specific beads at QC settings

QC Settings

%rCV Percent robust coefficient of variation of the bright beads

Linearity Min Channel The lower end of the linear range for the detector

Max Channel The upper end of the linear range for the detector

Resolution Sensitivity The ratio of the MFI of the bright bead to two times the
Actual standard deviation of noise of a given detector

Sensitivity % Percent difference from characterization QC value

Diff

Qr Relative fluorescence detection efficiency, used for describing

the light collection efficiency of a detector

Br Relative optical background signal, used for tracking the optical

background noise levels in a detector

Detector settings for characterization QC Report

This table displays information that is displayed in the characterization QC reports.
62      BD FACSLyric™ System Instructions For Use

Section Field Description

Detector Name Name for the detector

Mirror Name of the mirror used with the detector

Filter Description of wavelengths transmitted

Position Location of the filter holder with mirror

PMT Voltage at LW Measured PMT voltage at LW settings

Settings

Slope of Gain Slope of the PMT voltage vs brightness for bright beads (log
MFI vs log PMT voltages)

Bright Bead Median at LW Median fluorescence intensity (MFI) value of the specific
Settings beads at LW settings

Median at QC MFI value of the specific beads at QC settings

Settings

%rCV Percent robust coefficient of variation of the bright beads

Mid Bead Median at QC MFI value of the specific beads at QC settings

Settings

%rCV Percent robust coefficient of variation of the mid beads

Dim Bead Median at QC MFI value of the specific beads at QC settings

Settings

%rCV Percent robust coefficient of variation of the dim beads

Linearity Min Channel The lower end of the linear range for the detector

Max Channel The upper end of the linear range for the detector
 Chapter 4  Daily setup and QC    63

Section Field Description

Resolution Sensitivity The ratio of the MFI of the bright bead to two times the
standard deviation of noise of a given detector

Electronic noise Robust standard deviation (rSD) of the electronic noise in

rSD the particular detector, used to predict the minimum
acceptable signal levels required for the best attainable
resolution and sensitivity for the system

Qr Relative fluorescence detection efficiency, used for

describing the light collection efficiency of a detector

Br Relative optical background signal, used for tracking the

optical background noise levels in a detector

Laser settings
The measurements shown in this section of the report are cytometer-dependent.

Section Field Description

Laser Laser name

Position Location of each laser

Delay Trigger on Laser delay values when thresholding on FSC

FSC

Trigger on Laser delay values when thresholding on fluorescence

Fluorescence

Area Scaling Factor Area scaling factors that are determined by setting area and
height values equally on the bright 3-µm beads

Power Actual Laser power measured in milliwatts

(mW)
Spec Laser power specification in milliwatts

Current Actual Laser current measured in milliamperes

(mA)
Spec Laser current specification in milliamperes
64      BD FACSLyric™ System Instructions For Use

Info
This section displays information on the setup beads and the cytometer settings that
were used.

Field Description

Bead Lot ID Setup bead identifier on the kit label

Expiration date Date after which the bead activity is not guaranteed

Window The amount of time added to collect the signal pulse below the threshold
extension

FSC Area Area scaling factor that is determined by setting the FSC area and height
Scaling Factor values on the bright 3-µm beads

Comments
The Comments section displays comments that were previously added to the report.
Click the Comments icon to add a new comment to the report.

Linearity results
This section of the report shows linearity plots for each detector. They are included
only if the preference is turned on. See Specifying report preferences (page 224).
A detector’s linear range is determined by measuring the MFI ratio of bright beads to
mid beads across the detector’s dynamic range. The ratio values from the middle of
the range, which is known to be linear, are averaged and compared against individual
ratios. If the difference between the measured ratio and the averaged ratio is greater
than 2%, the results are not considered linear.

More information
 l Running daily performance QC (page 54)
 l About the Setup and QC workspace (page 57)
 5 
Experiment basics
This chapter applies to the BD FACSuite™ application only, and includes the following
topics:
 l About the experiment (page 66)
 l Using the Manage Experiments tab (page 68)
 l About tube properties (page 70)
 l About experiment panels (page 72)
66      BD FACSLyric™ System Instructions For Use

About the experiment

Introduction
This topic describes experiments, the Experiment workspace, and provides typical
workflow steps for creating, editing, and saving experiments. As with other topics in
this chapter, this topic applies to the BD FACSuite™ application only.
This workflow includes only the basic required elements for creating and acquiring
data in an experiment using BD default settings. See Using the Manage Experiments
tab (page 68) for more information about optional features and functions.

About the Experiments workspace

The Experiments workspace includes the Manage Experiments tab and Experiment
tabs, which represent an open experiment.
To open the Experiments workspace, click the Experiments icon on the navigation bar.
Use the Manage Experiments tab to create new experiments, preview and open
existing experiments, organize experiments, filter and search for experiments, and
share them with other users. Use the BD FACSuite™ menus to rename, import, or
export experiments.
 Chapter 5  Experiment basics    67

Use a named Experiment tab, such as Experiment_001, to develop your experiment,

adjust settings, set properties, acquire and visualize tube data, and analyze the data
using different analysis tools. A separate tab is created for each open experiment.

About experiment folders

The Experiments Browser panel in the Manage Experiments tab displays experiment
folders. Each user has a default experiment folder identified by the user login name.
You can create an unlimited number of subfolders and organize different experiments
within your default experiment folder.
You can rename experiments and folders, move experiments from one subfolder to
another, and delete, share, or make experiments private.

Locating existing experiments

Experiments are located in your user folder(s) and are listed by experiment name and
creation date. Private experiments are accessible only by their author. Shared
experiments are accessible by all users.
If your folders include numerous subfolders with many experiments, you can search
individual folders to locate experiments. Click a folder, type an experiment name,
number, date, or owner in the Search field and press Enter.
68      BD FACSLyric™ System Instructions For Use

If you cannot find a specific experiment, the experiment might not be shared. See
your Administrator or the experiment author for more information.

More information
 l About experiment panels (page 72)
 l Using the Manage Experiments tab (page 68)
 l Experiment building workflow (page 86)

Using the Manage Experiments tab

Introduction
This topic describes how to open, save, and delete experiments, and how to change
sharing settings. As with other topics in this chapter, this topic applies to the BD
FACSuite™ application only.

Opening the Experiment workspace

To open the Experiment workspace:
 1. On the navigation bar, click Experiments.
The Manage Experiments tab opens in the Experiment workspace.

Saving an experiment as a different experiment

To save an experiment (Save As) as a different experiment:
 1. In the Experiments Browser, right-click an experiment, then select Save As.
A Save Experiment As dialog opens.
 2. In the Experiment Name field, type a new experiment name.
 3. (Optional) If you want to save the experiment properties, plots, gates, and other
worksheet elements, but not the tube data, select the Save Experiment without
Data checkbox.
 4. Click OK to save a copy of this experiment with a new name.
 Chapter 5  Experiment basics    69

Changing sharing settings

Experiments are private by default. Only Administrators or experiment owners
(authors) can change share settings. Once an experiment is shared by the author, all
users can modify, rename, or export the experiment. Changes are saved to the
original, shared experiment. Only Administrators or experiment owners (authors) can
delete an experiment.
Shared experiments are listed in the Shared by Me and Shared by Others folders.
Private experiments are listed only in the All Experiments and Owned by Me
experiment folders.
To change the share setting for an experiment:
 1. In the Experiments Browser, right-click an experiment and select Make Private or
Share.

Exporting experiments
Export experiments so that you can import them onto a different BD FACSLyric™
workstation or to back up experiments as a part of your specific data management
process.
To export an experiment:
 1. In the Experiment workspace, click the Manage Experiments tab.
 2. In the Experiments Browser, click an experiment folder.
 3. Right-click an experiment.
 4. Select Export Experiments, then select one of the following options:
 l With Data. Saves all tube properties, instrument settings, worksheets, reports,
and acquired data.
 l Without Data. Saves tube properties, worksheets, and reports. Select this option
when you are creating tubes you want to reuse.
The Browse For Folder dialog opens.
 5. Navigate to a target export folder.
 6. Click OK to export the file.
 7. View the status bar to confirm that the files have exported successfully.
70      BD FACSLyric™ System Instructions For Use

More information
 l About the experiment (page 66)
 l Creating and opening an experiment (page 83)

About tube properties

Introduction
As with other topics in this chapter, this topic applies to the BD FACSuite™ application
only.
Tube properties define the identity and details for each tube and determine how tube
data is acquired and displayed. Tube properties can be modified at any time before
you acquire a tube. It can be useful to set some tube properties before you preview
data (for example, selecting tube settings or adding labels), while other properties
should be modified after plots and gates are created (for example, acquisition
stopping rules).
 Chapter 5  Experiment basics    71

Tube properties
The following table describes the tabs in the Tube Properties dialog.

Tab Description

General Use this tab to view or modify the tube name, tube ID, or sample ID, select tube
settings, and view other descriptive information about the tube.

See Setting general tube properties and applying tube settings (page 97)

Parameters Use this tab to change the current parameter names, area, height, and width,
PMT voltages, and thresholds for the tube.

See Viewing and adjusting cytometer settings (page 93)

Spillover Use this tab to view or modify the compensation matrix for the current tube.
Values
You do not need to modify this matrix for typical daily use.

See Modifying the compensation matrix (page 95)

Reagents Use this tab to select labels and lot IDs for fluorochromes used in this tube.

See Editing single-color reagent labels (page 101)

Keywords Use this tab to view and assign keywords and set keyword values to the
selected tube.

See Assigning and editing keywords (page 102)

Acquisition Use this tab to set acquisition stopping rules.

See Setting acquisition stopping rules (page 104)

More information
 l Experiment building workflow (page 86)
 l Modification of tube properties for multiple tubes (page 99)
72      BD FACSLyric™ System Instructions For Use

About experiment panels

Introduction
This topic describes the different panels in the Experiment tab and how to use them to
build, modify, and run experiments. As with other topics in this chapter, this topic
applies to the BD FACSuite™ application only.

About the Experiment tab

When you create a new experiment or open an existing experiment in the Manage
Experiments tab, a new Experiment tab opens.

The Experiment tab represents an experiment and includes the following panels:

No. Description

1 Data Sources

2 Acquisition Status

3 Cytometer Settings

4 Worksheets and reports

 Chapter 5  Experiment basics    73

You can drag the panels to organize them in any order within the workspace, or click to
minimize panels to maximize display space.

About the Acquisition Status panel

Use the Acquisition Status panel to view real-time status for time, event counts, and
aborts. You can also set flow rate and SIT flush options specific to an experiment.

This panel is open by default. You can show or hide this panel. When you hide (close)
the panel, an Acquisition Status button is displayed in a toolbar at the top of the
Experiment tab. Click the button to display the panel.
Acquisition data displays each time you preview or acquire data. The display is
refreshed (cleared) each time you preview or acquire a tube. You can also click to
expand Advanced Status to display the acquisition abort count and abort rate.
74      BD FACSLyric™ System Instructions For Use

You can select the following options in this panel.

Option Description

Flow Select the rate (low, medium, high, or high sensitivity) that the sample flows
Rate through the flow cell in the instrument. High and medium flow rates are typically
used for immunophenotyping experiments and to increase event throughput. Lower
flow rates are typically used when high precision is required (for example, DNA
experiments) to measure slight variations in fluorescence. The high-sensitivity
fluidics mode slows the sample and sheath flow. If selected in an experiment, high-
sensitivity fluidics mode must be enabled in the Setup and QC Preferences. Note:
High-sensitivity fluidics mode should not be used in clinical applications.

Events Select the maximum number of events to display in plots.

to
Display

Number By default, one SIT flush is performed after acquisition completes and after you
of SIT remove the tube from the manual tube port. Increase the number of flushes when
Flushes extra cleaning is required between acquisitions to reduce sample carryover.

If you create another tube using the Next button in the Data Sources panel, all the
settings in the Acquisition Status panel remain the same unless you change them.
If you create another tube using the New Tube button in the Data Sources panel, only
Events to Display remains the same; Flow Rate and Number or SIT Flushes revert to
default values.
 Chapter 5  Experiment basics    75

About the Data Sources panel

Use the Data Sources panel to add and delete tubes and FCS files for acquisition and
analysis. You can right-click tubes to set tube properties, duplicate tubes, create tube
settings, and create reference settings. The run pointer indicates which tube is being
previewed or acquired, and which tube’s data is applied to a plot.

No. Description

1 Run pointer
76      BD FACSLyric™ System Instructions For Use

The Data Sources table displays the tube name, sample ID, and acquisition date. The
following table describes the buttons in the Data Sources panel.

Button Description

New Click to add a new tube to the list.

Tube
A new default tube has the default Lyse/Wash (LW) or Lyse/No-Wash (LNW) tube
settings. You can select the default tube settings from the experiment preferences.

Import Click to display a dialog where you can select FCS files to import for analysis.
FCS
Files

Delete Select a tube or tubes in the list, then click this button to delete the tube.
Tube

Add Click to select tubes from a worklist and add them as tubes in an experiment.
From
See Creating and adding tubes (page 87).
Worklist

Preview Click to start the sample flow and to populate plots with event data. This does not
record event data.

Acquire Click to start the sample flow (if not already previewing) and record event data to
an FCS file.

Stop Click to stop the sample flow and the current preview or acquisition.

Next Click to set the run pointer to the next tube in the Data Sources table. You can also
click this button to add tubes. Note that this is the equivalent of duplicating without
data.

See Creating and adding tubes (page 87).

Pause Click during preview to pause the sample flow and event counters and timers.

Resume Click to resume a paused preview.

Restart During preview, click to clear the counters and timers. This clears the acquisition
data without pausing the fluid flow.

During acquisition, click to delete acquired events, clear counters and timers, and
clear the progress bar. This clears the acquisition data without pausing the fluid
flow.
 Chapter 5  Experiment basics    77

About the Cytometer Settings panel

Use the Cytometer Settings panel to view system status, run cleaning protocols, adjust
PMT voltages, and view laser delay and area scaling. This panel includes the following
sections:
 l Status
 l PMT Voltages
 l Lasers

Status
The Status section displays the system status, including real-time status for the SIT,
fluidics, and lasers. This section also indicates when you need to run system cleaning
protocols.

A checkmark indicates a ready status. You can click the arrow icon in the Status title
bar to expand or collapse this section.

PMT Voltages
Use the PMT Voltages section during preview to select the area, height, width, and
adjust the voltage and threshold for scatter or fluorescence parameters. You can also
add or remove parameters.
78      BD FACSLyric™ System Instructions For Use

If you are using the default tube settings and then adjust PMT voltages or other
cytometer settings, the changes apply only to the current tube. If you want to reuse
adjusted settings for additional tubes, especially outside the current experiment,
create a new tube setting.
 Chapter 5  Experiment basics    79

In the PMT Voltages section, you can perform the following actions. Select a
parameter by clicking to the right of the threshold control.

Button Description

Threshold Select And or Or to specify how multiple thresholds are combined logically.
Operation

Add Adds a new parameter to the PMT Voltages table. Click the arrow to select a
fluorochrome.

Remove Removes the selected parameter from PMT Voltages table.

Parameter Displays a list of available parameters. You can select the fluorochrome by
(Name clicking the arrow.
column)

A (Area), A (Area) is the default parameter that measures the entire voltage pulse. H
H (Height), (Height) is the peak of the voltage pulse, and W (Width) is the amount of time
and W taken for the event to pass through the laser (multiplied by a constant).
(Width)

Voltage Adjusting the voltage changes the amount of sensitivity used by the PMT to view
events.

 l Click the up and down arrows to adjust the value in increments of 1 V.

 l Ctrl+click the up and down arrows to adjust the value in increments of 10 V.
 l Drag the slider to adjust the voltage value in any increment.

Threshold An electronic threshold on a parameter is used to eliminate unwanted events.

Only events with parameter values above the threshold are acquired. Select the
checkbox to enable the threshold for the parameter.

 l Click the up and down arrows to adjust the value in increments of 100.
 l Ctrl+click the up and down arrows to adjust the value in increments of 10.
 l Drag the slider to adjust the voltage value in any increment.

You can click the arrow icon in the PMT Voltages title bar to expand or collapse this
section.
This page intentionally left blank
 6 
Data acquisition in an experiment
This chapter applies to the BD FACSuite™ application only, and includes the following
topics:
 l Data acquisition workflow (page 82)
 l Creating and opening an experiment (page 83)
 l Experiment building workflow (page 86)
 l Creating and adding tubes (page 87)
 l Creating plots and gates (page 88)
 l Viewing and adjusting cytometer settings (page 93)
 l Modifying the compensation matrix (page 95)
 l Setting general tube properties and applying tube settings (page 97)
 l Modification of tube properties for multiple tubes (page 99)
 l Editing single-color reagent labels (page 101)
 l Assigning and editing keywords (page 102)
 l Setting acquisition stopping rules (page 104)
 l Acquiring data in an experiment (page 105)
82      BD FACSLyric™ System Instructions For Use

Data acquisition workflow

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Introduction
This topic describes the typical workflow stages you need to complete to build an
experiment and acquire data. This is also the workflow for creating an assay, which
allows for data acquisition in the worklist. As with other topics in this chapter, this topic
applies to the BD FACSuite™ application only.

Typical workflow
Perform the following typical workflow stages for acquiring data in an experiment.

Stage Description

1 Create a new experiment or open an existing experiment.

See Creating and opening an experiment (page 83).

2 Build an experiment.

See Experiment building workflow (page 86).

3 Acquire data.

See Acquiring data in an experiment (page 105).

4 (Optional) Save, export, or print the experiment.

See Using the Manage Experiments tab (page 68).

More information
 l Daily workflow (page 45)
 l Performing system startup (page 48)
 Chapter 6  Data acquisition in an experiment    83

Creating and opening an experiment

Introduction
This topic describes how to create new experiments and how to open existing
experiments. As with other topics in this chapter, this topic applies to the BD
FACSuite™ application only.
You can have several experiments open at the same time. This allows you to compare
acquired data from different experiments.

Creating a new experiment

To create a new experiment:
 1. On the navigation bar, click Experiments.
The Manage Experiments tab opens in the Experiments workspace.
 2. In the Experiments Browser panel, click your default folder or subfolder.
 3. Click New.
A new experiment opens. The new experiment name and creation date are
displayed in the Experiments Browser, and a new tab opens in the Experiments
workspace.

Opening an existing experiment

To open an existing experiment:
 1. In the Experiments Browser, click your experiment folder or click an experiment
subfolder to display the available experiments.
84      BD FACSLyric™ System Instructions For Use

 2. (Optional) Click an experiment to display a snapshot of the experiment in the

Experiment Preview panel.
 3. Double-click an experiment to open the experiment in the Experiments workspace.

Opening multiple experiments

To open multiple experiments at the same time:
 1. In an experiments folder, Ctrl+click each experiment that you want to open.
 2. Right-click, then select Open Experiment.
All selected experiments open as individual tabs.

Creating a new experiment from an assay

If you want to modify a current BD assay or a user-defined assay, you can create a
new experiment from the assay, modify the experiment, then create an assay from
the modified experiment.
To create a new experiment from an assay:
 1. Click the Manage Experiments tab.
 2. From the menu bar, select File > New Experiment from Assay.
The Select an Assay dialog opens.
 3. Click an assay in the list, then click OK.
 Chapter 6  Data acquisition in an experiment    85

The new experiment is displayed in the Experiments Browser and the new
experiment opens.
If you intend to modify an existing user-defined assay and want to retain the same
assay name, you can overwrite the original by creating an assay with the same name
(but only if the original assay in the library does not have Shared status).
See Creating a user-defined assay from an experiment (page 112).

Next steps
 l If you want to create new tubes or delete existing tubes in your experiment,
continue with Experiment building workflow (page 86).
 l If your experiment has the correct tubes, plots, gates and properties, you can
acquire tubes, re-acquire existing tubes, or analyze the data. See Acquiring data in
an experiment (page 105).

More information
 l About the experiment (page 66)
86      BD FACSLyric™ System Instructions For Use

Experiment building workflow

Introduction
This topic provides the basic workflow for building an experiment. As with other topics
in this chapter, this topic applies to the BD FACSuite™ application only.

Typical workflow
Perform the following typical workflow stages for building an experiment.

Stage Description

1 Determine the experiment settings strategy.

2 Adjust cytometer settings as needed.

See Viewing and adjusting cytometer settings (page 93).

3 (Optional) Create tube settings and reference settings as needed.

See Creating tube settings (page 116) and Creating default reference settings (page
117).

4 Add tubes (if needed) with default tube settings, or apply existing tube settings.

See Creating and adding tubes (page 87).

5 Create and modify worksheet, reports, plots, and create gates and statistics views.

See Creating plots and gates (page 88).

6 (Optional) Create a user-defined assay from the experiment.

See Creating a user-defined assay from an experiment (page 112).

More information
 l Using the Manage Experiments tab (page 68)
 Chapter 6  Data acquisition in an experiment    87

Creating and adding tubes

Introduction
This topic describes how to create tubes in the Data Sources panel by adding or
duplicating tubes. This topic also describes how to delete tubes from an experiment.
As with other topics in this chapter, this topic applies to the BD FACSuite™ application
only.

Working with tubes

When you create a new experiment, one default tube is displayed in the Data Sources
panel.
To work with tubes, complete one of the following options in the Data Sources panel:

To... Then do this...

Create a new  1. Click New Tube.

tube.
A new default tube is displayed. The Lyse/Wash (LW) or Lyse/No-
Wash (LNW) tube settings are applied to all default tubes.

Add tubes from  1. Click Add From Worklist.

entries in a
worklist. The Add Tubes From Worklist dialog opens.

 2. Select one of the following:

 l Under Entries, click a worklist entry, then click Add Selected

Entry Tubes.
 l Under Entries, click a worklist entry. Under Tubes, click individual
tubes that are displayed in the entry, then click Add Selected
Tubes.
Use the Next  1. Click Next to move the run pointer to the next tube.
button to add
tubes If you click the last tube in the list, and then click Next, a new
duplicate tube without data is created and the run pointer moves to
the tube.
88      BD FACSLyric™ System Instructions For Use

To... Then do this...

Duplicate tubes  1. Before you can duplicate with data, acquire the tube.
with or without
See Acquiring data in an experiment (page 105).
data
 2. In the tube list, right-click the tube you want to duplicate.
 3. Select one of the following:

 l Duplicate with data. A duplicate tube is added to the list with

the same tube name and includes all data that is associated with
the source tube.
 l Duplicate without data. A duplicate tube is displayed with a
new name and includes all tube properties and settings except the
acquired data.

Clear data in a  1. Right-click a tube and select Clear Tube.

tube
All associated tube data is deleted and associated plots or statistics
are cleared.

Delete a tube  1. Click a tube in the list.

 2. Click Delete.

Next step
 l After you add tubes to the experiment, create plots on a worksheet to visualize
tube data. See Creating plots and gates (page 88).
 l If you want to adjust tube properties before creating plots, see Setting general
tube properties and applying tube settings (page 97), and Modification of tube
properties for multiple tubes (page 99).

Creating plots and gates

Introduction
As with other topics in this chapter, this topic applies to the BD FACSuite™ application
only. This topic describes how to create plots and basic gates. Gates allow you to
identify cells of interest, display these cells graphically in plots, and classify events into
populations which are used to calculate statistics.
 Chapter 6  Data acquisition in an experiment    89

Additional gate types including logical, interval, adaptive, and quad gates are
described in the BD FACSLyric™ Reference System.

About worksheets and reports

Worksheets and reports provide a canvas to lay out analysis elements such as plots,
statistics, and text. You use the Worksheets toolbar to add and adjust analysis
elements. Reports differ from worksheets because reports allow the use of an E-
Signature box, are shown as part of the report delay time, and are available for auto-
printing and exporting.

Before you begin

 l It is helpful to create tubes before you create plots associated with the tubes.
 l (Optional) You can also set tube properties before you begin, or at any time before
you acquire the tube. See Setting general tube properties and applying tube
settings (page 97).

Creating a plot
When you create a new experiment, one default tube is displayed in the Data Sources
panel and one default plot is displayed in the worksheet.
When you create additional plots, the plots display the default plot title and
parameter names. You can modify the plot title and select different parameters for
each axis after you create the plot.
To create a plot:
 1. Open an experiment.
 2. (Optional) Click Toggle Grid on the Worksheets toolbar to enable the grid.
A grid on the worksheet provides guidelines for plot size and placement.
 3. Click a plot tool on the Plot toolbar.
 4. Click in the worksheet to create the plot.
 5. Continue to add plots for your scatter and fluorescence parameters as needed.
The primary data source determines which tube is associated with a plot or plots in
the worksheet. If the run pointer is selected as the primary data source (default),
all plots display data from the tube that is indicated by the run pointer.
90      BD FACSLyric™ System Instructions For Use

You can change the primary data source for a plot from the run pointer to a
specific tube if needed.

Modifying plot parameters

To modify plot parameters:
 1. Select a plot in a worksheet.
 2. Right-click the x-axis parameter label, then select a parameter from the list.
 3. Right-click the y-axis parameter label, then select a parameter from the list.

Drawing gates
The following table describes how to draw basic gates in plots.
 Chapter 6  Data acquisition in an experiment    91

To draw a... Then do this...

Rectangle  1. Click this tool on the Worksheet toolbar.

gate  2. Click in the plot and drag diagonally to create and size the rectangle
around specific events in the plot.
 3. Release the mouse button to set the gate.

Polygon gate  1. Click this tool on the Worksheet toolbar.

 2. Click in the plot to specify a starting point. A vertex is displayed.
 3. Move the cursor to another position and click to add another vertex.
Repeat this step to create a minimum of three vertices around specific
events in the plot.
 4. Click the first vertex or double-click to set the last vertex to close the gate.
92      BD FACSLyric™ System Instructions For Use

To draw a... Then do this...

Ellipse gate  1. Click this tool on the Worksheet toolbar.

 2. Click in the plot and drag diagonally to create and size the ellipse around
specific events in the plot.
 3. Release the mouse button to set the gate.

Freehand  1. Click this tool on the Worksheet toolbar.

gate  2. In the plot, click and hold the mouse button, then move the cursor to draw
a freehand shape around specific events.
 3. Release the mouse button to set the gate.

New gates are added to the hierarchy and are applied to all tubes within the
experiment. The population hierarchy is updated to identify the new population.
 Chapter 6  Data acquisition in an experiment    93

Next step
 l If a tube contains acquired data, new plots automatically display data.
 l If you are working with un-acquired tubes, plots remain empty until you preview or
acquire the tube to populate the plots with data. Continue by acquiring data.

More information
 l Modifying the compensation matrix (page 95)
 l Setting general tube properties and applying tube settings (page 97)
 l See topics about plots in the BD FACSLyric™ Reference System for more
information about plot types and tools, and creating and modifying plots.
 l See topics about modifying tube properties in the BD FACSLyric™ Reference
System.

Viewing and adjusting cytometer settings

Introduction
This topic describes how to view the tube parameters for area, height, width, window
extension, area scaling factors, laser delay, PMT voltages, and threshold settings. As
with other topics in this chapter, this topic applies to the BD FACSuite™ application
only.
You can then adjust these settings in the Cytometer panel. Adjust the cytometer
settings for a tube to optimize the sample brightness and place the events on scale.

Viewing tube parameters

To view tube parameters for a tube:
 1. In the Data Sources panel, set the run pointer to the tube you want to modify (for
example, Tube_001).
 2. Double-click the run pointer, or right-click the tube and select Properties to open
the Tube Properties dialog.
 3. Click the Parameters tab.
94      BD FACSLyric™ System Instructions For Use

This tab displays only the parameters that are set for the current tube or an
acquired tube.

Adjusting cytometer settings

Perform the following adjustments as needed before or after you create gates in a
plot.
To adjust the cytometer settings:
 1. Preview the data. See Previewing data (page 105).
 2. Adjust the PMT voltages as needed to put all populations on scale.
 a. In a plot, click the PMTV button in the lower-left corner of the plot to enable
the data sliders.
 Chapter 6  Data acquisition in an experiment    95

 b. Drag the slider control for each axis parameter in the plot.
The PMTV value is displayed on the slider control.
 c. Click the PMTV button again to disable the slider control.
 3. Select a threshold operation as needed.
 4. Select a checkbox to enable a threshold, then adjust the threshold value as
needed.
 5. Select area, height, and width parameters as needed.
 6. Click Stop to stop previewing.

More information
 l Acquiring data in an experiment (page 105)
 l See topics about changing the primary data source for a plot in the BD FACSLyric™
Reference System.
 l See topics about populations and the population hierarchy in the BD FACSLyric™
Reference System.

Modifying the compensation matrix

Introduction
This topic describes how to view or modify the spillover matrix for your tube using the
Spillover Values tab in the Tube Properties dialog. As with other topics in this chapter,
this topic applies to the BD FACSuite™ application only.
96      BD FACSLyric™ System Instructions For Use

About the compensation matrix

The spillover matrix is automatically recalculated any time you adjust the PMT
voltages for a tube.
If you apply tube settings that do not have associated reference settings, the matrix is
calculated using the spillover values (SOVs) from the Lyse/Wash reference settings.
If you apply tube settings that have an associated reference setting, the matrix
reflects the measured SOVs created with the reference settings.
If the calculated SOVs work for your samples, you do not need to modify this matrix.

Procedure
To modify the SOVs matrix for a tube:
 1. In the Data Sources panel, set the run pointer to the tube you want to modify (for
example, Tube_001).
 2. Double-click the run pointer, or right-click the tube and select Properties to open
the Tube Properties dialog.
 3. Click the Spillover Values tab.
The matrix displays the SOVs associated with the acquired tube or the values that
will be used when a tube is acquired. The table shows how much of the row (for
example, FITC parameter) is spilling over into the column (for example, PE
parameter).
 4. Select the Enable Compensation checkbox to analyze with compensated data, or
clear the checkbox to analyze with uncompensated data.
 5. (Optional) Edit the SOVs as needed.
The goal is to ensure that a single-positive population and the negative population
are centered. For example, for a plot with FITC vs PE, the FITC mean on the y-axis
should not be higher or lower than the negative-population mean.
 a. Locate the row on the left, then move right across the table until you locate the
intersecting column.
 Chapter 6  Data acquisition in an experiment    97

 b. Type a new value (0.00 to 1000.00) in the table, or click the up and down arrows
to adjust the value.
If you adjust the values in this matrix, the values are applied to the current tube. If
you want to reuse these values, you need to save modified reference settings. Use
the Reset button to undo changes to the matrix. Use the Apply to Tubes button to
copy the SOV matrix from one tube in the experiment to another.
 6. Click Close.

More information
 l Saving modified reference settings (page 127)
 l Viewing and adjusting cytometer settings (page 93)
 l Editing single-color reagent labels (page 101)

Setting general tube properties and applying

tube settings
Introduction
This topic describes how to set general tube properties using the General tab in the
Tube Properties dialog and how to apply different tube settings from the library. As
with other topics in this chapter, this topic applies to the BD FACSuite™ application
only.

Setting general tube properties

To set general properties for a tube:
 1. In the Data Sources panel, double-click the run pointer, or right-click a tube and
select Properties to open the Tube Properties dialog.
98      BD FACSLyric™ System Instructions For Use

The Tube Properties dialog opens in the General tab.

 2. In the Tube Name field, use the current default name or type a new tube name.
 3. (Optional) In the Tube ID field, type a tube ID or click in the field and scan a
barcode.
 4. (Optional) In the Sample ID field, type a sample ID or click in the field and scan a
barcode.
Information for the following read-only fields is displayed when you acquire a tube:
 l Total Events (acquired for this tube)
 l Acquisition Date
 l Cytometer Name (the cytometer that was used for acquisition)

Applying existing tube settings

When you create a new tube, the default tube settings are applied—Lyse/Wash (LW),
or Lyse/No-Wash (LNW), based on the Experiment preferences. This section describes
how to apply a different tube setting from the library.
See Creating tube settings (page 116).
To apply existing tube settings:
 1. In the General tab, click Select in the Tube Settings field.
The Select Tube Setting dialog opens.
 2. Select a tube setting in the list.
 3. Click Select.
The tube settings are applied to the current tube.
If you modify any values that are part of a tube setting, a star icon is displayed in
the Tube Settings field indicating that you have modified tube settings. The
application automatically calculates modified SOVs based on the SOV column and
modified tube settings.
 Chapter 6  Data acquisition in an experiment    99

If you select a different tube setting, you will undo your current modified values
and the star will be removed. If you want to save these modified settings for future
use, create tube settings prior to selecting a different tube setting.

More information
 l Modification of tube properties for multiple tubes (page 99)
 l Viewing and adjusting cytometer settings (page 93)

Modification of tube properties for multiple

tubes
Introduction
This topic describes how to modify tube properties for multiple selected tubes. As with
other topics in this chapter, this topic applies to the BD FACSuite™ application only.
You can select multiple tubes and modify certain tube properties simultaneously. The
properties that can be modified are those for which the fields in the dialogs are
enabled for editing. If a field is not enabled, it will be dim and you cannot click in the
field.

Rules for tube property fields

The general rules for fields that are enabled are:
 l If the values are the same between the selected tubes, then the actual value
displays in the field.
100      BD FACSLyric™ System Instructions For Use

 l If the values are different between the selected tubes, then the field displays
<multiple> or <m>.

Details for Tube Properties tabs

The Tube Properties tabs have different behaviors depending on which one you are
trying to modify for multiple selected tubes. The following table describes what you
can and cannot modify when multiple tubes are selected.

Tab Description

General Tube name, tube ID, sample ID, and tube settings are editable if all the tubes
are unacquired.

Parameters PMTVs and threshold can be edited for multiple tubes if all the tubes are
unacquired.

Spillover Compensation takes into account labels, parameters, and lot IDs to determine
Values which values are editable.

Reagents All of the fields in this tab are editable for multiple tubes.

Keywords All of the fields in this tab are editable for multiple tubes.

Acquisition All of the fields in the Stopping Rules sub-tab are editable for multiple tubes.

More information
 l Setting general tube properties and applying tube settings (page 97)
 l Viewing and adjusting cytometer settings (page 93)
 Chapter 6  Data acquisition in an experiment    101

 l Creating tube settings (page 116)

Editing single-color reagent labels

Introduction
This topic describes how to view or edit single-color reagent labels for available
fluorochrome parameters in a tube. As with other topics in this chapter, this topic
applies to the BD FACSuite™ application only.

Procedure
To edit single-color reagent labels for available fluorochrome parameters in a tube:
 1. In the Data Sources panel, set the run pointer to the tube you want to modify (for
example, Tube_002).
 2. Right-click the tube and select Properties to open the Tube Properties dialog.
 3. Click the Reagents tab.
 4. In the Label column for each parameter, select an available reagent label.

 5. If your reagents require lot-specific SOVs (usually for tandem fluorochromes),
select a lot ID from the Lot ID column.
You must add reagents to the Library before you can use them. The values in the
102      BD FACSLyric™ System Instructions For Use

Library Reagents workspace populate the lot ID list.

If you do not select a lot ID from the list, then the generic SOVs are used.

Assigning and editing keywords

Introduction
This topic describes how to view or assign keywords to a tube and how to modify
keyword values using the Keywords tab in the Tube Properties dialog. As with other
topics in this chapter, this topic applies to the BD FACSuite™ application only.

About keywords
Keywords are unique fields for storing information in files. They are used to identify
particular data elements, both required and optional, and can be added to tubes in an
experiment. Keywords can include information such as patient information, dilutions,
and cell or sample types.

Before you begin

In the library, create any new keywords that you plan to assign to tubes.

Assigning new keywords to a tube

To assign a new (user-defined) keyword to a tube:
 1. In the Data Sources panel, set the run pointer to the tube you want to modify (for
example, Tube_001).
 2. Double-click the run pointer, or right-click the tube and select Properties to open
the Tube Properties dialog.
 3. Click the Keywords tab.
 4. Click Assign Keywords.
The Assign Keywords dialog opens.
 5. In the Assign column, select the checkboxes for keywords you want to assign to the
tube.
 Chapter 6  Data acquisition in an experiment    103

To locate or view detailed information on the keywords, you can perform the
actions in the following table.

To... Then do this...

Filter keywords by name or  1. In the Keyword Filter field, type the name or
display name display name criteria.
 2. Press Enter.

View the properties of a keyword  1. Click Keyword Properties.

 2. Select a keyword in the list to view its properties.

 6. Click OK.

The assigned user-defined keywords are displayed in the tab.

Changing values for assigned keywords

To change values for keywords assigned to a tube:
 1. In the Tube Properties dialog, click the Keywords tab.
Any currently assigned user-defined keywords are displayed.
 2. Click the user-defined keyword you want to modify.
 3. Click the Value field for that keyword and type a new value or select a new value
from the menu.
104      BD FACSLyric™ System Instructions For Use

More information
 l Running a worklist (page 157)
 l See the Keywords section in BD FACSLyric™ Reference System for more details on
keywords.

Setting acquisition stopping rules

Introduction
This topic describes how to set acquisition stopping rules using the Acquisition tab in
the Tube Properties dialog. As with other topics in this chapter, this topic applies to the
BD FACSuite™ application only.
If you want to assign a specific gate or gates to use as storage or stopping criteria,
these gates must first be created before setting acquisition properties.

Setting acquisition stopping rules for a tube

To set acquisition stopping rules for a tube:
 1. In the Data Sources panel, set the run pointer on the tube you want to modify (for
example, Tube_001).
 2. Double-click the run pointer, or right-click the tube and select Properties to open
the Tube Properties dialog.
 3. Click the Acquisition tab.
 4. If the experiment has multiple worksheets, click and select a worksheet in the
Worksheet to Display during Acquisition field.
 5. In the Storage Gate field, click and select an existing gated population if you want
to use a gate as the storage gate.
A storage gate identifies which data is stored when the tube is acquired. If you
select a gate for a subpopulation (P1, P2, etc), only events from that subpopulation
are stored in the FCS file.
 6. In the Stopping Rules tab, define the acquisition stopping rules.
BD FACSuite™ application always uses a combination of a time stopping rule and a
gate criteria rule using an OR operator. Use Time Stopping Rule to change the time
criteria. Use Create Gate Criteria and Combine Gate Criteria and Apply Rule to
change and apply the gate criteria. The current acquisition stopping rules are
displayed under Applied Stopping Rule.
 Chapter 6  Data acquisition in an experiment    105

More information
 l Setting general tube properties and applying tube settings (page 97)
 l See the BD FACSLyric™ Reference System for more details on stopping rules.

Acquiring data in an experiment

Introduction
This topic describes how to preview and acquire data in an experiment. You can
acquire data in an experiment as long as the experiment has at least one tube. As with
other topics in this chapter, this topic applies to the BD FACSuite™ application only.

About previewing data

Previewing data is the process of starting the sample flow and displaying event data.
Previewing does not record data. While previewing, you can adjust the PMT voltages
and modify the tube properties.
This example describes previewing data from a single (manually loaded) tube using the
run pointer as the primary data source. See topics about changing the primary data
source for a plot in the BD FACSLyric™ Reference System.

Before you begin

Create plots in the worksheet before you preview tube data.

Previewing data
To preview data in a specific tube:
 1. Load a tube on the manual tube port.
 2. In the Data Sources panel, set the run pointer to the tube you want to preview (for
example, Tube_002).
 3. Click Preview.
106      BD FACSLyric™ System Instructions For Use

During preview, the run pointer remains blue and displays an activity indicator.

Data is displayed in the plots.

Once data is displayed in plots, you can adjust the cytometer settings and draw
gates to identify populations of interest.
See Viewing and adjusting cytometer settings (page 93).

Acquiring data
To acquire data in an experiment:
 1. Complete the previewing procedure and adjust gates and cytometer settings as
needed.
 2. Click Acquire.
 Chapter 6  Data acquisition in an experiment    107

During acquisition, the run pointer turns orange and displays an activity indicator.

Acquisition continues until the stopping rules (defined in the Tube Properties
dialog) are satisfied.
The acquisition status is displayed in the Acquisition Status panel.

During acquisition, you can click Stop to manually stop acquisition, or click Restart
to clear the current acquisition.
When acquisition is complete, the tube icon displays as a filled tube to indicate
that data has been acquired.

 3. Click Next to move the run pointer to the next tube.
If no next tube exists, a new tube (duplicate without data) is created and the run
pointer moves to the tube.
108      BD FACSLyric™ System Instructions For Use

Next step
After you acquire data, you can analyze the data immediately, or open the
experiment later to analyze it.

More information
 l Data analysis workflow (page 110)
 l Creating and opening an experiment (page 83)
 l Experiment building workflow (page 86)
 7 
Data analysis in an experiment
This chapter applies to the BD FACSuite™ application only, and includes the following
topics:
 l Data analysis workflow (page 110)
 l Exporting and printing experiment worksheets and reports (page 111)
 l Creating a user-defined assay from an experiment (page 112)
110      BD FACSLyric™ System Instructions For Use

Data analysis workflow

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

Introduction
This topic describes the workflow for analyzing data acquired in an experiment. As with
other topics in this chapter, this topic applies to the BD FACSuite™ application only.

About analyzing experiments

When you create an experiment, you can preview data and perform basic analysis by
adding plots and drawing gates to define populations.
You can perform analysis on the workstation that is connected to the cytometer or
from a remote workstation with BD FACSuite™ application and exported FCS files.

Typical workflow
Perform the following tasks to analyze data in an experiment.

Stage Description

1 Open an existing experiment or import an experiment on a remote workstation.

See Creating and opening an experiment (page 83).

2 Create and modify reports.

See these topics in the BD FACSLyric™ Reference System:

 l Modifying experiment worksheets and reports

 l Setting and modifying the report header and footer

3 (Optional) Export or print reports.

See Exporting and printing experiment worksheets and reports (page 111).

4 (Optional) Save the experiment as an assay.

See Creating a user-defined assay from an experiment (page 112).

 Chapter 7  Data analysis in an experiment    111

Exporting and printing experiment worksheets

and reports
Introduction
This topic describes how to print or export worksheets or reports. As with other topics in
this chapter, this topic applies to the BD FACSuite™ application only.
Exporting in PDF format allows you to archive a page separately from the experiment.
If your experiment includes multiple worksheet or report tabs, you must select each
and export them separately.

Exporting a worksheet or report

To export:
 1. Open an experiment.
 2. Select the desired worksheet or report by clicking the tab.
 3. From the menu bar, select File > Export To PDF.
The Save As dialog opens.
 4. Navigate to the folder where you want to export the page.
 5. Type a file name.
 6. Click OK.

Printing a worksheet or report

To print:
 1. Select the desired worksheet or report by clicking the tab.
 2. Click the Print Current Tab tool.
 3. Preview the report and make sure that all analysis items are in the print area of the
page.
 4. Select Print on the Print Preview menu bar.
 5. Complete your typical printing process.
Note: The selected printer must be capable of accepting input in PDF format.
112      BD FACSLyric™ System Instructions For Use

Previewing a worksheet or report

To preview:
 1. Select the desired worksheet or report by clicking the tab.
 2. From the menu bar, select File > Print.
 3. Preview the report and make sure that all analysis items are in the print area of the
page.
You can print to a PDF-capable printer from the preview window using the Print
button on the Print Preview menu bar.

Creating a user-defined assay from an

experiment
Introduction
This topic describes how to create a user-defined assay from an experiment. User-
defined assays are used as templates in worklists to complete the same work on
multiple samples. As with other topics in this chapter, this topic applies to the BD
FACSuite™ application only.

About saving experiments

Experiments are automatically saved as you make changes to them. Creating a user-
defined assay from an experiment allows the assay to be used in the worklist, and is
useful when you or others must repeat an experiment often. The user-defined assays
provide uniform cytometer settings and format.
Some properties and parameters which are expected to be constant over time
become permanent in the assay.
If you want to edit these properties or parameters, you can create an experiment from
the assay, modify it, then save it as a user-defined assay again with the same name or
a new name.
If a tube uses a fluorochrome that is not contained in the tube settings of that tube,
then the assay cannot be created. Create tube or reference settings in order to create
the assay.
 Chapter 7  Data analysis in an experiment    113

Before you begin

 l If you create a report in the experiment, you can use auto-printing and auto-
exporting. You select these options in the assay properties.
 l If you are using statistics and auto-export or sending results to an LIS, you need to
define the properties for the statistics.

Procedure
To create a user-defined assay from an experiment:
 1. Build or open an experiment in the Experiment workspace.
See Creating and opening an experiment (page 83).
 2. From the menu bar, select File > Create Assay.
The Create Assay dialog opens.
 3. In the Name field, type a name for the new user-defined assay.
If you intend to modify an existing user-defined assay and want to retain the same
assay name, you can overwrite the original by creating an assay with the same
name. Note that you cannot overwrite BD assays, nor can you overwrite “Shared”
assays.
 4. (Optional) In the Description field, type a description of any details you want to
document for the assay.
 5. (Optional) Select the Share assay checkbox if you want this user-defined assay to
be shared with all users.
You can also make the assay shared from within the library after you save it.
 6. (Optional) Select a report to display in the Report to display after entry run list.
This sets the default report that opens after the worklist runs.
 7. (Optional) Select the Apply gate positions checkbox according to whether or not
changes to gate positions can be applied to the assay.
Note: Automatic approval of results is disabled when "Apply gate positions" is
selected.
Note: If, after creating the assay, you need to change the "Apply gate positions"
attribute, you can do so by editing the array in the Library.
 8. Click OK.
The user-defined assay is added to the library.
114      BD FACSLyric™ System Instructions For Use

More information
 l See topics about working with private and shared library resources in the
BD FACSLyric™ Reference System for more information about sharing user-defined
assays.
 l Specifying assay properties (page 231).
 8 
Experiment settings
This chapter applies to the BD FACSuite™ application only, and includes the following
topics:
 l Creating tube settings (page 116)
 l Creating default reference settings (page 117)
 l Creating user-defined reference settings (page 120)
 l Viewing tube and reference settings in the library (page 126)
 l Saving modified reference settings (page 127)
116      BD FACSLyric™ System Instructions For Use

Creating tube settings

Introduction
This topic describes how to adjust the position and brightness of the positive
population and how to create tube settings. As with other topics in this chapter, this
topic applies to the BD FACSuite™ application only.
A tube must contain at least two fluorochromes to create tube settings.

Before you begin

 l Prepare a tube of BD® CS&T Beads according to the instructions in the technical
data sheet.
 l Run performance QC.

Optimizing the positive population

To optimize the position and brightness of the positive population:
 1. Create a new experiment.
 2. In the Data Sources panel, select a tube, or add a new tube.
 3. Load a tube of your sample onto the manual tube port.
 4. Click Preview to start the sample flow and preview the data.
 5. In the Acquisition Status panel, adjust the flow rate or fluidic mode as needed.
 6. In the PMT Voltages panel, adjust the PMT voltages and threshold as needed.

Creating tube settings

The following procedure describes the typical method for creating tube settings
without measured SOVs. Creating tube settings is available only for tubes without
data. If your tube has data, duplicate it without data or clear the tube (by right-
clicking in the Data Sources panel).
To create tube settings:
 1. Right-click the tube and select Create Tube Settings.
The Create Tube Settings wizard opens.
 Chapter 8  Experiment settings    117

 2. The CS&T lot ID field displays the BD CS&T bead lot to be used for this tube
setting.
If you want to use a different bead lot, click and select a different BD CS&T bead
lot. If the appropriate lot is not listed, add the lot to the library.
 3. Load a tube of BD® CS&T Beads onto the manual tube port.
 4. Click Acquire.
When acquisition completes, the Name and Description dialog opens.
 5. In the Tube Settings Name field, type a meaningful name.
 6. (Optional) In the Description field, type a meaningful description that helps to
differentiate between similarly named tube settings.
 7. Click Finish.
The new tube settings are saved in the library.

More information
 l See Tube settings overview in the BD FACSLyric™ Reference System.
 l Importing or adding a CS&T bead lot (page 238)

Creating default reference settings

Introduction
This topic describes how to create reference settings using the Create Reference
Settings wizard. As with other topics in this chapter, this topic applies to the BD
FACSuite™ application only.
Note that if your system uses multiple optical configurations, each configuration
requires its own default reference settings.

Before you begin

 l Make sure the kit information for your BD® FC Beads is entered into the FC Bead
reagent section in the library.
 l Make sure that bead lots for BD® CS&T Beads and BD® FC Beads are current.
 l Prepare the BD® CS&T Beads according to the instructions in the technical data
sheet.
 l Prepare BD® FC Beads according to the instructions in the technical data sheet.
118      BD FACSLyric™ System Instructions For Use

 l Prepare BD® CompBead particles according to the instructions in the technical

data sheet.
 l Ensure that the performance QC is current.
The default LW/LNW reference settings are created by a BD Field Service Engineer
when the BD FACSLyric™ system is installed for the first time, or when a system is
reconfigured.
A user with Administrator privileges can create new default LW/LNW reference
settings if needed.
Note: Creating these new settings affects the performance of the system and must
be done carefully. Make sure to follow the instructions for the beads to insure that the
new settings are accurate.

Using the BD FACS™ Universal Loader

To create new default LW/LNW reference settings using the BD FACS™ Universal
Loader:
 1. On the navigation bar, click Setup & QC.
 2. Select Create LW/LNW Reference Settings from the Task menu.
 3. For Loading Option, select Universal Loader.
 4. Select the Carrier Type corresponding to the tube capacity of the rack that you
are using.
 5. Verify that you have selected the correct Lot ID numbers for the BD® FC Beads
you will be using.
 6. Click Start to open the Create LW/LNW Reference Settings dialog. Panels on the
left of the dialog indicate how the tube rack needs to be loaded. For example, if a
BD® FC Beads 7-Color IVD Kit was selected in step 5 and a 40 Tube Rack was
selected in step 4, the panels would appear as follows:
 Chapter 8  Experiment settings    119

 7. Load the BD® CS&T Beads and BD® FC Beads into the tube rack as specified in
the tube-identifier and Carrier Layout panels on the left of the Create LW/LNW
Reference Settings dialog. Place the rack in the Loader and close the Loader door.
 8. (Optional) Change the default values for mix settings by clicking the Mix Settings
button. Default value for initial mixing is 4 seconds at 1,400 rpm and then
10 seconds at 1,250 rpm every 4 minutes thereafter.
 9. (Optional) Click Print/Export to print or export as a PDF file the carrier layout and
list of tube names.
 10. Click the Acquire button to create the LW/LNW settings.
Once all the tubes have been acquired, a message displays to confirm that the new
settings have been successfully created.
 11. (Optional) Click Print/Export to print/export the Carrier Layout and the associated
table of tube names and carrier locations and a snapshot of the plot displays for
each tube recorded during data acquisition.
 12. Click Finish.
120      BD FACSLyric™ System Instructions For Use

Using the manual tube port

To create new default LW/LNW reference settings using the manual tube port:
 1. On the navigation bar, click Setup & QC.
 2. Select Create LW/LNW Reference Settings from the Task menu.
 3. Verify that you have selected the correct Lot ID numbers for the FC Beads you will
be using.
 4. For Loading Option, select the Manual loader.
 5. Click Start.
The Create LW/LNW Reference Settings dialog opens.
 6. Click Acquire.
The Load Tube dialog opens.
 7. Load the BD® CS&T Beads on the cytometer and click Continue.
The system detects the tube, and the process begins.
 8. Follow the on-screen instructions to load each sample tube of BD® FC Beads.
The on-screen instructions display which tube should be loaded in the exact order
required by the application. Note that by default the application asks for all the
colors available in the system configuration and depends on the FCB kit
configuration.
Once all the BD® FC Beads tubes have been acquired, a message displays to
confirm that the new settings have been successfully created.
 9. (Optional) Click Print/Export to print/export the a snapshot of the plot displays for
each tube recorded during data acquisition.
 10. Click Finish.

Creating user-defined reference settings

Introduction
This topic describes how to create user-defined reference settings from existing tube
settings. As with other topics in this chapter, this topic applies to the BD FACSuite™
application only.
 Chapter 8  Experiment settings    121

Setting tube properties

To create user-defined reference settings:
 1. Create a new experiment.
 2. In the Data Sources panel, click an existing tube or add a new tube.
 3. Right-click the tube and select Properties.
The Tube Properties dialog opens.
 4. In the Tube Settings field, select appropriate tube settings as a starting point: Lyse
Wash, Lyse No Wash, or previously created user-defined tube settings.
 5. Close the Tube Properties dialog.
 6. Preview the tube data and modify the cytometer settings.
 7. Right-click the tube and select Create Reference Settings.
The Create Reference Settings wizard opens.
 8. Type a name in the Reference Settings Name field. The reference settings will be
stored in the library, separated into new tube settings of the same name and SOVs.
You can also type the name of an existing user-defined tube setting, to override
that setting in the library.
 9. (Optional) Add a description using up to 300 characters to help differentiate
between similarly named tube settings.
 10. Click Next to continue.
The Create Reference Settings wizard displays a window that prompts for the
CS&T Bead Lot ID, provides a tube-loading option, and displays a Control Tubes
table.
122      BD FACSLyric™ System Instructions For Use

 11. The CS&T Lot ID field displays the bead lot used for the latest performance QC. If
you want to use a different bead lot, click and select a different entry.
 12. For Loading Option, select between Universal Loader and Manual. If you select
Universal Loader, select the Carrier Type corresponding to the tube capacity of
the rack that you are using.

Selecting control tubes

The Control Tubes table displays the fluorochromes of the beads included in each
BD® FC Beads kit. Control types include: BD® FC Beads, BD® CompBead particles,
and fluorescence controls.
 l BD® FC Beads FC beads are supplied by BD.
 l BD® CompBead particles These particles include two separate beads, a negative
bead and a capture bead. These beads need to be stained with the specific
antibodies for fluorochromes that are being added to the reference setting. You
can choose to have a separate unstained tube or add the negative bead to the
positive capture beads.
 l Fluorescence control (FC). These controls are user-defined fluorescent control
particles that can be cells, beads, or anything else (for example, nuclei for DNA
staining). They can have a separate unstained tube or include unstained particles in
the stained tube. This is useful when the fluorochrome/dye of interest is stained on
a specific particle other than BD® FC Beads or BD CompBeads particles.
To define control tubes:
 1. In the Label column, select to use a generic or specific label.
Generic labels apply to any antibody or label. Use Specific labels when
compensation requirements are different between labels (for example, for tandem
dyes). The available selection is based on the reagents in the library. For example,
you must create CD3 PE-Cy™7 reagent to select CD3 as a label for PE-Cy7.
BD® FC Beads can only define generic controls.
 2. In the Lot ID column, select a lot ID if you want to designate a specific reagent lot
ID for the fluorochrome label combination.
The available selection is based on the fluorochrome and reagent already selected.
For example if you select PE-Cy7  CD3, only lot IDs for that reagent are available.
Defining the label and lot ID creates a lot-specific SOV column in the SOV matrix.
This can be necessary for tandem reagents, for example, because the reagent
emission can change from lot to lot.
 Chapter 8  Experiment settings    123

In the following example, PE-Cy7 and APC-H7 fluorochromes are changed to

BD CompBeads that are tandem reagents with lot-specific SOVs.

 3. In the Unstained column, select an unstained control type:

 l Blank Leave this column blank if your tube contains both positive and negative
controls. No unstained control tube is created.
 l Unstained Select this when you have one unstained tube you plan to use as a
universal negative control and your remaining tubes contain only positive
controls. A universal unstained control tube (specific to the control type) is
created.
 l Fluorochrome-Unstained Select this when you have an unstained tube you plan
to use as a negative control only for a specific fluorochrome. An unstained
control tube for the specific fluorochrome is created.
 4. (Optional) If you want to add new fluorochromes or control types:
 a. Under Control Tubes, click Add to add a new fluorescence control.
 b. In the Fluorochrome column, select a fluorochrome for the new control tube.
 c. In the Control Type column, select the control type (FC Beads, FC, or
CompBeads).
 d. Repeat steps 1 to 3 for each added control.
Once the controls have been added, you can reorder them using drag and drop. The
order of the controls is persistent for the Update Reference Settings and Add
Fluorochromes tasks.
 5. Click Next.
The next wizard page displays a list of control tubes to acquire.

Acquiring control tubes using the BD FACS™ Universal Loader

To acquire the control tubes using the BD FACS™ Universal Loader:
 1. Place the BD® CS&T Beads and control beads into the tube rack as shown in the
left two panels of the Create Reference Settings dialog.
124      BD FACSLyric™ System Instructions For Use

 2. (Optional) Change the default values for mix settings by clicking the Mix Settings
button. Default value for initial mixing is 4 seconds at 1,400 rpm and then
10 seconds at 1,250 rpm every 4 minutes thereafter.
 3. (Optional) Click Print/Export to print or export as a PDF file the carrier layout and
list of tube names.
 4. Click Acquire and, when prompted, put the carrier onto the Loader and close the
Loader door. After dismissing the Load Carrier dialog, acquisition starts
automatically.
As the acquisition of each tube completes, a provisionally colored checkmark is
displayed in the tube status and Carrier Layout panels (green for success and red
for failure). When prompted, after acquisition of all tubes is complete, remove the
carrier from the loader and click Continue.
Note: SOV recalculations are performed after acquisition of all tubes is complete.
This can change the success/failure status for individual tubes.
 5. Click Finish.
The BD FACSuite™ application saves the tube settings and SOVs that comprise the
reference settings into the library.
 Chapter 8  Experiment settings    125

Acquiring control tubes using the manual tube port

To acquire the control tubes using the manual tube port:
 1. Click Acquire.

 2. When prompted, load the indicated tube onto the manual tube port.
When the acquisition of the tube completes, a green checkmark is displayed.
 3. When prompted, unload the indicated tube from the manual tube port.
 4. Repeat steps 2 and 3 until all of the tubes have been acquired.
 5. Click Finish.
The BD FACSuite™ application saves the tube settings and SOVs that comprise the
reference settings into the library.
126      BD FACSLyric™ System Instructions For Use

More information
 l Creating tube settings (page 116)
 l See Reference settings overview in the BD FACSLyric™ Reference System.

Viewing tube and reference settings in the

library
Introduction
This topic describes how to view tube and reference settings in the library. As with
other topics in this chapter, this topic applies to the BD FACSuite™ application only.

Procedure
To view the settings:
 1. In the Library panel, double-click Tube Settings, then click User-Defined.
The BD FACSuite™ application displays a Tube Settings table in a large panel to
the right of the Library panel. Entries in the table that are reference settings are
indicated by an X in the Reference Settings column.
 2. Click an entry in the Tube Settings table.
The tube settings for the selected entry in the Tube Settings table display in a
panel below the table.
Reference settings are split into tube settings and spillover values, which appear
under separate tabs in the lower panel.
 3. (Optional) Print tube settings or SOVs:
 a. Click the Tube Settings or Spillover Values tab.
 b. Click Print.
The print dialog includes a toolbar that allows you to change the print layout
and to either send the data to a PDF-capable printer or export the data to a
PDF file.

More information
 l Creating tube settings (page 116)
 l Creating default reference settings (page 117)
 l Creating user-defined reference settings (page 120)
 Chapter 8  Experiment settings    127

Saving modified reference settings

Introduction
This topic describes how to save modified reference settings when you adjusted
compensation but did not modify the cytometer settings (PMT voltages, thresholds,
window extension, flow rate, or area scaling factors). As with other topics in this
chapter, this topic applies to the BD FACSuite™ application only.

Example of the correct use of Save Modified Reference Settings

Saving modified reference setting works correctly for the tube (shown in the following
figure) if the reference settings have been applied to the tube and then adjustments
to the fluorochromes were made (FITC and PE in this example).

The FITC and PE labels and lot IDs in the Tube Properties dialog match what was in
the Create Reference Settings dialog. The rest of the parameters use the generic
SOVs from when the reference settings were created.

Procedure
To save modified reference settings:
 1. In the Data Sources panel, click a tube and apply tube settings to the tube.
 2. Right-click the tube and select Properties.
 3. Click the Spillover Values tab. If necessary, delete any non-lot specific labels
assigned to the parameters for which you will be adjusting compensation.
 4. Adjust the compensation values as needed and click Close.
 5. Right-click the tube, then select Save Modified Reference Settings.
128      BD FACSLyric™ System Instructions For Use

The Save Modified Reference Settings dialog opens.

 6. In the Reference Setting Name field, type a name for the reference settings that
are being modified.
If you began with LW/LNW reference settings, then you must give them a new
name.
 7. (Optional) In the Description field, type a meaningful description to help
differentiate between similarly named reference settings.
 8. Click Finish.
If you do not update the name for the reference settings other than LW or LNW,
the Save Settings dialog opens.
 9. Click Yes to overwrite the existing reference settings, or click No to enter a new
name and create new reference settings.
The modified reference settings are saved in the library with their associated tube
settings and adjusted SOVs.
 10. Add any deleted labels back to the tube properties.
 11. Acquire tubes or create an assay that will use the modified reference settings.

More information
 l Creating default reference settings (page 117)
 9 
Worklist overview
This chapter includes the following topics:
 l About the worklist (page 130)
 l Using the Manage Worklists tab (page 132)
 l About the Worklist Entries table (page 134)
 l About the Worklist Controls bar (page 140)
 l About worklist entry controls (page 142)
 l About Entry Details panel controls (page 145)
 l About Worklist panels (page 147)
130      BD FACSLyric™ System Instructions For Use

About the worklist

Introduction
Samples are acquired and data is analyzed using a worklist. A worklist is a list of tasks
to be performed for sample acquisition and analysis. Tasks include the assays being run
and other operations such as daily clean, SIT flush, and shutdown. The worklist
organizes multiple entries, which include sample IDs, tubes, tasks, status, and other
information about the sample.
You can acquire individual entries, tubes, or an entire worklist, then perform individual
sample analysis or batch analysis.
To open the Worklists workspace, click the Worklists icon on the navigation bar, or click
either the Acquire Data in Worklist or Analyze Data in Worklist shortcuts on the home
page.

Worklists workspace
 Chapter 9  Worklist overview    131

No. Description

1 Manage Worklists tab

2 Worklist tab

3 Worklist controls bar

4 Worklist entry controls

5 Worklist entries table

6 Worklist panels

7 Entry Details panel controls

Manage Worklists tab

The Worklist workspace includes the Manage Worklists tab, which contains a list of all
worklists.

Use the Manage Worklists tab to create new worklists, open existing worklists, and
filter, search, and share worklists with other users. Use the menu bar to create,
rename, import, and export worklists. The Action column displays actions needed for
worklists, such as approval required or acquisition required.
132      BD FACSLyric™ System Instructions For Use

Worklist tabs
Each worklist opens in a separate tab.

Use the worklist tabs to build your worklist, and acquire and analyze data.

More information
 l Using the Manage Worklists tab (page 132)

Using the Manage Worklists tab

Introduction
Use the Manage Worklists tab to create, open, import, share, sort, filter, delete, and
export worklists.

Creating a worklist
To create a worklist:
 1. On the navigation bar, click Worklists.
The Manage Worklists tab opens.
 2. Click New.
The new worklist opens in a new tab in the Worklist workspace.
 Chapter 9  Worklist overview    133

Opening a worklist
To open a worklist:
 1. On the navigation bar, click Worklists.
The Manage Worklists tab opens.
 2. In the Manage Worklists tab, double-click a worklist in the table.
The worklist opens in a new tab in the Worklist workspace.

Importing a worklist
To import a worklist from a folder:
 1. On the navigation bar, click Worklists.
The Manage Worklists tab opens.
 2. From the menu bar, select File > Import Worklist.
The Import Worklist dialog opens.
 3. Navigate to the folder that contains the worklist you want to import and select the
worklist.
 4. Click Open.
The worklist is displayed in the Worklist table.

Viewing worklist outstanding actions

If a worklist has outstanding actions that need to be performed on it, the Action
column under the Manage Worklists tab displays one or more of the following icons:
Icon Action status

Not all entries have been acquired.

Not all entries have been approved.

Unable to send LIS test result.

Deleting a worklist
Deleting a worklist makes the data files associated with the worklist inaccessible in the
database. When you delete a worklist, the entry run packages (ERPs) for the worklist
134      BD FACSLyric™ System Instructions For Use

are automatically exported to the default export folder (as defined in worklist
preferences). You can navigate to the export folder to locate and import the ERPs.
Worklist owners (authors) who are Operator users can change or delete only their
worklists. Administrators can change or delete all worklists.
To delete a worklist:
 1. Select a worklist.
 2. Click Delete.
The Delete Worklist dialog opens.
 3. Click Yes.
The worklist is deleted.

Exporting a worklist
To export a worklist:
 1. In the Manage Worklists tab, select a worklist.
 2. From the menu bar, select File > Export Worklist > With Data.
The Export Worklist path dialog opens.
 3. Navigate to an export target folder.
 4. (Optional) Modify the name of the worklist.
 5. Click Save.

More information
 l About the worklist (page 130)
 l See these topics in the BD FACSLyric™ Reference System:
Setting worklist preferences, Sharing a worklist, Sorting worklists in the table, and
Defining search criteria.

About the Worklist Entries table

Introduction
Within the Worklist tab, the Worklist Entries table organizes multiple entries to be
acquired or analyzed, and displays status and other information about each entry. The
Worklist Entries table is where you add, modify, and select entries.
 Chapter 9  Worklist overview    135

About entries and tubes

The worklist is a set of entries which are specific to your samples. Each entry is either a
fluidic task or an assay. Sample IDs must be entered for assay tasks, but not for fluidic
tasks.
Each entry has an ID number. Each tube within an entry is a child of the entry. For
example, if the entry number is 1, then the tube numbers are 1.1, 1.2, and 1.3.
Entries are collapsed by default, but can be expanded to show the tubes in each entry.
You can drag entries in the Worklist Entries table to change the run order.

Selecting entries and tubes

You can select one or more entries or tubes in a worklist. Any actions selected from the
Worklist Entry Control toolbar are applied to all selected entries.
To select an entry:
 1. Click between the entry number and the Sample ID column.

You can select multiple entries by holding down the Shift key to select a range of
entries, or the Ctrl key to select individual entries.
To select a tube:
 1. Expand an entry by clicking the arrow next to the entry number.
 2. Click between the tube number and the Sample ID number.
You can select multiple tubes by holding down the Shift key to select a range of
tubes, or the Ctrl key to select individual tubes.

About the run pointer

The run pointer is used to select:
 l Which entry to display in the Entry Details panel.
 l Which entry an acquisition run starts with (only when you select Run from Pointer).
136      BD FACSLyric™ System Instructions For Use

Worklist Entries table columns

The Worklist Entries table includes the following columns.
 Chapter 9  Worklist overview    137

Column Description

Sample ID Each entry for an assay task requires a sample ID. You can specify a sample ID
by typing in the Sample ID column for an entry, or by clicking in the column and
scanning a barcode. By default, autonumbering is enabled and a sample ID is
added when you select a task. By default, in the BD FACSuite™ application,
autonumbering is enabled and a sample ID is added when you select a task.

Task A task is an action that is performed when you run a worklist. Tasks can be
assays or fluidics actions.

The list of installed assays is displayed in the Task column. Fluidics tasks
include:

 l Perform Daily Cleaning

 l Perform SIT flush
 l Shutdown
Assays consist of one or more tubes. When you add a task in the Task column,
all tubes associated with the task are added to the entry.
138      BD FACSLyric™ System Instructions For Use

Column Description

Status The current entry status is displayed in the Status column. Icons displaying audit
(entry) trail, E-Signature, and LIS status are also displayed in the Status column.

 l Ready. Indicates that the entry will be acquired during the worklist run.
 l Not Ready. Indicates that the entry does not have a sample ID or task, or
another requirement of the assay is not met. Mouse over the status to view
the condition that is not met.
 l Incomplete. Indicates that the acquisition of the entry has not been
completed.
 l Ready For Approval.Indicates that the entry has been acquired and
requires approval. This is displayed when automatic approval is disabled for
the assay (default), or after modification of the entry removes the Approved
status.
 l Approved.Indicates that the entry has been approved. This is displayed
when automatic approval is enabled for the assay. For the BD
FACSuite™ Clinical application, an additional requirement for Approved
status is that no report includes QC messages that trigger the Needs Review
status. It is also displayed when an entry has been approved manually.
 l Needs Review.Indicates that there are instrument errors that need to be
addressed. For the BD FACSuite™ Clinical application, this status is also set
when there are QC messages for the entry specifying what should be
reviewed before the entry is approved. This status requires manual approval.

Status The current tube status is displayed in the Status column.

(tube)
 l Ready to Acquire.Indicates that the tube is ready to be acquired and has
all required information.
 l Complete. Indicates that the tube has been acquired.
 l Stopping Criteria not met. Indicates that there were insufficient events to
meet the stopping rule.

Indicators A worklist entry that allows gate sizes and positions to be modified displays a
gating control status icon:

All matching gates are at their last applied positions.

All matching gates are at their last applied positions and the entry was the
source of the last applied positions.
 Chapter 9  Worklist overview    139

Column Description

At least one of the matching gates is different from last applied gate positions.

Location The tube location on the Loader rack or the well location on a plate a specified
for the entry.

Carrier ID The sample carrier ID for the entry.

You can select different sample carrier types using the Loading Options panel.
You can select a specific carrier using the Layout View panel.

Acquisition The date and time of acquisition for the data file.
Time

Tube ID The ID number of the tube.

a Well locations should not be used for BD IVD assays

Note: Other assay-specific keywords may be displayed to the right of the

Tube ID column.

Printing a worklist
To print a worklist:
 1. Open the worklist you want to print.
 2. From the menu bar, select File > Print > Worklist.
The Print dialog opens.
 3. Complete your typical printing procedure.
Note: The selected printer must be capable of accepting input in PDF format.

More information
 l BD FACS™ Universal Loader (page 197)
 l Defining sample carrier layouts (page 205)
140      BD FACSLyric™ System Instructions For Use

About the Worklist Controls bar

Introduction
The Worklist Controls bar is displayed at the top of the Worklist tab and includes
options for different worklist acquisition, analysis, and stopping actions.

Worklist controls
The following table describes the worklist controls.
 Chapter 9  Worklist overview    141

Control Description

Load/Unload Click to load or unload the sample carrier (tube rack or platea) with the
Loader.

Mix Click to perform mixing actions on the sample carrier (based on default
sample carrier preferences).

Run Click to start an acquisition run of unacquired entries or tubes, or to start an

analysis run of previously acquired entries. Click the arrow to select options
(Run All, Run from Pointer, or Run Selected). A worklist run begins with
preview mode, then begins acquiring after the Acquisition Delay Timer
expires.

Re-Acquire Click to re-acquire any previously acquired entries, or tubes, or wellsa. Click
the arrow to select options (Re-acquire Selected, Re-acquire All, or Re-acquire
from Pointer).

Analyze Click to start a batch data analysis run of previously acquired entries. Click
the arrow to select options (Analyze All, Analyze from Pointer, or Analyze
Selected).

Skip Tube Click to skip a tube during an acquisition or analysis run. Click the arrow to
select to skip entries or sample carriers.

Stop Tube Click to stop a tube immediately. Click the arrow to select to stop the run
after a tube completes or after an entry completes.
142      BD FACSLyric™ System Instructions For Use

Control Description

Stop Before acquisition

Timer/Resume
During preview mode, the Stop Timer button controls the Acquisition Delay
Timer.

Click this button to manually stop the timer countdown and pause the
worklist in preview mode before acquisition begins. You can stop the timer if
you need to make adjustments.

If you make changes to instrument settings, a dialog prompts you to select

how to apply the changes to the other entries in the worklist.

After acquisition

After acquisition, the Stop Timer button controls the Report Delay Timer. The
report displays data from an acquired entry until the timer expires. You can
click Stop Timer (before time expires) to continue viewing the report and
making adjustments.

You can adjust the duration of the Acquisition and Report Delay timers in
the Preferences dialog.
a Plates should not be used with BD IVD assays.

More information
 l Worklist run options (page 161)
 l Setting worklist preferences (page 226)
 l See the BD FACSLyric™ Reference System for topics about using the layout view
with the worklist.

About worklist entry controls

Introduction
The controls at the top of the Worklist Entries table allow you to perform actions on
selected worklist entries.
 Chapter 9  Worklist overview    143

Worklist entry controls

Clicking the Approve, Audit Trail, or E-Sign control applies the next logical action to
some or all of the selected entries based on the state of the entries. For example, if
any of the selected entries are ready for approval, then clicking the Approve control
approves all entries which are ready for approval.
This following table describes what each control does when you click it, based on the
status of the selected entries.
144      BD FACSLyric™ System Instructions For Use

Control When... Then...

Approve One or more selected entries Click this button to approve any entries that are
are ready for approval ready for approval. Entries not ready for approval
are unaffected.

Audit To view the log Click this button to view the Audit Trail Report.
Trail
An audit trail item in a After clicking this button:
worklist entry requires a
 l Select one or more entries that require a
reason for change
description in the Reason column of the audit
report.
 l Click the button Provide Reason for Change
to open the dialog.
 l Type the reason for change.
The same change text will be applied to each
selected entry.

E-Sign An entry has E-Signature Click to open the E-Signature dialog.

enabled

More NA Click to select one of the following actions:

 l Assign Keywords
 l Show/Hide Columns
One or more entries must be selected for the
following functions to be enabled:

 l Export Entry Run Packages

 l Export Results
 l Export FCS Files
 l Export Assay Reports
 l Print Assay Reports
 l Send Results to LIS
 l Delete
 Chapter 9  Worklist overview    145

Control When... Then...

Reset This control only displays if Click to display a dialog that allows you to select
Gate the current worklist contains the tubes where positions and sizes of gates need
Positions at least one entry using an to be reset to their last applied positions.
assay with the Apply Gate
Applying gate positions using this button results in
Positions attribute enabled.
the audit-trail text "Gate positions were reset to
It is only enabled when last applied gate positions" for each affected
acquired entries are not in the assay in the worklist. The user can overwrite the
Approved state and gates audit-trail text on a per-assay basis.
are not in their last applied
positions.

More information
 l Working with audit trails (page 179)
 l Using E-Signature (page 182)

About Entry Details panel controls

Introduction
The controls in the Entry Details panel allow you to display data from a specific tube,
approve an entry, and print a report, as well as adjust how the report is displayed on
the screen.

Entry Details panel controls

The following figure shows the controls in the Entry Details panel.

The following table describes the controls in the Entry Details panel.
146      BD FACSLyric™ System Instructions For Use

No. Description

1 Displays the sample ID and assay used to create the report or worksheet, overwriting
the name of the Entry Details panel.

2 Click to view the tube properties for that tube.

3 Click to select which tube to view.

4 Click to apply an e-signature to the entry, if enabled.

5 Click to approve the entry, if enabled.

6 Only shown if the assay for the worklist entry allows gates to be repositioned and
resized. Click to apply the gate positions in this entry to other entries in this worklist that
use the same assay.

7 Only shown if the assay for the worklist entry allows gates to be repositioned and
resized. Only enabled if the entry has not been approved and the gates are not in their
last applied positions. Click to reset the gates to the last applied positions.

8 Click to undo the last action.

9 Click to redo the last action.

10 Click to change to Select mode.

11 Click to change to Navigate mode.

12 Click to print the current tab to a PDF-capable printer.

13 Click to add a new worksheet.

14 Click to delete the currently selected worksheet.

15 Click to add a new report.

16 Click to edit the header and footer (BD FACSuite™ application only).

17 Click to add a new page (BD FACSuite™ application only).

18 Click to make the report fit the pane below.

19 Click to zoom in or zoom out.

20 Click to view a grid in the report background.

 Chapter 9  Worklist overview    147

No. Description

21 Click to toggle the layout of multiple pages between horizontal (side by side) and
vertical (top to bottom).

22 Click to change page orientation between landscape and portrait (BD FACSuite™
application only).

More information
 l For details about gates, see Drawing gates (page 90).
 l Reviewing reports (page 176)

About Worklist panels

Introduction
The worklist workspace is made up of a series of panels that can be expanded,
collapsed, or closed. When closed, the panel names are displayed as buttons across the
top of the worklist workspace.

Carrier Layout panel

The Carrier Layout panel displays the carrier ID of the tube rack or plate1 and the tube
or well layout. The order of tubes is based on their order in the worklist. You can right-
click in the layout to display properties of the rack.

1Do not use plates with well layouts with BD IVD assays.
148      BD FACSLyric™ System Instructions For Use

If you are using the Loader, you can use the Carrier Layout panel to view tubes and
wells as they are ordered in the worklist. Carriers can be locked, which means that the
physical tube position will not change, regardless of the acquisition order. If a carrier is
not locked, modifying the position of entries in the worklist also modifies the physical
tube location. Carriers are automatically locked when acquisition starts.

Acquisition Status panel

Use the Acquisition Status panel to view real-time status for time, event counts, and
aborts. You can also set events to display and SIT flush options specific to an
acquisition.
 Chapter 9  Worklist overview    149

The settings apply to the entire worklist except for the number of SIT flushes, which
applies to the current tube only. Also, the assay can control the number of SIT flushes
per tube. Changing the number of SIT flushes in the worklist Acquisition Status panel
overrides the assay value for the current tube.
The fluidic mode controls the speed that the combination of sheath and sample
passes through the flow cell in the instrument. These modes include:
 l Normal (uses low, medium, or high flow rates)
 l High-sensitivity (uses a flow rate that obtains a better separation between the
negative and positive fluorescence populations)
High-sensitivity mode should not be used for BD IVD applications.
Flow rates (low, medium, or high) determine the rate that the sample flows through
the flow cell in the instrument.
Note that you cannot apply different fluidic modes to separate entries within the
same worklist. Changing from one fluidic mode to another causes the cytometer
settings to recalculate and requires time for the fluidics to stabilize.
150      BD FACSLyric™ System Instructions For Use

Tasks panel
The Tasks panel allows you to add multiple entries of a task at once.

You can select one or more tasks to add at once. You can also specify how many of
each selected task to add to the worklist.
In the BD FACSuite™ application, you can also designate a sample ID prefix to be
added to the beginning of the sample ID. Sample ID autonumbering needs to be
enabled if you are using the prefix.
In the example, a prefix is entered and three tasks are added.
 Chapter 9  Worklist overview    151

Loading Options panel

Use the Loading Options panel to select the carrier type, loading mode (manual or
Universal Loader), whether to automatically unload the carrier at the end of a run, and
whether to lock the positions of tubes or wells. The default is defined by the Loader
preferences.

Selecting the Lock Positions checkbox maintains the physical location of the target
tubes or wells—even if you re-order or add new entries in the worklist. This can be
helpful when you are manually preparing samples to run using the Loader. Note that
you cannot unlock the positions for a worklist once you lock them.

Cytometer panel
Use the Cytometer panel to view system status, run cleaning protocols, and adjust
PMT voltages.
The Status section displays the system status, including real-time status for the
manual tube port, Loader, fluidics, and lasers. A checkmark indicates a ready status.
This section also indicates when you need to run system cleaning protocols.

Use the PMT Voltages section to indicate whether or not to collect data for area (A),
height (H), width (W)1; view and adjust PMT voltages; and adjust the threshold.

1Area, height, and width options are available in the BD FACSuite™ application only.
152      BD FACSLyric™ System Instructions For Use

In the BD FACSuite™ application, you can also add or remove parameters before you
run a worklist.

During preview mode, you can adjust threshold and PMT voltages (as applicable) and
the system will automatically adjust spillover values (SOVs).
 10 
Data acquisition in a worklist
This chapter includes the following topics:
 l Data acquisition overview (page 154)
 l Creating a worklist (page 155)
 l Running a worklist (page 157)
 l Worklist run options (page 161)
 l Re-acquiring entries in a worklist (page 164)
 l Concatenating FCS files (page 165)
 l Deleting Concatenated FCS files (page 170)
154      BD FACSLyric™ System Instructions For Use

Data acquisition overview

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

About data acquisition

Acquisition consists of creating or opening a worklist, adding keywords, then running
the worklist to acquire data from samples.

Workflow stages
Perform the following workflow to acquire data using a worklist.

Stage Description

1 Open an existing worklist, or create a new worklist and create new entries.

See Creating a worklist (page 155).

2 (Optional) Assign keywords to entries and tubes.

See topics about assigning keywords in the BD FACSLyric™ Reference System.

3 Run the worklist.

See Running a worklist (page 157).

More information
 l Worklist run options (page 161)
 l Re-acquiring entries in a worklist (page 164)
 Chapter 10  Data acquisition in a worklist    155

Creating a worklist
Introduction
This topic describes how to create a worklist from scratch. You can also open an
existing worklist and make modifications or start by importing saved entry run
packages into the worklist. An entry run package includes all information needed to
replicate an entry in a different worklist, including acquired data.
In addition to manually adding entries to a worklist, you can add entries from LIS test
orders or import entry run packages (ERPs).

Creating a worklist
To create a worklist:
 1. In the Manage Worklists tab, click the New button.
A blank worklist opens in a new tab.
 2. Add entries to the worklist by doing one of the following:
 l Use the Worklist Entries table to type a sample ID or scan a barcode in the
Sample ID column. In the Task column, select an assay or fluidics task.
 l Use the Tasks panel to select one or more tasks to add. You can specify how
many of each task you want to add. For each entry, type a sample ID or scan a
barcode in the Sample ID column. If autonumbering is enabled in the BD
FACSuite™ application, the sample ID is automatically entered after you add a
task.
Note: A Sample ID is not required for fluidics tasks.
All tubes associated with the task(s) are added to each entry.
 3. (Optional) Assign keywords to an entry or tube.
See topics about assigning keywords to entries or tubes, and working with audit
trails in the BD FACSLyric™ Reference System.
 4. Modify the loading options in the Loading Options panel as needed.
 5. If the worklist is in the BD FACSuite™ application, modify worksheet or report
elements, instrument settings, or SOVs (as permitted by the assay type or your user
privileges).
 6. Save the worklist by selecting File > Save.
156      BD FACSLyric™ System Instructions For Use

Adding entries from an LIS

BD FACSLink™ software is used to communicate with an LIS (laboratory information
system) and can access sample information for use in building worklists.
To add entries from an LIS to the worklist:
 1. In the Worklist Preferences dialog, verify that there is a connection to the LIS.
Check the lower status bar for the status of the BD FACSLink™ connection.

 2. In the Worklist Entries table, type in the field or scan a barcode to enter a sample
ID in the Sample ID column.
The sample and assay are added as a task in the Worklist Entry table.
If multiple test orders are available for the sample ID, or if the order is already
accessioned, the Add Test Orders dialog opens with the Sample ID and the
requested test orders.
 3. If necessary, in the Add Test Orders dialog, select the assay(s) and click Add
Selected or Add All.

The Worklist Entries table now displays the samples and assays from the LIS with
an icon in the status column.
 Chapter 10  Data acquisition in a worklist    157

 4. For each entry, verify that the information entered for each sample ID (for
example, sample name and case number) is correct, and that the correct task is
assigned.

Saving a worklist
Worklists are automatically saved as you add entries, make changes, or when you close
the worklist.
To save without closing:
 1. Select File > Save.

Renaming a worklist
To rename a worklist:
 1. Select File > Rename.
 2. Type a new name, then click OK.
If you create a new worklist, you need to create at least one entry before you can
rename the new worklist.

More information
 l See the BD FACSLyric™ Reference System for more information about sorting,
exporting, and deleting worklists, the Layout View panel, and entry run packages.

Running a worklist
Introduction
This topic describes how to acquire samples using the worklist.

About worklist run order

Acquisition is performed in the order that entries are listed in the worklist. However,
you can run the worklist entries in a different order based on the acquisition status of
the tubes and where you set the run pointer. Once you start a worklist run, you cannot
re-order tubes or entries during acquisition unless you first stop the run.
158      BD FACSLyric™ System Instructions For Use

Before you begin

 l Set or verify your worklist preferences for acquisition delay and report delay timers,
exporting, and printing in Worklist preferences.
 l Set or verify your assay report and results export preferences in the library.
 l If you include cleaning tasks, make sure that the tube racks include a tube with
10% bleach and a tube with DI water in the locations identified in the Layout View.

Running a worklist
To run a worklist:
 1. Verify that the Status column displays Ready for all entries.

 2. In the Worklist Controls bar, click Run All to run the entire worklist from the
beginning, or click the arrow on the Run All button to select a different run option.
If you select Run from Pointer, acquisition begins with the tube where the run
pointer is set. If you select Run Selected, acquisition begins with the first of the
selected entries.
 3. Load the first tube or sample carrier.
 l (Loader) When prompted, place the carrier onto the Loader tray, then click
Continue in the Add Carrier dialog.
 l (Manual loading) When prompted, ensure that the LED light on the manual
tube port is green, then place a tube onto the manual tube port, pressing the
top of the tube onto the gasket until you feel a click.
The worklist run starts, indicated with a circle on the run pointer.
 Chapter 10  Data acquisition in a worklist    159

As acquisition progresses, the Acquisition Status panel displays the time, events,
and an acquisition progress bar. Events are displayed in plots in the acquisition
report and, in the case of the BD FACSuite™ application, in the worksheet.
 4. If necessary, adjust voltages, threshold, or SOVs.
 a. Click Stop Timer on the Worklist Controls bar.
This stops the acquisition delay timer, but sample is still being aspirated into the
cytometer.
 b. Adjust the threshold and FSC, SSC, and PMT voltages, or adjust SOVs.
You cannot modify both SOVs and threshold/voltages.
 c. Click Resume.
The Apply Changes dialog opens.
 d. Select how to apply the adjusted instrument settings, then click OK to start
acquisition.
 5. (Optional) Make adjustments to gates.
 a. Click Stop Timer when the lab report is displayed after the tube has been
acquired.
 b. Examine each gate and make adjustments as necessary.
 c. Click Resume to continue to the next entry.
 6. Follow the prompts to load subsequent tubes or carriers.
 l (Loader) If selected in the Loading Options panel, the Loader will automatically
unload after the last sample in the carrier has been acquired. If not, click
Unload and remove the first carrier, then load the next carrier and click Load.
 l (Manual tube loading) When prompted, carefully remove the first tube from the
manual tube port. Be sure to wait until the LED light on the manual tube port
turns green before loading the next tube.
Acquisition continues until the last entry has been acquired.
160      BD FACSLyric™ System Instructions For Use

Running part of a worklist

If you don’t want to run the entire worklist from start to finish, you can perform one of
the following actions.

To... Then do this...

Run from a specific entry or  1. Set the run pointer to a specific entry or tube.
tube and all subsequent tubes  2. Click the arrow next to the Run All button and select
Run from Pointer.
The worklist starts with the specified tube or entry, then
runs all subsequent tubes in the worklist.

Run a specific entry or tube in  1. Select either entries or tubes.

the worklist
The entries or tubes do not need to be adjacent in the
worklist.

 2. Click the arrow next to the Run All button and select
Run Selected.
The worklist starts with the selected tube or entry and
continues with the next selected entry or tube in the
worklist.

More information
 l Worklist run options (page 161)
 l Re-acquiring entries in a worklist (page 164)
 l About the Worklist Controls bar (page 140)
 l See the BD FACSLyric™ Reference System for topics about worklist preferences,
modifying tube properties, and approving entries in a worklist.
 Chapter 10  Data acquisition in a worklist    161

Worklist run options

Optional tasks while running the worklist
You can perform the following additional tasks while running the worklist.
162      BD FACSLyric™ System Instructions For Use

To... Then do this...

Pause the worklist in  1. Click Stop Timer to manually stop the acquisition delay timer
preview mode countdown and pause the worklist in preview mode.

While the timer is paused, you can adjust PMT voltages and
thresholds, or SOVs.

 2. If you make changes, click Resume to open the Apply Changes
dialog.
 3. Select how you want to apply the changes to the worklist, then
click OK.

Acquisition resumes according to tube type and preferences.

Review the entry once After acquisition, the report displays data from an acquired entry
the report is populated until the timer expires. The Stop Timer button controls the report
with data delay timer.

 1. Click Stop Timer (before time expires) to continue viewing the
report and modify the analysis.
 2. Click Resume to allow the worklist to move to the next entry.

View the reports for an  1. After acquisition, set the run pointer to an entry to manually
entry after a worklist display the reports. For the BD FACSuite™ application, the run
run pointer also displays the worksheets.

Click the arrow buttons on the right side of the toolbar in the
Entry Details panel to view results for the previous or next entry.

View tube properties  1. If needed, expand an entry to view the tubes for that entry.
 2. Set the run pointer to a tube in the Worklist Entry table.
 3. Right-click next to the tube number and select Tube Properties.

View stopping rules  1. Open the tube properties for a tube.
 2. Click the Acquisition tab and then click the Stopping Rules
tab.
 Chapter 10  Data acquisition in a worklist    163

To... Then do this...

Print spillover values  1. Open the tube properties for a tube.
matrix for a tube  2. Click the Spillover Values tab.
 3. Click Print.

The Print dialog opens.

 4. Select a PDF-capable printer and complete your typical printing

procedure.

Skipping tubes, entries, and carriers

You can skip tubes, entries, or carriers during a worklist run. If you skip during preview,
then no data is saved. If you skip during acquisition, then an FCS file is saved, but the
stopping criteria will not be met.
To skip tubes, entries, and sample carriers during a worklist run, complete one of the
actions in the following table.

To... Then do this...

Skip a tube in a  1. Click Skip Tube.

worklist
The tube where tube pointer is set will be skipped.

Skip an entry  1. Click the arrow on the Skip Tube button and select Skip Entry.

Skip a carrier This applies only to systems using the Loader.

 1. Click the arrow on the Skip Tube button and select Skip Sample
Carrier.

Stopping a worklist run

You can stop a worklist run at any time. If you stop a run during preview, then no data
is saved for the current tube. If you stop a run during acquisition, then an FCS file is
saved for the current tube, but the stopping criteria will not be met.
164      BD FACSLyric™ System Instructions For Use

To stop the worklist run, complete one of the actions in the following table.

To... Then do this...

Stop the worklist immediately  1. Click Stop Tube.

Stop the worklist after the  1. Click the arrow next to the Stop Tube button and click
current tube completes Stop After Tube Completes.
Stop the worklist after the  1. Click the arrow next to the Stop Tube button and click
current entry completes Stop After Entry Completes.
The tube with the run pointer completes, then the
worklist run stops.

Re-acquiring entries in a worklist

About FCS files for entries and worklists
Entries and tubes can be re-acquired using the Re-acquire options.
After an entry or tube is re-acquired, the new FCS file is saved along with the previous
FCS file. Each file is date and time stamped.

Procedure
To re-acquire entries in a worklist, complete one of the actions in the following table.

To... Then do this...

Re-acquire an entire  1. Click Re-Acquire All.

worklist
This re-acquires all tubes in the worklist that have an FCS file.

Re-acquire from a  1. Set the run pointer to a specific tube or entry.
specific starting point  2. Click the arrow next to the Re-Acquire All button, then click
Re-Acquire from Pointer.
This re-acquires the current tube and all subsequent tubes in the
worklist which have an FCS file.
 Chapter 10  Data acquisition in a worklist    165

To... Then do this...

Re-acquire specific  1. Ctrl+click to select specific tubes that have an FCS file.
entries or tubes
The selected entries or tubes do not have to be adjacent.
However, you cannot select a mix of tubes and entries.

 2. Click the arrow next to the Re-Acquire All button, then click
Re-Acquire Selected.
Restart a partially  1. Select the tube that was stopped.
acquired tube  2. Click the arrow next to the Re-Acquire All button, then click
Re-Acquire Selected.

More information
 l Data analysis overview (page 174)
 l Worklist run options (page 161)

Concatenating FCS files
About FCS file concatenation
FCS files may need to be concatenated to record sufficient events of interest to allow
a scientifically or clinically meaningful analysis of a test sample. There are multiple
scenarios and reasons why you may not be able to acquire sufficient events of interest
in a single FCS file. These include:
 l Stopping the instrument mid-acquisition during long acquisitions (e.g. for rare
populations) to clear or prevent clogging and then acquire further events from the
same tube that was being acquired at the time that acquisition was stopped.
 l Due to incomplete RBC lysis, a bad sample preparation, or a medical condition
where the number of cells of interest are unexpectedly reduced in a patient's
sample, the usual stopping criteria of 100,000 events or 5 minutes may stop the
acquisition before sufficient events of interest have been acquired. In such cases,
re-acquisition may be needed to record as many events as possible from the
remaining sample.
166      BD FACSLyric™ System Instructions For Use

Note: FCS file concatenation is subject to the following constraints:

 l Concatenation of acquired and re-acquired data can only be performed if
concatenation is enabled in the assay being used.
 l The assay constraint also applies to assays used in imported Entry Run Packages
(ERPs). In addition, concatenation is only enabled if the ERP supports FCS 3.1 or
later.
 l For imported FCS files, concatenation is disabled regardless of the
concatenation configuration in the assay.

Concatenation Procedure
To concatenate acquired and re-acquired samples for an entry in a worklist:
 1. Set the run pointer to the tube where samples have been re-acquired.
 2. Right-click in the Worklist Entries cell containing the run pointer to display the
context menu.
 3. Select the Concatenation menu item.
The system displays a Concatenation dialog.
 4. Select the samples to concatenate.
Note: After you select the first FCS file for concatenation, the BD FACSuite™
software checks that other FCS files for the sample are compatible. If an FCS file is
not compatible with the first selected item, selection of the file will be disabled
and an information icon will be displayed next to it. Clicking the icon will display the
reasons why the two FCS files are incompatible for concatenation purposes.
Possible reasons include different Performance QC date, PMT voltage changes, and
different spillover values.
 Chapter 10  Data acquisition in a worklist    167

 5. If a relatively long period has elapsed between acquisitions in comparison to the
combined acquisition times, click Minimize time gaps in concatenated file.
 6. Click Done to concatenate the selected files.
The message bar displays the message "Concatenated file successfully created".
 7. (Optional) To confirm that the FCS files have been concatenated as expected, add
a time-based histogram to the worksheet or any other plot with a Time parameter
for the x-axis.
Example:

The FCS filename of the composite file, after running the File > Export > FCS Files
command, will end with the suffix concatnnn.fcs where nnn is a 3-digit integer that
increments by one for each concatenation operation.

Handling of keyword values in concatenated FCS files

The following table lists how common keywords are handled in concatenated FCS files.
168      BD FACSLyric™ System Instructions For Use

Keyword Application to concatenated FCS file

$OP Name of person logged in when the file was created.

OPERATOR EMAIL Email address of person logged in when file was created.

Last_Modifier Name of person logged in when the file was created.

Last_Modified Date and time the file was created.

GUID The GUID in the composite file is auto-generated and is

not the same as any of the values in the component
FCS files.

$FIL The filename of the composite file is auto-generated and

is not the same as any of values in the component
FCS files.

AUTOBS At the time of concatenation, the AUTOBS keyword will

match the tube properties. If scaling is set after
concatenation, the AUTOBS value will be true if
biexponential autoscaling was selected or false if
biexponential scaling is set manually.

$BEGINDATA Value reflects the address of the first event data in the
composite file. However, if the size of the file exceeds the
default limit of 99,999,999 bytes, the Begin Data value
given in the header segment will remain at zero.

$ENDDATA Value reflects the address of the last event data in the
composite file. However, if the size of the file exceeds the
default limit of 99,999,999 bytes, the End Data value
given in the header segment will remain at zero.

$COM If there are no comment values in the files concatenated

into the composite file, there will be no keyword value. If
the comments are the same in each of the component
files, the $COM value will be the same as the value
shown in a single component file. If one or more
$COM values differ between component files, the
$COM value in the composite file will be concatenated
values (including duplicates) of the component files in
the order that they were acquired, separated by a
suitable separator character.
 Chapter 10  Data acquisition in a worklist    169

Keyword Application to concatenated FCS file

$WELLID If the files concatenated into the composite file were all
acquired manually, there will be no $WELLID value in the
composite file. If at least one of the concatenated files
was acquired using the loader, the $WELLID in the
composite file will be the same as the value in the
concatenated file or files acquired using the loader.

$DATE Value reflects the $DATE value from the first acquired

component FCS file.

$TOT Value reflects the sum of all $TOT values in the

concatenated component files.

$ABRT Value reflects the sum of all $ABRT values in the

concatenated component files.

ORIGINALITY Value is data modified.

PnBS Value will match that of the tube properties at time of

acquisition of the component FCS files.

PnMS Value will match the tube properties at the time of

concatenation.

PnDISPLAY Value will match current tube properties.

CONCATENATIONSOURCEINFO Value will be the GUID, $BTIM, and $ETIM data from

each of the concatenated component files in acquisition
order. The three keywords from each component file will
be comma-separated, and the pipe character will
separate the combined keyword values from each
component file.

User-defined keywords If a user-defined keyword is the same in each of the

component files, the value in the composite file will be
the same as the value shown in a single component file.
If one or more of the values differ between component
files, the value in the composite file will be concatenated
values (including duplicates) of the user-defined keyword
in the component files in the order that they were
acquired, separated by a suitable separator character.
170      BD FACSLyric™ System Instructions For Use

Keyword Application to concatenated FCS file

QCMESSAGES Contain a list of all the QC messages in the source files

minus duplicates. Where a message is duplicated, the
QCMn
timestamp will be taken from the first occurrence of the
message. The messages will be in timestamp order.

In a report, QC messages are re-ordered by priority (high

priority first) as the primary sort order and timestamp
as the secondary sort order.

More information
 l Specifying assay properties (page 231) for details about viewing or setting
concatenation preferences.
 l For details about drawing plots and keywords, refer to the BD FACSLyric™
Reference System.

Deleting Concatenated FCS files

Note: Approved concatenated files cannot be deleted. Only files that have not yet
been approved can be deleted. Deletion of concatenated files is permanent.
To delete a concatenated FCS file:
 1. Set the run pointer to the tube where FCS files were concatenated.
 2. Right-click in the Worklist Entries cell containing the run pointer to display the
context menu.
 3. Select the Concatenation menu item.
The system displays a Concatenation dialog.
 4. Click the Delete tab.
 5. Select the FCS file or files to delete from the displayed list.
An information icon is displayed beside each list entry, indicating the acquisition
dates and times recorded in the concatenated file.
 6. Click Delete to permanently delete the selected files.
The message bar displays the message "Concatenated file(s) deleted".
 Chapter 10  Data acquisition in a worklist    171

The audit trail for the worklist records the deleted FCS file and the associated tube
name.
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 11 
Data analysis in a worklist
This chapter includes the following topics:
 l Data analysis overview (page 174)
 l Working with assay reports (page 175)
 l Reviewing reports (page 176)
 l Approving entries in a worklist (page 177)
 l Working with audit trails (page 179)
 l Using E-Signature (page 182)
 l Running batch data analysis (page 183)
174      BD FACSLyric™ System Instructions For Use

Data analysis overview

Start up Perform Shut down
Acquire data Analyze data
the system Setup & QC the system

About data analysis

After entries have been acquired, perform analysis by reviewing reports and
worksheets1, adjusting plots and gates, approving entries, and e-signing reports. Entries
can be automatically exported and printed before approval if the assay is set to do so
in the Library. Approve an entry to send results to the LIS according to the assay
properties and preferences.
You can analyze any individual entry or tube that has been acquired, or use batch
analysis to analyze all acquired entries in a worklist.
Batch analysis in worklists1 is an automated process that results in automatically
generated and/or exported reports and statistics files. Batch analysis allows you to
increment files and print automatically.
Acquisition and batch analysis cannot run simultaneously for the same worklist.

Analysis workflow
The following table describes the analysis workflow stages.

1Worksheet analysis features are only available in the BD FACSuite™ application.

 Chapter 11  Data analysis in a worklist    175

Stage Description

1 Review reports and worksheets, and modify analysis elements or instrument settings
(as permitted).

See Reviewing reports (page 176).

2 Approve the results.

See topics about approving entries in a worklist in the BD FACSLyric™ Reference

System.

3 E-sign reports.

See Using E-Signature (page 182).

More information
 l Working with audit trails (page 179)
 l Running batch data analysis (page 183)

Working with assay reports

About assay reports
Reports must be created in an experiment. When you create a user-defined assay from
an experiment, the report is included in the new assay. If your assay includes a report,
the plots and statistics automatically display data when you acquire or analyze a
worklist.
If you are using a BD IVD assay, reports are included in the assay. The plots and
statistics automatically populate with data when you acquire or analyze a worklist.
If you want to modify an assay report, you must create a new experiment from the
assay, modify the report, then re-create a new user-defined assay from the modified
experiment. When you create an experiment from a BD-defined assay, the reports and
data are removed. When you create an experiment from a user-defined assay, the
report and data are included.

More information
 l Experiment building workflow (page 86)
 l Creating a user-defined assay from an experiment (page 112)
176      BD FACSLyric™ System Instructions For Use

Reviewing reports
Introduction
Reports are already defined for each BD IVD assay. In the BD FACSuite™ application,
you can also create reports for user-defined assays. The plots and results table
automatically populate with data when you acquire or analyze a worklist. Reports are
automatically saved with the worklist.
Reports are displayed in the Entry Details panel based on where the run pointer is set.
The plots and statistics are populated with the acquired data.
You can review the plots during acquisition or once acquisition is complete. We
recommend that you inspect all plots to verify that all gates include the appropriate
populations.

Procedure
To review reports:
 1. If necessary, open the worklist that you want to review.
The status of each entry is displayed in the Status column.
 2. Set the run pointer to view the reports for that entry in the Entry Details panel.
 3. Click the tab for the report you want to view.
 4. Visually inspect the plots and verify that all gates fully encompass the appropriate
populations, or adjust if necessary.
 5. Review the following:
 Chapter 11  Data analysis in a worklist    177

 l Plots
 l Gates
 l Statistics
 l QC results (for BD assays only)
 l Results summary (for BD assays only)
 6. Click Approve to approve the entry.
Approving an entry triggers the automatic export, printing, and sending of results
to the LIS according to the assay properties and preferences.
Note: An assay property can be set up for auto-approval, where automatic export
will occur without needing to manually approve the entry. This option is only
available if e-signatures are not required.
 7. Repeat steps 2 through 6 for the remaining entries.

More information
 l Data analysis overview (page 174)
 l Approving entries in a worklist (page 177)
 l Using E-Signature (page 182)
 l Specifying report preferences (page 224)
 l Setting worklist printing preferences (page 231)

Approving entries in a worklist

Introduction
This topic describes how to approve entries after analysis.
Approving an entry triggers the automatic export, printing, and sending of results to
the LIS according to the assay properties and preferences.
178      BD FACSLyric™ System Instructions For Use

Entry approval status

After an entry is acquired in a worklist, the Status column displays one of the following
status messages.

Status Condition
message

Approved This message is displayed when automatic approval is enabled for the assay and
there are no errors reported for this entry, or when you manually approve the
entry.

Ready This message is displayed when automatic approval is disabled for the assay and
For when no errors are reported for this entry.
Approval

Needs This message is displayed when there is an error with the entry, including a QC
Review message which requires review.

If your laboratory workflow requires manual approval of an entry, you can manually
approve it. You can also save a worklist without approving, then return to the worklist
at a later time and finalize the status.

Manually approving an entry

To manually approve an entry:
 1. Select one or more entries that have a Needs Review or Ready For Approval status.

 2. Do one of the following:

 l To approve one or more entries, select the entries, then click the Worklist Entries
Approve button.
 l To approve only the currently selected entry, click the Approve button in the
Entry Details panel.
Approval triggers the export and printing of reports, as well as the automatic
export, printing, and release of results to the LIS.
 Chapter 11  Data analysis in a worklist    179

Confirming results are sent via BD FACSLink™

Approve the entries you want to send manually or by using automatic approval in the
assay properties. Confirm that the results were successfully transmitted to
BD FACSLink™ software by checking for the confirmation icon in the entry.

Viewing the BD FACSLink™ results history log

To view the BD FACSLink™ results history:
 1. From the main menu, select Tools > BD FACSLink Test Results History.
The BD FACSLink™ Test Results History log displays all entries that have been sent
to BD FACSLink™ or are in queue. You can sort the columns and delete entries from
the table.

More information
 l Using E-Signature (page 182)
 l Data analysis overview (page 174)

Working with audit trails

About audit trails
Audit trails track changes to entries. Any changes that affect the data (for example,
modifying instrument settings, changing keyword values, or changing gate locations)
are listed as changes in the audit trail report. Audit trails are automatically enabled for
all entries in all worklists.
The following information is tracked for each change:
 l Date and time of changes
 l User ID
 l Details of the changes
180      BD FACSLyric™ System Instructions For Use

Requiring the user to provide the reason for change can be enabled or disabled on a
per-assay basis. Once an entry in a worklist has been acquired or modified, its reason-
for-change requirement can no longer be changed, even if the reason-for-change
requirement of the corresponding assay is subsequently modified.

Providing a reason for change

When a reason for change requirement is enabled and a modification is made, a
yellow A (audit) icon is displayed. The icon remains until you provide a reason for
change.

To provide a reason for change:

 1. Select the entry in the Worklist Entries table, click Audit Trail and, in the Audit log,
click the Provide Reason for Change button.
The Reason for Change dialog opens.
 2. Under Enter Reason, type a reason for changing the selected entry.
 3. Click OK.
The reason is added to the audit trail report and the audit icon is removed.

Reviewing the audit trail report

To review the audit trail report:
 1. Select an entry in the worklist.
 2. Select Audit Trail.
The Audit Trail Report dialog opens.
 Chapter 11  Data analysis in a worklist    181

The audit trail report displays the history of changes and the reason for each
change.

Printing the audit trail report

To print the audit trail report:
 1. Click Print in the lower-right corner of the dialog.
The Audit Trail Viewer Print View dialog opens.
 2. Click the Print icon.
The system Print dialog opens.
 3. Select a PDF-capable printer and complete your typical printing procedure.

Exporting the audit trail report

To export the audit trail report as a PDF:
 1. Click Export in the lower-right corner of the Audit Trail Report dialog.
The Export Audit Trail Report dialog opens.
 2. Provide a meaningful name in the File name text box and click Save.
The PDF is exported to the default worklist reports folder.
Note: Setting up an assay to automatically export/print applies to the audit trail
reports as well as other assay reports.

More information
 l Approving entries in a worklist (page 177)
 l Using E-Signature (page 182)
 l For details about setting audit trail preferences in an assay, refer to the
BD FACSLyric™ Reference System
182      BD FACSLyric™ System Instructions For Use

Using E-Signature
Introduction
E-signature allows you to electronically sign reports. When E-signature is enabled for
an assay, the signature box is displayed at the bottom of the report and a yellow E icon
is displayed in the Status column for the entry.

E-Signature is an assay property that can be enabled in the library.

E-signing a report
To e-sign a report:
 1. Select an entry, then click the E-Sign button.
The E-signature dialog opens.
 2. Select a user ID.
 3. Type your password.
 4. (Optional) Enter any comments.
 5. Click Sign.
The E-signature icon in the Worklist Entries table turns green, and the E-signature
box at the bottom of the report displays the signer’s user ID, date and time, and
comments that were entered.
If you modify the gate position, keywords, worksheet or report layout1, or any other
analysis elements or settings that affect the data after you e-sign the report, the
report is automatically un-signed and must be e-signed again.

More information
 l Approving entries in a worklist (page 177)
 l Data analysis overview (page 174)

1Worksheet analysis and report layout preferences are available in the BD FACSuite™ application only.
 Chapter 11  Data analysis in a worklist    183

 l For instructions on enabling E-Signature, see “Editing assay properties” in the

BD FACSLyric™ Reference System.

Running batch data analysis

Introduction
Batch analysis allows you to automatically export and print all items in a worklist that
have already been approved. To begin batch analysis, you need to have acquired data
from at least one entry or tube. Analysis is performed only on entries or tubes that
have an associated FCS file. Tubes that do not have an FCS file are skipped.

Running batch analysis on selected entries or tubes

To run batch analysis on selected entries or tubes:
 1. Click an entry or tube in the worklist that has been acquired and includes an FCS
file.
This is indicated by a Complete status in the Status column for the entry or tube, as
well as a black tube icon in the Task column.

 2. Click Analyze on the worklist control bar.

The analysis preview opens in the report.
 3. (Optional) Click Stop Timer to pause the run and make any changes.
Click Resume to resume the run.
When all entries have been run, results are automatically generated, and reports
and statistics files are printed or exported according to assay preferences.
184      BD FACSLyric™ System Instructions For Use

Running batch analysis on an entire worklist

To run batch analysis on an entire worklist:
 1. Click Analyze on the worklist control bar.
Batch analysis begins and analyzes entries and tubes with acquired data.
 12 
BD IVD assays
This chapter covers the following topics:
 l Overview of BD IVD assays (page 186)
 l Creating an assay worklist (page 187)
 l About lab reports (page 188)
 l About physician reports (page 191)
 l About supplemental reports (page 193)
Note: BD IVD assays are for use in the BD FACSuite™ Clinical application only.
186      BD FACSLyric™ System Instructions For Use

Overview of BD IVD assays

Introduction
BD IVD assays are designed for use only with the BD FACSuite™ Clinical application
application and the appropriate process controls.

Contents
Each assay contains the following elements:
 l Predefined tubes for samples or controls
 l Tube settings and keywords
 l Acquisition properties and stopping rules
 l Lab report with plots, gates, results, and QC messages
 l Physician report with reportable results
 l Supplemental report (for selected assays)

Workflow
The following table describes the workflow for running BD IVD assays.

Stage Description

1 Create an assay worklist.

See Creating an assay worklist (page 187).

2 Prepare controls or samples for the assay according to the directions in the product
kit’s Instructions For Use.

3 Acquire the samples.

See Data acquisition in a worklist (page 153).

4 Analyze the data.

See Data analysis in a worklist (page 173).

 Chapter 12  BD IVD assays    187

Creating an assay worklist

Before you begin
 l Verify that the lot information for the reagents and BD Trucount™ tubes (if
applicable) that you are using matches the information entered into the library.
 l Verify that all QC required for the IVD assays was performed and passed within the
last 24 hours.
 l For assays that do not use BD Trucount™ tubes, obtain complete blood counts
(CBCs) from a hematology analyzer for all samples. The application uses the WBC
count and percent lymphocytes, or the lymphocyte count, to calculate absolute
counts.
 l Prepare and stain your samples according to the reagent instructions for use (IFU).

Procedure
To create an assay worklist:
 1. Open an existing worklist, or create a new one.
 2. In the worklist, type a sample ID for the first entry.
 3. Select an assay from the Task menu.
 4. If you selected an assay without a BD Trucount™ tube, enter one of the following
in the designated keywords field(s) in the worklist:
 l WBC (x1000) and percent lymphocytes
 l Lymphocyte count (x1000)

Note: If you enter values in all three keyword fields, the application checks to
ensure that WBC x % lymphocytes is equal to the lymphocyte count. If the
calculation is incorrect, the absolute count results are suppressed.
 5. Repeat step 2 through 4 for the remaining samples.
 6. Save the worklist with a unique name.
188      BD FACSLyric™ System Instructions For Use

More information
 l Creating a worklist (page 155)
 l Running a worklist (page 157)
 l Worklist run options (page 161)

About lab reports

Introduction
The lab report summarizes data analysis of the stained sample. The following is an
example lab report for the 6 Color TBNK + Truc assay. The table contains a description
of the elements in the report.
 Chapter 12  BD IVD assays    189

Example lab report

The following is an example of a BD clinical report.
190      BD FACSLyric™ System Instructions For Use
 Chapter 12  BD IVD assays    191

No. Element Description

1 BD Displays the assay name and report type.

banner

2 Report Lists information about the sample, the BD Trucount™ tubes (if applicable),
header the logged-in user, the system, and the date and time the report was
approved.

3 Tube Displays information about the tube and its acquisition. If the assay was
header run without BD Trucount™ tubes, the WBC count, lymphocyte percentage,
and lymphocyte count are displayed for each entry.

4 Analysis Displays the plots with gates.

plots

5 Report Displays the assay name, print date and time, regulatory status of the
footer results, and the report page number.

6 Results Summarizes the results for each tube acquired.

summary
table

7 QC Displays the 4/8 ratio, %T-Sum value, and lymphosum values with
results recommended ranges.

8 QC Displays all QC messages that were generated during the run.

messages

9 E- Displays the electronic signature and any comments added by the reviewer,
signature if applicable.

More information
 l Reviewing reports (page 176)

About physician reports

Introduction
The physician report contains a results summary table and provides space to write
comments and sign the report.The following is an example physician report for the 6
Color TBNK + Truc assay. The table contains a description of the elements in the
report.
192      BD FACSLyric™ System Instructions For Use

Example physician report

 Chapter 12  BD IVD assays    193

No. Element Description

1 BD banner Displays the assay name and report type.

2 Report header Lists information about the sample, the date and time the report was
approved, and institution information.

3 Acquisition Displays the tube name (for some assays), and acquisition date and
information time.

4 Results Summarizes the results for each tube acquired.

summary
table

5 Signature Provides space to sign the report.

6 Comments Provides a space for comments.

7 Report footer Displays the assay name, print date and time, regulatory status of the
results, and the report page number.

More information
 l Reviewing reports (page 176)

About supplemental reports

Introduction
The following is an example supplemental report for the 6 Color TBNK + Truc assay.
The report displays the analysis plot and results of the CD3+CD16+CD56+ population.
The table contains a description of the elements in the report.
Caution! The information in the supplemental report is for Research Use Only. Not
for use in diagnostic or therapeutic procedures.
194      BD FACSLyric™ System Instructions For Use

No. Element Description

1 BD banner Displays the assay name.

2 Report Displays the report type. Lists information about the sample, the
header BD Trucount™ tubes (if applicable), the logged-in user, and the system
at the time of acquisition.

3 Tube header Displays information about the tube and its acquisition. If the assay
was run without BD Trucount™ tubes, the WBC count, lymphocyte
percentage, and lymphocyte count are displayed for each entry.

4 Analysis plot Displays the CD3 vs CD16+CD56 plot with gate.

5 Supplemental Displays the percent lymphocytes and absolute counts in cells/µL of the
information CD3 +CD16+CD56 + population. Caution: The supplemental information
is not for diagnostic use.

6 Report footer Displays the assay name, print date and time, regulatory status of the
results, and the report page number.
Chapter 12  BD IVD assays    195
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 13  
BD FACS™ Universal Loader
This chapter includes the following topics:
 l BD FACS™ Universal Loader overview (page 198)
 l Sample carrier specifications (page 201)
 l Placing carriers into the Loader (page 203)
 l Defining sample carrier layouts (page 205)
 l Cleaning the Loader (page 207)
198      BD FACSLyric™ System Instructions For Use

BD FACS™ Universal Loader overview

About the Loader
The BD FACS™ Universal Loader is an optional automated loading system that mixes
samples and delivers tube racks and plates1 to the BD FACSLyric™ cytometer for
acquisition. The Loader can be included as an option on a new system or it can be
ordered and installed at a later time by a BD field service engineer.

External components
The following figure shows the location of the Loader’s external components.

1Plates should not be used with BD IVD assays.

 Chapter 13  BD FACS™ Universal Loader    199

No. Description

1 Status indicator

2 Loader

3 Eject button

4 Cover

Status indicator
The status indicator uses illumination and color to show the status of the Loader.

Condition Status

Off Ready to operate

Note: If main power to the system is off, this indicator is off.

Blue Cover is locked and system is running

Blinking blue Loading or unloading

Red Error condition

Eject button
The Eject button should be used if there is a problem during operation. Pressing this
button stops acquisition and moves the carrier out to the loading position.
200      BD FACSLyric™ System Instructions For Use

Internal components
The following figure shows the location of the internal components.

No. Description

1 A1 location

2 Gripper mechanism

3 Carrier nest

4 Carrier release lever

Overhead imaging system

The Loader has an internal overhead imaging system that can detect:
 l The presence and location of tubes in racks
 l The correct type and orientation of carriers
 l Lids on plates
Only compatible carriers can be used for this system to work.
 Chapter 13  BD FACS™ Universal Loader    201

Recommendations for using the Loader

Follow these recommendations to ensure that the Loader operates correctly.
Note: Plates should not be used with BD IVD assays.
 l Do not use any plates, tubes, or racks that are not listed as compatible carriers. See
Sample carrier specifications (page 201).
 l Do not use black plates.
 l Keep the top surface of tube racks clean so that the camera imaging system works
properly.
 l Inspect the flange, upper lip, and barcode label on all tube racks for signs of wear
and replace them if excess wear is found. See Placing carriers into the Loader (page
203).
 l Inspect the numbers on the top surface of tube racks to make sure they are legible
and not faded.
 l Keep all barcode labels clean and dry.
 l Do not use CONTRAD® detergents for any cleaning procedures when using the
Loader.
 l Do not autoclave tube racks.
 l When using the Loader, leave a tube of DI water on the manual tube port.

Sample carrier specifications

Carrier type compatibility
The following tables list the carrier types that are compatible with the Loader. The
tube racks are available only from BD.
For information on part numbers and additional details on compatible carriers, see the
BD FACSLyric™ section of the BD website.
The minimum and maximum volumes for tubes and wells are shown. Volumes below
the minimum may need additional diluent to resuspend the sample. Using volumes
above the maximum could result in cross-contamination and spillage during mixing.
202      BD FACSLyric™ System Instructions For Use

Carrier type for tubes a Recommended minimum volume Maximum volume

(µL) (µL)

30-tube rack (12 x 75 100 2,000

mm)

40-tube rack (12 x 75 100 2,000

mm)
a For polystyrene, polypropylene, and BD Trucount™ tubes.

Carrier type for Bottom Material b Recommended Maximum

platesa geometry minimum volume volume (µL)
(µL)

BD 96 standard Round PS 55 200

height

BD 96 standard Flat PS 55 200

height

BD 96 standard Round PP 55 200

height

BD 96 standard Conical PP 55 200

height

384 standard Flat PS 40 75

height

96 half deep Conical PP 55 500

96 deep Conical PP 55 1,000

96 matrix tube N/A N/A 55 700

rack

96 filter bottom N/A PS 150 200

a Plates should not be used with BD IVD assays.
b PS = polystyrene, PP = polypropylene
 Chapter 13  BD FACS™ Universal Loader    203

Barcode reading
The system can read barcodes on plates, tube racks, and individual tubes in 30-tube
racks. To confirm the identification of racks, the barcode must first be entered into the
Carrier ID field in the Layout View of the worklist.
To confirm the identification and correct location of tubes in racks, the barcodes must
first be entered into a worklist with the handheld barcode reader or entered into the
Tube ID column manually. Then the readers in the Loader can confirm that the correct
barcode has been recognized.

More information
 l See topics about barcode label specifications in the BD FACSLyric™ Reference
System for more information about barcode scanning and barcode labels.
 l See Loader preferences in the BD FACSLyric™ Reference System for more
information about setting preferences for the Loader.

Placing carriers into the Loader

Procedure
To place a carrier into the Loader:
 1. Verify that the carrier type you are using is compatible with the Loader.
See Carrier type compatibility (page 201).
 2. Open the cover.
 3. Install the carrier into the carrier nest with the carrier centered on the nest.
This is especially important with heavier carriers such as tube racks, deep-well
plates, and matrix tube racks. Make sure that the flange along the perimeter of
the carrier is held securely in the gripper mechanisms, as shown in the following
figure. The grippers close automatically when the Loader cover is closed.
204      BD FACSLyric™ System Instructions For Use

No. Description

1 Gripper mechanism

2 Flange

The following figure shows a tube rack loaded onto the nest.

More information
 l Sample carrier specifications (page 201)
 Chapter 13  BD FACS™ Universal Loader    205

Defining sample carrier layouts

Introduction
This topic describes how to define sample carrier layouts for a worklist. This applies
only to systems that include the Loader option.
You need to perform this procedure only if you want to define a layout different from
the default. The default is set as a preference in the Preferences dialog. Layouts are
saved with a worklist.

Defining a carrier layout

To define a carrier layout:
 1. In the Loading Options panel, in the Carrier Type field, click and select a carrier
type (for example, 40 Tube Rack).
 2. (Optional) In the Carrier Layout panel, change the three-digit carrier ID in the text
box.

 3. In the Carrier Layout panel, right-click the carrier diagram and select Display
Layout Settings…
The Layout Settings for Carrier dialog opens.
 4. Under Carrier Layout, click the drop-down arrow and select a linear vertical,
serpentine vertical, linear horizontal (factory default), or serpentine horizontal
layout.
206      BD FACSLyric™ System Instructions For Use

 5. (Optional) Make the following selections:

 l If you do not want to include the tubes on the horizontal or vertical edges,
select the Don’t use edge positions checkbox.
 l Select the number of empty positions in the layout between each tube.
 l Select the number of empty positions in the layout between worklist entries.
 6. (Optional) If you have defined multiple carriers in the worklist, use the Apply
properties to checked carrier(s) table to apply the carrier settings to all or selected
carriers. The checkbox in the table header controls the property settings for all
carriers simultaneously.

 7. Click Apply.

Changing barcode settings

To enable or disable barcode reading:
 1. Right-click the carrier diagram in the Carrier Layout panel and select Display
Barcode Settings…
 2. To read the carrier barcode label during loading, select the Read Carrier Barcode
Label checkbox.
 3. For 30-tube racks only, select or clear the Read Tube Barcode Labels checkbox, as
needed.

More information
 l The Loader can be used for creating or updating reference settings. For details, see
the following:
 o Creating default reference settings (page 117)
 o Creating user-defined reference settings (page 120)
 Chapter 13  BD FACS™ Universal Loader    207

 l For details about using the BD FACS™ Universal Loader when updating reference
settings or adding fluorochromes to a reference setting, see the BD FACSLyric™
Reference System.

Cleaning the Loader

Introduction
This topic describes how to clean the Loader. It is a good practice to perform this
cleaning daily.

Required materials
 l 10% bleach solution in a squirt-type bottle
 l DI water
 l Disposable towels or wipes

Caution
Caution! Do not use a spray bottle to spray the 10% bleach solution because the
mist can get into areas and can cause problems. Instead, use a squirt-type
(squeeze) bottle to distribute the solution.

Caution! All biological specimens and materials can transmit potentially fatal
infection. Use proper precautions and wear suitable protective clothing, eyewear,
and gloves. Dispose of waste in accordance with local regulations.

Procedure
To clean the Loader:
 1. Apply the 10% bleach solution to a disposable towel, then wipe down the following
areas:
 l Top surface of the carrier nest
 l Inside surfaces of the cover
 l Outside surfaces of the cover
 l Outside surfaces of the Loader chassis
 2. Use the DI water on the same areas to remove the bleach, then wipe them dry
208      BD FACSLyric™ System Instructions For Use

with a towel.
 3. Dispose of used cleaning materials following biohazard precautions.
For any major spills of liquids down into the interior of the Loader, contact BD
technical support.

More information
 l Performing manual system shutdown (page 49)
 14 
User management
This chapter includes the following topics:
 l Managing user accounts (page 210)
 l Managing departments (page 211)
 l Managing users (page 213)
 l Setting operator permissions (page 216)
210      BD FACSLyric™ System Instructions For Use

Managing user accounts

Introduction
This topic describes the user management tools in the BD FACSuite™ and BD
FACSuite™ Clinical applications.
Administrators can use the User Management window to create and manage user
accounts in the software, as well as manage and assign corresponding departments to
user accounts and create passwords.

User account types

The software includes the following user account types:
 l Administrator This account can administer and manage all accounts (except BD
Service) and has complete access to administrator and operator accounts.
 l Operator This account can only edit its own profile with certain limitations.
See topics about managing a profile in the BD FACSLyric™ Reference System.

About the User Management window

The User Management window can be accessed only by Administrator user accounts.
The window is divided into two panels: a Master panel that displays a table of current
users and user information, and a Details panel for creating or editing information
about the user.
 Chapter 14  User management    211

User management tasks

The following table lists the user management tasks.

To... See...

Add or edit the department that is Managing departments (page 211)

associated with a user

Add or edit user profiles Managing users (page 213)

Set the password policy for users Topics about setting user login and password policies in
the BD FACSLyric™ Reference System.

Export or import user accounts Topics about importing and exporting users in the
BD FACSLyric™ Reference System

Set operator permissions Setting operator permissions (page 216)

More information
 l Setting administration preferences (page 219)

Managing departments
Introduction
This topic describes how to manage departments by adding, editing, and deleting their
information.
Departments must be created before you can assign users. This is an Administrator
task.

Adding new departments

To add a new department:
 1. From the menu bar, select Tools > User Management.
The User Management panel opens.
 2. In the Departments tab, click New.
The New Department detail panel displays at the bottom of the tab.
212      BD FACSLyric™ System Instructions For Use

 3. Enter values in all required fields and optional fields, as needed.
All values are alphanumeric text. All fields have a 30-character limit, except the
Address field, which has a 40-character limit, and the URL field, which has a 200-
character limit.
 4. (Optional) Add a custom department field.
 a. Click the Settings tab.
 b. Under Custom Department Fields, click in a field and type a category (for
example, Supervisor).
 c. Click the Department tab.
The new department field is displayed in the Department detail panel.
 5. Click Done to add the new department settings to the table.

Editing departments
To edit a department:
 1. In the Departments tab, select a department to edit.
The Department detail panel displays at the bottom of the tab.
 2. Click Edit.
 3. Edit the information as necessary.
 4. Click Done.

Deleting a department
To delete a department:
 1. In the Departments tab, select the department to delete.
You can only delete one department at a time. All users must be deleted from a
department before a department can be deleted.
 2. Click Delete.
The Delete Department dialog opens.
 3. Click Yes to confirm the deletion.
 4. The department is deleted.

More information
 l Managing user accounts (page 210)
 l Managing users (page 213)
 Chapter 14  User management    213

Managing users
Introduction
This topic describes how Administrators can add new users in the BD FACSuite™ and
BD FACSuite™ Clinical applications and edit their information later.
Users must be assigned to a department in an institution. The value for the
department can be None.

Adding a new user

To add a new user:
 1. From the menu bar, select Tools > User Management.
 2. In the Users tab, click New.
The New User detail panel opens at the bottom of the tab.
 3. Enter values for all required fields, and the optional fields as needed.
Values are alphanumeric text.
214      BD FACSLyric™ System Instructions For Use

In the Enter the value for...

field...

First Name First name for the user (1-20 characters).

(Required)

Last Name Last name for the user (1-20 characters).

(Required)

User ID A user ID for the user (1-25 characters), must be unique.

(Required)

Title The user’s job title.

Status A status for the user:

 l Active. For users who are granted access to the software.

 l Inactive. For users who are no longer granted access to the software.
 l Locked. For active users with expired passwords, or users who have
exceeded the maximum number of failed login attempts.

Department A department for the user, as defined in the Departments tab. The value
(Required) can be None.

Institution An institution for the user, as defined in the Departments tab. If the
(Required) Department value is None, then the Institution value is None.

Phone A phone number for the user.

Email An email address for the user (must be 1–60 characters and include the @
symbol and a period).

Role A role for the user: Administrator or Operator (default).

Password The date that the user password expires, set in number of days. This is a
Expiration calculated value. Password details are defined in the Settings tab.
Date

Temporary A temporary (initial login) password. Administrators can type specific

Password passwords (case-sensitive, 8–16 characters, no spaces, and at least one of
(Required) each of the following: lowercase, uppercase, number, and a special
character), or generate a random password by clicking Generate Password.

At first login, the user is prompted to enter a new password.

 Chapter 14  User management    215

In the Enter the value for...

field...

Notes Any notes to document history, or other descriptions of the new user
(maximum of 250 characters).

 4. (Optional) Add a custom user field if needed.

 a. Click the Settings tab.
 b. Under Custom User Profile Fields, click a field and type a category (for
example, Supervisor).
 c. Click the Users tab.
The new user profile field is displayed in the User detail panel.
 5. Click Done to save the new user to the Users table.

Editing user details

To edit user details:
 1. In the Users tab, select a row in the Users table.
 2. Click Edit.
 3. Edit the information as needed.
 4. Click Done.

Resetting a user password

To reset a user password:
 1. In the Users tab, select a row in the Users table.
 2. Click Edit.
 3. In the User detail panel, click Generate Password to generate a random password,
or type a new password in the Temporary Password field.
 4. (Optional) Click the Settings tab to view the password policies.
 5. Click Done.

Making users inactive

To make a user inactive:
 1. In the Users tab, select a row in the Users table.
 2. Click Edit.
216      BD FACSLyric™ System Instructions For Use

 3. In the User detail panel, select Inactive in the Status menu.
 4. Click Done.
The user status becomes inactive in the Users table and access is denied.

More information
 l Managing user accounts (page 210)
 l Managing departments (page 211)

Setting operator permissions

Introduction
This topic describes how an Administrator can set operator permissions for users
constrained to the operator role. These settings are global, and changes affect all
users in the operator role. These permissions control whether or not an operator can
delete or rename worklists or worklist entries that have data. In addition, in the BD
FACSuite™ application, the permissions control whether or not an operator can change
the gate sizes and positions in an assay, and whether or not they can access
experiments.

Procedure
To set operator permissions:
 1. From the menu bar, select Tools > User Management or click the Manage Users…
button in the Quick Start panel on the home page.
 2. Click the Operator Permissions tab.
 3. Set or clear the checkboxes in the Assay Worklists Workspace and Experiments
Workspace1 panels as needed.

More information
 l Managing user accounts (page 210)
 l Managing departments (page 211)

1The Experiments Workspace is in the BD FACSuite™ application only.

 15 
Preferences
This chapter includes the following topics:
 l Preferences overview (page 218)
 l Setting administration preferences (page 219)
 l Setting system preferences (page 220)
 l Setting setup and QC preferences (page 222)
 l Setting experiment preferences (page 225)
 l Setting worklist preferences (page 226)
 l Specifying assay properties (page 231)
218      BD FACSLyric™ System Instructions For Use

Preferences overview
Introduction
This topic describes what preferences are and how they are managed.

About preferences
Preferences specify administration settings, display options, schedules for automatic
actions, notifications, and other functions. They include settings for the System,
Worklist, Experiments, Setup & QC, and BD FACS™ Universal Loader Once set,
preferences persist until modified.
The ability to edit preferences is defined by your assigned role. Administrators can set
and edit preferences for all users, but operators can set and edit only their user-
defined preferences.
You can access the Preferences dialog by selecting Tools > Preferences.

Types of preferences
The following table describes the various preferences.

Preference Description

Administration Controls connected systems and software, and generates a system health
report.

System These global preferences set system startup and behavior, programmed
startup and shutdown, and other general system settings.

Setup & QC These preferences set automatic printing for Setup and QC reports, exported
file locations, QC expirations, QC dot plot parameters for specific cytometer
configurations, and Universal Loader preferences for any reference-setting
tasks.

Experiments These preferences define the default tube settings for experiments.

Worklist These preferences set the acquisition and report delay timers, define
exported file names and locations, set printing options, and set Universal
Loader default preferences for new worklists. The BD FACSLink™ connection
information is set here as well.
 Chapter 15  Preferences    219

More information
 l See topics about preferences in the BD FACSLyric™ Reference System

Setting administration preferences

Introduction
This topic describes how Administrators can set administration preferences.
Administration preferences are global settings that specify where files are saved and
when the system health reports are generated for the cytometer.
You can set up the directory path to the FCAP Array software executable. After the
path is set, create a worklist and start FCAP Array software from the Tools menu in the
BD FACSuite™ or BD FACSuite™ Clinical application.

Procedure
To set administration preferences:
 1. From the menu bar, select Tools > Administration.
The Administration dialog opens.

 2. Under Logs, select the Generate System Health Report checkbox to automatically
create system health reports.
 3. (Optional) Specify a different destination folder for system health reports.
220      BD FACSLyric™ System Instructions For Use

 a. Click the Browse button to open the Browse for Folder dialog.
 b. Select a folder and click OK.
 4. Enter or select a value in the Every x Day(s) field to specify the frequency for
generating system health reports.
The default schedule is every 30 days.
 5. Select the Include CMSLog checkbox to include the Cytometer Management
Service (CMS) Log in the System Health Report.
This log contains information about the hardware and firmware details in the
system and can be helpful when trying to diagnose problems with the system.
 6. If FCAP Array software is installed on your system, click the FCAP Array Software
browse button and navigate to the FCAP.exe file.
 7. Click OK to save your administration preferences and close the dialog.

More information
 l Preferences overview (page 218)

Setting system preferences

Introduction
This topic describes how to set the system general preferences.
These preferences are global and are applied to all users. We recommend that only
administrators or lab supervisors set these preferences.

Setting system general preferences

This procedure describes how to set the system general preferences for the default
startup view, a notification type to indicate completion of a task, language selection,
and information that displays on assay and Setup and QC reports.
To set the system general preferences:
 1. From the System tab, select General in the left panel.
 2. Under Startup, select a default startup view from the Default Startup View menu.
The selected workspace is displayed when the software opens.
 Chapter 15  Preferences    221

 3. Under Audible Notifications, select a sound for each notification type, or leave the
value as None.
(Optional) Click the Play button (triangle to the right of the field) to hear the
selected sound for each notification type.

 4. Under Print Options, select the paper size for your printer.
 5. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting cytometer schedule preferences

This procedure describes how to specify the cytometer shutdown and automatic
startup schedules. Setting shutdown sets the time that the cytometer can stay idle
before the system shuts down. Setting preprogrammed startup sets the times when
the system automatically starts. When the schedules are set, the cytometer
automatically starts at the scheduled time and shuts down after the defined idle time.
The default setting is unprogrammed (manual).
To set cytometer schedule preferences:
 1. In the System tab, select Hardware in the left panel.
 2. Under Cytometer Startup Schedule, select the Preprogrammed Startup checkbox.
The Startup Schedule fields are enabled.
 3. Specify the startup days and times by selecting checkboxes for the days and then
entering times. You can also use the current time icon (clock at right side of field)
to set the time to the current time.
222      BD FACSLyric™ System Instructions For Use

 
 4. Under Cytometer Shutdown Schedule, select the Preprogrammed Shutdown
checkbox.
The Hours After Cytometer Idle field is enabled.
 5. Specify the length of time that the system can be idle before shutting down (1–24
hours).
 6. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

More information
 l Preferences overview (page 218)

Setting setup and QC preferences

Introduction
This topic describes how to specify setup and QC preferences.
Since most of these preferences are associated with each user ID, you can customize
them without affecting other users.
When setting a preference for an export folder, everyone using the system should
have access to write to that folder.

Setting expiration preferences

This procedure describes how to specify the expiration preferences for
characterization QC, performance QC, and LW/LNW and user-defined reference
 Chapter 15  Preferences    223

settings. This task is available only to Administrators, although Operators can view the
settings. See the following table for the maximum time for each setting's expiration.
To set expiration preferences:
 1. In the Setup & QC tab, select the General option.
 2. Under the Expiration Options section, enter the expiration durations for
characterization QC, performance QC, and LW/LNW (default reference settings)
and user-defined reference settings.
Note that controls created with BD CompBeads or user-defined fluorescence
controls do not contribute to the reference setting expiration. The expiration is
calculated based on the last updated date for the individual FC Beads in each
setting.

Item Expiration
limit

Performance QC 24 hours

Characterization QC 6 months

Lyse/wash and lyse/no-wash settings and user-defined reference 60 days

settings

 3. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting the high-sensitivity fluidics mode preference

By default, high-sensitivity fluidics mode is excluded when performing setup and QC
tasks.
To change the fluidics mode preference:
 1. In the Setup & QC tab, select the General option.
 2. Under the Fluidics Mode section, click the Include High Sensitivity checkbox to
include or exclude high-sensitivity fluidics mode.
Note: The system will display an error message if you attempt to run an experiment
that has tube settings with flow rate set to high-sensitivity mode, and high-sensitivity
Characterization QC (CQC) and Performance QC (PQC) tasks have never been run, or if
previously run CQC/PQC tasks have expired.
224      BD FACSLyric™ System Instructions For Use

Specifying report preferences

This procedure describes how to specify setup and QC preferences for printing reports
and including linearity charts in characterization QC reports.
To specify setup and QC report preferences:
 1. Select the Automatically print Setup & QC reports checkbox to automatically print
the setup and QC report, once it is generated, on the default printer. The default
printer must be capable of accepting input in PDF format.
 2. Select the Include linearity charts in the Characterization QC reports checkbox to
include linearity charts in the characterization QC report.
This selection is available to Administrators only.
 3. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Specifying file export locations

This procedure describes how to specify the file locations for the file types generated
during setup and QC. Default locations can be specified for both automatically and
manually exported files.
To specify file locations:
 1. In the Export Options section, specify a file location (storage) path for each
generated file type.
 a. Click the Browse button to display the Browse For Folder dialog.

 b. Select a folder and click OK.

The new file path with the new folder name is displayed.
 2. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting dot plot parameter preferences

This procedure describes how to specify the default x and y dot plot parameters for
each installed laser on the system for viewing during setup and QC.
 Chapter 15  Preferences    225

To set dot plot parameter preferences:

 1. In the Setup & QC tab, select Dot Plot Parameters in the left panel.
 2. In the Cytometer Configuration field, select a cytometer configuration from the
list.
 3. In the Parameters table, double-click any parameter in the X Axis or Y Axis column
to enable editing.

 4. Select a different parameter for the other axis.

Plots display these parameters during characterization QC and performance QC for
this configuration.
 5. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Universal Loader preferences

The Universal Loader preferences for Setup & QC tasks can be set independently from
Universal Loader preferences for worklists.

More information
 l Preferences overview (page 218)
 l For Loader and mix preferences, refer to the Preferences section in the
BD FACSLyric™ Reference System.

Setting experiment preferences

Introduction
This topic describes how to set experiment preferences. Experiment preferences can
be set for each user and apply to all experiments created and run by that user.
226      BD FACSLyric™ System Instructions For Use

Since these specific preferences are associated to each user ID, you can customize
them without affecting other users.

Procedure
To set experiment preferences:
 1. Click the Experiments tab.
 2. In the Default Tube Settings field, select a tube setting from the list.
 3. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

More information
 l Preferences overview (page 218)

Setting worklist preferences

Introduction
This topic describes how to set preferences for running a worklist, details for exporting
entry run packages, FCS files and results, and printing options.
Since these specific preferences are associated to each user ID, you can customize
them without affecting other users.
When setting a preference for an export folder, everyone using the system should
have access to write to that folder.

Setting worklist acquisition preferences

To select worklist acquisition preferences:
 1. From the left panel in the Worklist Preferences dialog, select General.
 2. Under Acquisition Delay Timer:
 a. Enter a value in the Preview for field to set how long to preview. This is the
time to update PMT voltages and move gates before data is acquired.
 b. Select one of the following options:
 l Use timer for the first tube in each entry (audible alarm will sound)
 l Use timer for all tubes
 Chapter 15  Preferences    227

 3. Under Trucount Acquisition Delay Timer, enter a value in the Preview for field to
set how long to preview.
The minimum delay time for assays using BD Trucount™ tubes is 17 seconds.
 4. Under Report Delay Timer, in the Preview for field, enter a delay value.
This time is the duration that the report is displayed before the next tube or entry
acquisition is started.
 5. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting the autonumber preference for sample IDs

You can select a worklist preference that enables automatic generation of sample IDs
for worklist entries. This automatically assigns a sample ID when adding an entry
manually or by adding tasks from the Worklist task panel. Autonumbering is enabled
by default.
To set the autonumber preference for sample IDs:
 1. From the menu bar, select Tools > Preferences.
 2. Click the Worklist tab.
 3. Select General from the left panel.
 4. Under Sample ID Assignment, select the Autonumber Sample ID checkbox.
The first auto-generated sample ID will be 001. The next one will be 002, and so
on.
If you change the sample ID to 100 for the first entry, then the next one will be
101, and so on.
 5. Click OK to close the Preferences dialog.

Setting the BD FACSLink™ connection

To configure BD FACSLink™ connection preferences:
 1. From the left panel in the Worklist Preferences dialog, select General.
 2. Under BD FACSLink™ connection, enter the following information in the
appropriate fields. Contact the person responsible for the BD FACSLink™ server at
your location for this information.
 l BD FACSLink™ username
 l BD FACSLink™ password
228      BD FACSLyric™ System Instructions For Use

 l TCP/IP address for the BD FACSLink™ server

 l Port number assigned to your instrument
 3. Click the Test Connection button to ensure that the BD FACSuite™ or BD
FACSuite™ Clinical application can connect to the BD FACSLink™ server.
A BD FACSLink™ connected message displays in the status bar when the
connection is active.

Setting entry run package export preferences

An entry run package includes all the information needed to replicate an entry in a
different worklist. This includes acquired data.
To set entry run package export preferences:
 1. In the Worklists tab, double-click Export, then click Entry Run Package to view the
export options.
 2. Under Auto Export Options, select the Export Entry Run Package after acquisition
checkbox to automatically export the entry run package, the FCS file, and
metadata, which are generated and saved to the specified folder location when
the entry status is Approved.

 3. In the Location field, specify the folder where the exported entry run packages are
stored. Click the Browse button to display the Browse for folder dialog.
 4. If you want to create separate dated folders for exported files, select the Create
dated subfolder checkbox.
A folder with the current date in yyyymmdd format is added to the Location field.
For example, if the folder location field is BDExport\ERP\Worklists and the
checkbox is selected, then the folder location becomes:
BDExport\ERP\Worklists\20110701.
 5. Under Naming Format, click one or more name fields, then select a naming
element.
The naming elements you select are displayed in the Example based on selected
choices field as an example. The selections are used in setting the name of the
entry run package.
 Chapter 15  Preferences    229

Note: Tube or assay names with prohibited Windows OS file name characters, such
as CD3\CD4, will be replaced by a dash (for example CD3-CD4).

 6. Click the Delimiter field and select a delimiter to display between naming
elements in the file name.
 7. Select the Autonumber starting with checkbox to add auto numbering to the file
name.
The example field shows an example of the resulting name (for example, Worklist
Name_001_Sample ID_001).
 8. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting FCS export preferences

An FCS file is a file that contains the raw data. In the BD FACSuite™ and BD
FACSuite™ Clinical applications, the FCS standard is 3.1.
To set FCS export preferences:
 1. In the Worklists tab, select Export > FCS.
 2. Under Auto Export Options, select the Export FCS after acquisition checkbox to
automatically export the FCS file that is generated when you run a worklist.
 3. In the Location field, specify the folder where to export the FCS files. Click the
Browse button to display the Browse for folder dialog.
 4. If you want to create separate dated folders for exported files, select the Create
dated subfolder checkbox.
A folder with the current date in yyyymmdd format is added to the Location field.
For example, if the folder location field is BDExport\FCS\Worklists and the
230      BD FACSLyric™ System Instructions For Use

checkbox is selected, then the folder location becomes:

BDExport\FCS\Worklists\20110701.
 5. Under Naming Format, click one or more name fields, then select a naming
element.
The naming elements you select are displayed in the Example based on the
selected choices. The selections are used in setting the name of the FCS file.
Note: Tube or assay names with prohibited Windows OS file name characters, such
as CD3\CD4, will be replaced by a dash (for example CD3-CD4).
 6. Click the Delimiter field and select a delimiter to display between naming
elements in the file name.
The example field shows an example of the resulting name.
 7. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting result export preferences

Results are generated by running entries in a worklist. One CSV file is created for the
worklist. The file contains a column header row that contains the sample ID, assay
name, export date, and the name of each exported result from all assay tasks in the
worklist.
To set result export preferences:
 1. In the Worklists tab, select Export > Results.
 2. Under Auto Export Options, select the Automatically export results checkbox to
automatically export the results.
 3. In the Location field, specify the folder to export results to. Use the Browse button
to display the Browse for folder dialog.
 4. If you want to create separate dated folders for results files, select the Create
dated subfolder checkbox.
 5. Continue with additional preferences, or click OK to save your preferences and
close the dialog.
 Chapter 15  Preferences    231

Specifying an assay setup report

To generate an assay setup report:
 1. In the Worklists tab, select Assay Setup.
 2. Select the checkbox for Generate assay setup report if none exists for the current
assay setup.
 3. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Setting worklist printing preferences

To set worklist printing preferences:
 1. In the Worklists tab, select Print.
 2. Under Print Options, select the Automatically print report for entries checkbox to
automatically print a report to the default printer when the entry status is
approved. The default printer must be able to accept input in PDF format.
 3. Continue with additional preferences, or click OK to save your preferences and
close the dialog.

Universal Loader preferences

The Universal Loader preferences for worklist tasks can be set independently from
Universal Loader preferences for setup & QC tasks, but the options in each case are
the same.

More information
 l For Loader and mix preferences, refer to the Preferences section in the
BD FACSLyric™ Reference System.

Specifying assay properties

About assay properties
Assay properties specify results approval, export, and LIS options, and report print,
export, and E-signature options. Assay properties are set by an administrator or a user.
Once set, assay properties persist until modified.
232      BD FACSLyric™ System Instructions For Use

Assay properties, together with worklist preferences, define the behavior of your
system when running an assay. However, worklist preferences take precedence over
assay properties.

Procedure
To specify assay properties:
 1. In the library, double-click Assays, and then click the BD icon or User-Defined.
The BD Assays window displays a list of installed BD assays.The User-Defined
Assays window displays a list of user-defined assays.
 2. In the Name column, select an assay and right-click the entry.
 3. Enable/disable the features Require Reason for Change in Audit Trail and Require
Approval for Auto Export/Print as required.
 4. With the assay still selected, click Edit.
 5. Click the General tab. Depending on the user permissions, some or all of the fields
may be read-only.
 a. If you want to automatically approve results without review, select the
Automatically Approve checkbox.
Note: Automatic approval is disabled if certain QC messages are generated
during acquisition or if e-signatures are required for one or more reports.
 b. To allow gate positions and sizes to be modified and applied to other samples
using the same assay, select the Apply gate positions checkbox.
Note: Automatic approval is disabled if the "Apply gate positions" attribute is
set.
 c. For each assay tube, select the number of Tube SIT Flushes in the range 1–6.
 d. Check the Allow Concatenation checkbox if the events of interest are so rare
that there may not be sufficient to be of value in one acquisition.
 6. Click the Export Results tab.
 7. Remove or add any statistics, keywords or expressions for export.
 8. Click the Reports tab, and select print, export, and E-signature options for the
reports. Up to three E-signatures can be specified for each report.
 9. (Optional) Click the Send to LIS tab and select from Keywords & Expressions and
Statistics1.

1Statistics are only available in the BD FACSuite™ application.

 Chapter 15  Preferences    233

 10. Remove any keywords, expression results, or statistics that you do not want to send
to your LIS.
 11. (Optional for the BD FACSuite™ application) Click the Assign Lot ID tab and select
specific lots and labels for lot-specific compensation. This is only for tubes with
labels assigned. Use the Assign Lot buttons to select a lot for all tubes, or use the
individual drop-down menu to select per tube.
 12. To save all changes, click Done.

More information
 l Creating and opening an experiment (page 83)
 l Creating a user-defined assay from an experiment (page 112)
 l For more details about editing assay properties, refer to the Library section in the
BD FACSLyric™ Reference System.
 l Setting worklist preferences (page 226)
This page intentionally left blank
 16 
Periodic Setup and QC
This chapter includes the following topics:
 l Cytometer Setup and QC overview (page 236)
 l Importing or adding a CS&T bead lot (page 238)
 l QC tracking overview (page 239)
 l Setting Levey-Jennings charts preferences (page 240)
236      BD FACSLyric™ System Instructions For Use

Cytometer Setup and QC overview

Introduction
This topic describes periodic setup and quality control (QC) procedures for the
cytometer.
Use the Setup & QC workspace to perform these tasks. After you perform setup and
QC tasks, you can view the results summary or view a detailed report of the task.
For information about daily setup and QC tasks, see Daily setup and QC workflow
(page 54).

Periodic setup and QC tasks

The following setup and QC tasks should be performed only as needed.
 Chapter 16  Periodic Setup and QC    237

Setup and QC Purpose Who

task

Import or add a As bead lots near their expiration date, new bead lots will All users
a CS&T bead lot need to be added to the system for use.
(done in the
You can import bead lot ID information from the BD
library)
website or add bead lot ID information by scanning the
bead lot file card in a kit.

Assay and tube Run assay and tube settings setup to determine the PMT All users
settings setup voltages needed to meet the median fluorescence
determined by the tube target values in the tube settings.

This is completed automatically for LW and LNW tube

settings as part of performance QC, but is available to run
separately.

CS&T bead lot The CS&T bead lot transfer ensures consistency across All users
transfer bead lots by comparing the old lot to the new lot. Existing
tube settings and reference settings can be used without
additional work.

Characterization This task establishes the measured cytometer Administrator

QC performance baseline that is used for all subsequent
performance QC runs. Characterization QC is performed at
installation and every six months.

Characterization QC should not be performed with bead

lots for which the bead lot transfer task has not been
completed. The existing tube settings and reference
settings may no longer be accurate.

Update This task updates either the default LW or LNW reference Administrator
reference settings. In the BD FACSuite™ application, the task also
settings updates the user-defined reference settings.

Setup Cleanup This task purges Performance QC reports that are older Administrator
than a specified number of days, which by default is 30.
Make sure that you back up the database using the
Backup and Restore utility before starting this task.
238      BD FACSLyric™ System Instructions For Use

Setup and QC Purpose Who

task

Add This task adds new secondary fluorochromes and lot- All users
fluorochromes specific fluorochromes to the LW or LNW reference
settings. In the BD FACSuite™ application, the task also
adds the fluorochromes to the user-defined reference
settings.

Laser setup This task initiates an automatic re-alignment of the Administrator

lasers, followed by performance QC to update settings.
Run this procedure if the laser alignment check fails during
performance QC, or if the %rCV is out of range.

More information
 l About QC reports (page 59)
 l See the BD FACSLyric™ Reference System for more information about periodic set
and QC tasks.

Importing or adding a CS&T bead lot

Introduction
This topic describes how to import or add a new CS&T bead lot prior to your existing lot
expiring.

Importing CS&T bead lots

Import CS&T bead lots if you do not have the optional barcode reader. CS&T bead lot
files can be downloaded from the BD website. See the information included in the
BD® CS&T Beads kit for the specific URL, and instructions for downloading bead lot
files.
To import a CS&T bead lot:
 1. On the navigation bar, click Library.
The Library workspace opens.
 2. In the Library panel, double-click Beads and Reagents, then click CS&T.
The CS&T bead information is displayed in the upper-right panel.
 Chapter 16  Periodic Setup and QC    239

 3. From the menu bar, select File > Import.

The Import dialog opens.
 4. Navigate to the CS&T bead lot file location and select the appropriate CS&T bead
lot file.
 5. Click Open.
The new bead lot file is displayed in the table. The Import confirmation dialog
opens if there are warnings or errors.

Adding a new CS&T bead lot

To add a new CS&T bead lot using the barcode reader:
 1. On the navigation bar, click Library.
The Library workspace opens.
 2. In the Library panel, double-click Beads and Reagents, then click CS&T.
 3. In the CS&T Bead Lots table, click Scan barcode and scan the new bead lot
barcode card inside the BD® CS&T Beads kit.
The information is automatically displayed in the CS&T Bead Lots table.

More information
 l For more information on transferring CS&T bead lots, see the BD FACSLyric™
Reference System.

QC tracking overview
Introduction
This topic describes the tasks needed to set up and view Levey-Jennings charts, which
are used to track QC results.

About QC tracking
Using the QC Tracking tab, you can set the performance values you want to display in
the Levey-Jennings (LJ) charts. LJ charts and reports provide a visual display of
instrument performance over time. Time is plotted on the x-axis. A data point is
plotted, indicating its position relative to the mean.
When the system is functioning at peak performance, the variability will be small
(within one SD). If the performance declines, the variability and SD range will increase.
240      BD FACSLyric™ System Instructions For Use

Only Administrators can set alarm and scaling ranges, but any user can choose which
data to view.

QC tracking tasks
The following QC tasks can be performed as needed.

QC Description For more

tracking information
task

Set Levey- These preferences determine which set of data is See Setting Levey-
Jennings displayed in LJ charts and reports based on different Jennings charts
chart filters including bead lot, date range, and filter status. preferences (page
preferences These preferences are specific to each user ID. 240).

Setting The alarm and scaling ranges for LJ charts and reports See topics on setting
alarms and determine which alarm criteria are used and how the alarms and scaling
scaling performance data is scaled in LJ charts and reports. This ranges in the
ranges determines when to flag data points as out of range in BD FACSLyric™
reports. Reference System.

Viewing Levey-Jennings reports contain information about the See topics on Levey-
Levey- system, detector settings, lasers, setup bead lots, and Jennings reports in
Jennings cytometer settings. the BD FACSLyric™
reports Reference System..

Setting Levey-Jennings charts preferences

Introduction
This topic describes how to set the data display and tracking preferences for Levey-
Jennings (LJ) charts and reports. These preferences are specific to the user currently
logged in.

Setting data display preferences

To set data display preferences for LJ reports:
 1. On the navigation bar, select Setup & QC.
The Setup & QC workspace opens.
 Chapter 16  Periodic Setup and QC    241

 2. Click the QC Tracking tab.

 3. In the Cytometer Configuration field, select an available cytometer configuration
from the list.

 4. Click the LJ Charts tab.

The LJ Charts tab opens with a Preferences panel on the left and a Charts panel on
the right.
 5. In the Preferences panel, click and expand the Data Display box to view the list of
preferences.

 6. In the CS&T Bead Lot ID(s) field, select a bead lot ID.
 7. If high sensitivity fluidics mode is enabled in the Tools > Preferences menu, the
LJ Charts Preferences panel includes Fluidics Mode options. Select between
Normal and High Sensitivity.
 8. Under Filter by Date Range, select a date filtering preference.
 9. Under Filter By Status, select a status filtering preference.
 10. Under X-Axis Label, select a label preference.

Setting data tracking preferences

To set data tracking preferences for LJ reports:
 1. On the navigation bar, select Setup & QC.
The Setup & QC workspace opens.
 2. In the QC Tracking tab, click the LJ Charts tab.
242      BD FACSLyric™ System Instructions For Use

 3. In the left panel, click and expand the Data Tracking section to view the list of
performance measurements.

 4. Under Channel Data, select an option checkbox to display the channel data you
want to view in an LJ chart, either using the controls for columns, rows, or individual
checkboxes.
 5. Under Laser Data, select an option checkbox to display the laser data you want to
view in an LJ chart, either using the controls for selecting all lasers, columns, rows,
or individual checkboxes.
 Chapter 16  Periodic Setup and QC    243

As measurements are selected for display, their corresponding LJ charts are

displayed in the Charts panel.
 6. Complete any of the following actions as needed:
 l Click View Report to view the selections in a sample report.
 l Click Comments to add a comment to the report.
 l Use the icons on the top right of each chart to copy or zoom in on the charts
individually.
 l Use the slider to the right of the Charts panel to vary the zoom of the panel.
This page intentionally left blank
 17 
Maintenance
This chapter includes the following topics:
 l Maintenance overview (page 246)
 l Running the daily clean procedure (page 247)
 l Refilling the sheath tank (page 248)
 l Emptying the waste tank (page 250)
 l Performing the monthly clean procedure (page 252)
 l Replacing the sheath filters (page 256)
 l Managing your database (page 259)
 l Archiving procedure for worklists (page 261)
 l Archiving procedure for experiments (BD FACSuite™ application only) (page 262)
 l Performing disk cleanup (page 263)
 l Decommissioning the instrument (page 263)
246      BD FACSLyric™ System Instructions For Use

Maintenance overview
Daily maintenance
Daily maintenance is part of the shutdown procedure.

Procedure When

Running the daily clean procedure (page 247) Daily

Performing manual system shutdown (page 49) Daily

Unscheduled maintenance
The following table lists unscheduled maintenance that you might have to perform.

Procedure When

Refilling the sheath tank (page 248) As needed

Emptying the waste tank (page 250) As needed

See topics about unscheduled maintenance in the BD FACSLyric™ Reference System

for information about additional maintenance procedures.

Scheduled maintenance
Scheduled maintenance should be performed according to the following table.

Procedure When

Performing the monthly clean procedure (page 252) Monthly

Replacing the sheath filters (page 256) Every 3 months

 Chapter 17  Maintenance    247

Running the daily clean procedure

Introduction
This topic describes how to run the daily clean procedure. This procedure is part of the
daily system shutdown. You can also use this procedure to clean the system whenever
it is needed.

Required materials
 l 2 mL of 10% bleach solution
 l 3 mL of DI water
Caution! Do not use the same tube repeatedly for DI water or bleach during the
daily clean procedure. Repeated use can cause wear on the tube, and resulting
particles can damage the tube sensor in the manual tube port or BD FACS™
Universal Loader.

Procedure using the manual tube port

To run the daily clean procedure using the manual tube port:
 1. From the menu bar, select Cytometer > Daily Clean.
The Daily Clean dialog opens.
 2. Make sure that the Universal Loader checkbox is clear. To use the loader, see
Procedure using the universal loader (page 248).
 3. Place a tube containing 2 mL of 10% bleach solution on the manual tube port, then
click Continue.
 4. When prompted, place a tube containing approximately 3 mL of DI water on the
manual tube port, then click Continue.
 5. When prompted by the system, unload the DI water from the manual tube port.
The dialog closes when the process is complete.
Note: You must complete this entire procedure. If the procedure is interrupted or not
completed, the system prevents any other actions from happening. This is to avoid the
possibility of bleach remaining in the fluidics path.
248      BD FACSLyric™ System Instructions For Use

Procedure using the universal loader

To run the daily clean procedure using the universal loader:
 1. From the menu bar, select Cytometer > Daily Clean.
The Daily Clean dialog opens.
 2. Make sure that the Universal Loader checkbox displays a checkmark and the
appropriate option button is set for the size of tube rack that you will use.
 3. Place the tubes of bleach solution and DI water on the tube rack according to the
instructions given in the dialog, then click Continue.
The dialog closes when the process is complete.

More information
 l Fluidics components (page 31)
 l Performing manual system shutdown (page 49)

Refilling the sheath tank

Introduction
This topic describes how to check the sheath fluid level, illustrates sheath tank
components, and describes how to refill the sheath tank.
The sheath and waste tanks must be placed at a level even with, or below, the
cytometer. Placing the tanks higher than the cytometer can cause uncontrolled
siphoning.

Checking the sheath fluid level

The standard sheath tank is translucent so you can visually check the fluid level. In
addition, a message in the software alerts you when the tank is close to empty and
starts a 10-minute timer. You must refill the tank before the 10 minutes elapses to
avoid acquisition being interrupted. The system stops operation when the timer
expires.
 Chapter 17  Maintenance    249

Sheath tank components

The following figure shows the parts of the standard sheath tank.

No. Description

1 Connector

2 Filler cap

3 Standard sheath tank in dock

Required materials
 l BD FACSFlow™ sheath fluid to fill the sheath tank (5 L or 10 L, depending on which
tank is being used). Do not use sheath fluid with surfactant.

Procedure
To refill the sheath tank:
 1. Disconnect the connector from the sheath tank by turning it counter-clockwise.
The following figure shows the connector disconnected from the tank.
250      BD FACSLyric™ System Instructions For Use

 2. Remove the sheath tank from the dock and take it to a filling station.
 3. Remove the filler cap and fill the tank with BD FACSFlow™ sheath fluid.
 4. Re-install the filler cap and place the tank in the dock.
 5. Re-install the connector and turn clockwise to tighten it.

More information
 l Replacing the sheath filters (page 256)
 l Fluidics components (page 31)
 l Emptying the waste tank (page 250)

Emptying the waste tank

Introduction
This topic describes how to check the waste tank level, illustrates the waste tank
components, and describes how to empty the waste tank.
The sheath and waste tanks must be placed at a level even with, or below, the
cytometer. Placing the tanks higher than the cytometer can cause uncontrolled
siphoning.

Checking waste tank level

The standard waste tank is translucent so you can visually check the fluid level. In
addition, a message in the software alerts you when the tank is close to full, and starts
 Chapter 17  Maintenance    251

a 10-minute timer. If the tank is not emptied within 10 minutes, the system prevents
further operation.

Waste tank components

The following figure shows the parts of the standard waste tank.

No. Description

1 Connector

2 Filler cap

3 Standard waste tank in dock

Required materials
 l Enough bleach solution to equal 10% of volume of waste tank

Procedure
Caution! All biological specimens and materials can transmit potentially fatal
infection. To prevent exposure to biohazardous agents, expose waste container
contents to bleach (10% of total volume) before disposal. Dispose of waste in
accordance with local regulations. Use proper precautions and wear suitable
protective clothing, eyewear, and gloves.
252      BD FACSLyric™ System Instructions For Use

To empty the waste tank:

 1. Verify that the system is not processing any samples.
 2. Disconnect the connector from the waste tank by turning it counter-clockwise.
The following figure shows the connector disconnected from the tank.

 3. Remove the tank from the dock and take it to a dumping station.
 4. Remove the filler cap and empty the tank.
Hold the tank at an angle as you empty it and pour slowly to avoid splashing the
contents.
 5. Add bleach to the tank to equal 10% of the volume.
 6. Re-install the filler cap and install the tank in the dock.
 7. Re-install the connector and turn clockwise to tighten it.

More information
 l Fluidics components (page 31)
 l Refilling the sheath tank (page 248)

Performing the monthly clean procedure

Introduction
This topic describes how to perform the monthly clean procedure. This procedure
should be performed at least once per month. It can be performed more often if the
system is heavily used or if any contamination is suspected.
 Chapter 17  Maintenance    253

Description
The monthly clean procedure rinses the fluidics system with a 10% bleach solution,
followed by another rinse with DI water and sheath fluid. The procedure takes about
20 minutes to complete.

Required materials
 l 2 mL of 10% bleach solution
 l 3 mL of DI water
 l 2 L of 10% bleach solution
 l Sheath filter bypass assembly
 l BD FACSFlow™ sheath fluid to fill the sheath tank (5 L or 10 L)

Procedure
Caution! All biological specimens and materials can transmit potentially fatal
infection. To prevent exposure to biohazardous agents, expose waste container
contents to bleach (10% of total volume) before disposal. Dispose of waste in
accordance with local regulations. Use proper precautions and wear suitable
protective clothing, eyewear, and gloves.

To perform the monthly clean procedure:

 1. Verify that the system is in idle mode (not acquiring or performing any other fluidic
task).
 2. From the menu bar, select Cytometer > Monthly Clean.
The Monthly Clean dialog opens.
 3. Load a tube with 2 mL of 10% bleach onto the manual tube port.
 4. Fill a tank with 2 L of 10% bleach solution.
 l We recommend using an extra tank dedicated for 10% bleach for this
procedure. If you have this tank, remove the connector from the sheath tank
and install it on the dedicated bleach tank.
 l If you do not have a dedicated bleach tank, then empty the sheath fluid from
the sheath tank and fill it with 10% bleach solution.
 5. Empty the waste tank.
 6. Remove the sheath filter and store it carefully for putting it back in place at the
end of this procedure.
254      BD FACSLyric™ System Instructions For Use

No. Description

1 Vent line

2 Vent line connector nut

3 Sheath filter

 a. Open the door on the left side of the chassis.

 b. Disconnect the vent line on the top of the filter by unscrewing the connector
nut.
 c. Press the quick-disconnect tabs at the top and bottom of the filter and remove
the filter from the chassis.
 7. Install the sheath filter bypass assembly onto the two quick-connects and the vent
line connector.
Caution! Installing the bypass assembly is a critical step. Failure to do this can
damage the system.
 Chapter 17  Maintenance    255

The bypass assembly is shown installed in the following figure.

No. Description

1 Vent line connector nut

2 Bypass assembly installed

 8. Click Continue in the dialog to start the cleaning process.

A progress bar in the dialog shows the status of the process.
 9. When the bleach cycle is done, remove the tube that contained bleach and replace
it with a tube containing 3 mL of DI water.
 10. Remove the bleach tank and connect the sheath tank.
 l If you are using a dedicated bleach tank, disconnect it and install the connector
on the sheath tank.
 l If you are not using a dedicated bleach tank, empty any remaining bleach from
the sheath tank, rinse it thoroughly with DI water, and refill it with sheath fluid.
 11. Click Continue to continue the cleaning process.
A message is displayed when the process is complete, and the software records the
time and date of the completed procedure.
 12. Remove the bypass assembly and re-install the sheath filter.
256      BD FACSLyric™ System Instructions For Use

 13. Select Cytometer > Fluidics > Purge Sheath Filter and run this command twice to
remove any air bubbles that might have formed during the process.
You can also tap the filter gently to help remove bubbles.

More information
 l Fluidics components (page 31)
 l Replacing the sheath filters (page 256)

Replacing the sheath filters

Introduction
This topic describes how to replace the sheath filter on the side of the cytometer. It
also describes how to replace the sheath supply-line filter in the sheath tank. You
should replace these filters every three months.

Required materials
 l 1 new sheath filter
 l 1 new sheath supply-line filter

Replacing the sheath filter

To change the sheath filter:
 1. Verify that the system is in idle mode (not acquiring or any other fluidic mode).
 2. Open the door on the left side of the chassis.
You might have to move the fluidics tanks dock if it is positioned next to the
cytometer.
 3. Disconnect the vent line on the top of the filter by unscrewing the connector nut.
 Chapter 17  Maintenance    257

No. Description

1 Vent line

2 Vent line connector nut

3 Sheath filter

 4. Press the quick-disconnect tabs at the top and bottom of the filter and remove the
filter from the chassis.
 5. Discard the used filter.
 6. Install a new filter assembly, with the flow arrow pointing up, by inserting each end
into the connectors.
 7. Reconnect the vent line on the top of the filter by screwing on the connector nut.
 8. Select Cytometer > Fluidics > Purge Sheath Filter to bring sheath fluid into the
new filter.
This process takes about one minute to complete.
 9. Repeat step 8 to fill the filter.
You should see fluid in the vent line when it is done.
 10. Close the door and resume normal operation.
 11. Select Cytometer > Maintenance > Replace Sheath Filter.
 12. Enter the information about the new filter, then click OK.
258      BD FACSLyric™ System Instructions For Use

Replacing the sheath supply-line filter

The sheath supply-line filter is located inside the sheath tank in the tube that draws up
the sheath fluid.
To change the sheath supply-line filter:
 1. Disconnect the connector from the sheath tank by turning it counter-clockwise.
 2. Remove the base connector from the sheath tank by unscrewing it and pulling out
the connector and supply-line assembly that includes the supply tube and the filter.
 3. Place the connector and supply-line assembly on clean, lint-free disposable towels
so that you can work on it.
 4. Twist open the supply-line filter holder and pull it apart to access the filter. See the
following figure.

No. Description

1 Base connector

2 Supply-line filter holder

 5. Remove the used filter and install a new filter.

 6. Push the two halves of the filter holder back together and twist to close it.
 7. Place the supply-line assembly back into the sheath tank and screw on the base
connector until it is secure.

More information
 l Fluidics components (page 31)
 l Refilling the sheath tank (page 248)
 Chapter 17  Maintenance    259

Managing your database

Introduction
This topic describes the tasks involved in managing your database. The BD FACSuite™
Backup and Restore utility allows you to back up and restore your database. Two
utilities are provided: the BD FACSuite™ Backup and Restore Utility and the BD
FACSuite™ Clinical Backup and Restore Utility.

About the Backup and Restore utility

Use the appropriate Backup and Restore utility to back up or restore all data that is
stored in the BD FACSuite™ application database or BD FACSuite™ Clinical application
database, along with all FCS files located in the application-defined directories.
With this utility, you can create a single backup set which contains a backup of the
database, along with experiment and worklist FCS files. The utility maintains backup
sets indefinitely. It displays how much disk space each set is taking and how much disk
space is left. You can discard existing backup sets to free up space.
Since the Experiment and Worklist workspaces save FCS files to different locations,
these folders are handled separately when the backup is created.
You can also use any backup set to restore the database and FCS files. When you
restore, you erase any new data created since the backup was created.

Creating a new backup set

To create a new backup set:
 1. Start the BD FACSuite™ Backup and Restore or BD FACSuite™ Clinical Backup and
Restore utility from the icon on the desktop, depending on which application
database you want to back up.
 2. Click Back Up.
The Back Up window opens, indicating the required disk space. If the estimated
space required is greater than the amount available, the software prompts you to
free up additional space and try again.
 3. Verify that adequate disk space is available and click Back Up.
The backup process starts and displays a progress bar. A completion dialog is
displayed and indicates success or failure. If the backup succeeds, the timestamp
260      BD FACSLyric™ System Instructions For Use

of the new backup is provided. If the backup fails, the reason is indicated.
 4. Click Finish to close the window.

Restoring a backup set

To restore a backup set:
 1. Click the BD FACSuite™ Backup and Restore or BD FACSuite™ Clinical Backup and
Restore utility icon on the desktop, depending on which application database you
want to restore.
 2. Select the backup set to restore.
 3. Click Restore.
The Restore window opens, indicating the timestamp of the selected backup set
and the required disk space. If the estimated space required is greater than the
amount available, the system prompts you to free up additional space and try
again.
The estimated space required takes into account the files that will be removed
during the process, and it is possible that this number could be negative. In that
case, 0 KB is used.
 4. Select one of these actions:
 l Back Up and Restore
 l Restore
A confirmation dialog is displayed. The restore process begins and displays a
progress bar. A completion dialog is displayed and indicates success or failure.
 5. Click Finish to close the window.

Deleting a backup set

To delete a backup set:
 1. Click the BD FACSuite™ Backup and Restore or BD FACSuite™ Clinical Backup and
Restore utility icon on the desktop, depending on which application database
backup image you want to delete.
 2. Select the backup set to delete.
 3. Click Delete.
A confirmation dialog is displayed to verify that the selected backup set needs to
be deleted.
 4. Click OK.
 Chapter 17  Maintenance    261

More information
 l Maintenance overview (page 246)

Archiving procedure for worklists

Introduction
Worklists that are no longer being used should be archived at least once per month, or
more frequently as defined by lab-validated procedures. This will allow the software to
perform optimally.
Worklists should be archived to a known location, preferably not on the hard drive of
the BD FACSLyric™ workstation.

Procedure
To archive worklists not actively in use:
 1. Perform a BD FACSuite™ and/or BD FACSuite™ Clinical database backup and
export it to a known location, preferably not on the hard drive of the
BD FACSLyric™ workstation.
 2. Navigate to the Worklist Management page.
 3. Select the worklists you would like to archive.
 4. In the File menu, select Export Worklist > With Data to export the selected
worklists to the desired known location.
 5. Confirm that the files were successfully exported.
 6. In the Edit menu, select Delete to delete the selected worklists that have been
exported.
 7. Exit the software.
 8. To show hidden files and folders in Windows 10:
 a. In the Search box, type Show hidden files and folders, then press Enter.
 b. In the View tab, select Show hidden files and folders, then click OK.
 9. Navigate to C:\ProgramData\BD\FACSuite\Worklists\Deleted Worklists or
C:\ProgramData\BD\FACSuite Clinical\Worklists\Deleted Worklists, according to
which application worklist was archived and delete the contents of that directory.
 10. Perform a database backup again and export it to a known location, preferably not
on the hard drive of the BD FACSLyric™ workstation.
262      BD FACSLyric™ System Instructions For Use

If you need to retrieve one or more of the worklists from the archive, use the Import
Worklist functionality to import the desired worklist(s) from the archiving location.

Archiving procedure for experiments (BD

FACSuite™ application only)
Introduction
Experiments that are no longer being used should be archived at least once per month,
or more frequently as defined by lab-validated procedures. This will allow the software
to perform optimally.
Experiments should be archived to a known location, preferably not on the hard drive
of the BD FACSLyric™ workstation.

Procedure
To archive experiments not actively in use:
 1. Perform a BD FACSuite™ database backup and export it to a known location,
preferably not on the hard drive of the BD FACSLyric™ workstation.
 2. Navigate to the Manage Experiments workspace.
 3. Select the experiments you would like to archive.
 4. In the File menu, select Export Experiments > With Data to export the selected
experiments to the desired known location.
 5. Confirm that the files were successfully exported.
 6. In the Edit menu, select Delete to delete the selected experiments that have been
exported.
 7. Exit the BD FACSuite™ application.
 8. To show hidden files and folders in Windows 10:
 a. In the Search box, type Show hidden files and folders, then press Enter.
 b. In the View tab, select Show hidden files and folders, then click OK.
 9. Navigate to C:\ProgramData\BD\FACSuite\Experiments\Deleted Tubes and
delete the contents of that directory.
 10. Perform a database backup again and export it to a known location, preferably not
on the hard drive of the BD FACSLyric™ workstation.
 Chapter 17  Maintenance    263

If you need to retrieve one or more of the experiments from the archive, use the
Import Experiment functionality to import the desired experiment(s) from the
archiving location.

Performing disk cleanup

Introduction
During normal operation, the software generates intermediate files in your local
temporary folder. We recommend running the Disk Cleanup tool on a regular basis to
scan your disks to find and remove unnecessary temporary files to free up some disk
space.

Procedure
To run disk cleanup:
 1. Close the BD FACSuite™ or BD FACSuite™ Clinical application, if it is open.
 2. In Windows 10, click the bottom-left Start button, type administrative and click
Administrative Tools, and then press Enter.
 3. Double-click Disk Cleanup.
 4. In the Disk Cleanup dialog, select the Temporary files checkbox if it is not
selected.
 5. Click OK.
A confirmation dialog opens.
 6. At the prompt, Are you sure you want to permanently delete these files? select
Delete Files.

Decommissioning the instrument

Instrument disposal and parts removal
A BD Field Service Engineer is required to perform any necessary decontamination and
safe removal and/or disposal of the instrument, or any of its non-consumable parts or
accessories.
This page intentionally left blank
 18 
BD FACSLyric™ technical
specifications
This section includes the following topics:
 l Software and data specifications (page 266)
 l Physical specifications (page 267)
 l Transportation and storage (page 268)
266      BD FACSLyric™ System Instructions For Use

Technical specifications
Software and data specifications

Parameter Value

Software BD FACSuite™ and BD FACSuite™ Clinical applications version 1.4

Operating system Microsoft Windows 10

Data resolution Uncompensated data has a range of 0 to 262143, which is 18 bits

FCS format FCS 3.1 for export

 Chapter 18  BD FACSLyric™ technical specifications    267

Physical specifications

Parameter Value

Operating The cytometer has an operating range between 15°C (59°F) and 30°C
temperature (86°F). We recommend that the lab temperature fluctuate less than
5°C within a day for best operation.

Humidity The operating humidity tolerance is between 15% and 85% relative
humidity (non-condensing).

Dimensions (W x D x H)

Cytometer 63.3 x 57.9 x 57.9 cm

(24.93 x 22.8 x 22.8 in.)

Cytometer with 85.2 x 57.9 x 57.9 cm

standard tanks
(33.5 x 22.8 x 22.8 in.)

Cytometer with 107.2 x 57.9 x 57.9 cm

standard tanks and
(42.2 x 22.8 x 22.8 in.)
Loader

See the BD FACSLyric™ Site Preparation Guide for additional information on dimensions and
clearances.

Weight Cytometer: 56.02 kg (123.5 lb)

Loader: 13.2 kg (29 lb)

Voltage 100–240 ±10% VAC

Frequency 50–60 ±10% Hz

Current 2A

Power 200 W

Heat dissipation Less than 498 BTU/hour at ambient temperature with the cytometer
and Loader running.

Noise Less than 55 dBA over 8 hours under normal operating conditions with
the cytometer and Loader running.
268      BD FACSLyric™ System Instructions For Use

Transportation and storage

This product does not require any special environmental conditions (for example, cold
chain) for transport or storage.
 Index
%
%rCV  61-62, 238

A BD-defined  39, 175
BD IVD  25, 185, 194
accounts, user  210, 213-215
report  58
acquisition
user-defined  25, 112, 114
status  73, 107
Assurity Linc software  36
stopping criteria  165
audit trail
acquisition properties  104
export  181
acquisition status  148, 159
modify  180
adapter, tube  33
print  181
Add Test Orders dialog  156
review  180
administration preferences  219-220
audit trail log  180
administrator  134, 210, 216, 240
auto export options  228, 230
alphanumeric text  212-213
automated system shutdown  51
analysis preview  183
autonumbering  229
analyze  184
apply gate positions  113 B
approve  138
background signal  61, 63
approving entries  177
backup  259, 261
archiving
backup directory  16
experiments  262
barcode  98
area scaling factor (ASF)  63
label  203, 206
area, voltage pulse  79
scanner  35
assay
scanning  239
properties  231
batch analysis  174, 183
worklist  187
BD-defined assay  84, 175
assays
BD Assurity Linc software  36
about  37
BD CompBeads  122
270      BD FACSLyric™ System Instructions For Use

BD FACS Universal Loader C

about  36
cap, filler  250, 252
carrier  201
carrier
cleaning  207
ID  147
imaging system  200
layout  205-206
status indicators  199
Loader  203-204
BD FACS Workflow Manager
placement  203
software  36
types  201, 205
BD FACSFlow sheath fluid  48, 249-
carrier layout  147
250
channel data  242
BD FACSLink
characterization QC  237
preferences  227
cleaning
BD FACSLink connection  156
daily  50, 247
BD FACSLink software  36
Loader  207
BD FACSLyric cytometer  20, 36
monthly  252
BD FACSuite/BD FACSuite Clinical
colors  29
application  20
comments  64, 243
BD FACSuite/FACSuite Clinical
compensation  95
application  20, 24, 36, 48
components
BD FC Beads  25
system  25, 200
BD IVD assay  39
window  42
BD IVD assays  37, 185, 194
configuration
BD Trucount  33
cytometer  59
bead See CS&T beads  48
laser  29
bleach  158
optical  57, 117
daily clean  48, 247-248
options  34
loader  207
system  29
monthly clean  253
connected status  49
system shutdown  49-51
control tube  122, 125
waste tank  252
CS&T beads  117
Br  61, 63
about  48
browse  69
QC  55
bypass assembly  254-255
 Index    271

CS&T Beads detectors  59

about  36 disk cleanup  263
importing  238-239
transferring  237 E
CSV  230 e-Signature
cubitainer  35 about  37
current time  221 using  182
current, laser  63 electronic noise  63
cytometer email  214
configuration  59 emptying waste tank  250
panel  57, 151 entries, worklist  135
settings  59, 77 entry detail
cytometer schedule preferences  221 toolbar  162
entry detail controls  145
D
entry run package  166
daily clean procedure  50, 137, 247 entry run package (ERP)  226
daily maintenance  246 entry run package export
data preferences  228
acquisition  154 Eppendorf tubes  33
analysis  174 ERP  133
channel  242 ESignature option  37
tracking  242 events to display  74
data resolution  266 experiment
data sheet  116 about  37
data sources  75, 89, 93, 96-97, 101- acquiring  106
102, 104-105 browser  83
database  259, 261 creating  83-84
delay timer  141, 226 exporting  69
delay, laser  63 opening  68, 83
delimiter  229-230 preview  84
departments  211-212 saving  68, 112
detector settings  58 sharing  69
272      BD FACSLyric™ System Instructions For Use

tab  72 Flow Cytometry Standard See FCS

workspace  66 file  226
experiment folder  67 fluidics  28, 49
experiments browser  67, 85 fluids  35
expiration date  64 fluorochrome  59, 101, 122

F G
FACS Workflow Manager software  36 gain See PMTV  62
FACSFlow sheath fluid  249-250 gate  104
FACSLink connection  156 gates  88, 110
FACSLink software  36 global settings  219
FACSLyric cytometer  20
FACSuite application  12 H
FACSuite Clinical application  12 hazard symbol definitions  14
FACSuite/FACSuite Clinical heat dissipation  267
application  20, 24, 36, 48 height, voltage pulse  79
Falcon tube  33 Help menu  44
FCAP Array software  35, 219-220 high sensitivity  56
FCS  75-76, 110, 164 home page  39
concatenation  165 FACSuite  39
FCS file FACSuite Clinical  40
export  229 humidity specifications  267
worklist preference  226
FCS format  266 I
filler cap  250, 252
imaging system, Loader  200
filter
institution  214
optical  61-62
IVD assays
sheath  253, 256
overview  186
sheath supply line  258
workflow  186
flow
rate  74
Flow Cytometry Standard  75, 110
 Index    273

K Lyse Wash  226
Lyse/no-wash  87
keyword  102-103
Lyse/wash  87
assigning  155
concatenated FCS file  167 M
L maintenance
daily  246
lab reports  188
scheduled  246
language selection  220
unscheduled  246
laser
manage experiments tab  66-67, 83-84
data  242
manage tab  131
delay  63
Manage Worklists tab  131
report  59
managing user accounts  210
settings  63
manual tube port  31, 50, 52
setup  238
manually approving an entry  178
layout, carrier  205-206
matrix  71, 96
Levey-Jennings charts  37, 239, 241
median fluorescence intensity
library
(MFI)  61-62, 64
about  38
menu bar  43
bead lot  238-239
message bar  43
linearity
Microsoft Windows  24
chart  224
mirror, detector  61-62
plot  64
monthly clean  253
LIS  156, 178
my profile  44
LNW  87, 98
Loader See BD FACS Universal N
Loader  141
navigation bar  43
loading options  151, 205
nest, carrier  203
lock positions  151
noise specifications  267
login  48, 67
noise, electronic  63
logout  44
notes  215
LW  87, 98
notification type  221
Lyse No Wash  226
274      BD FACSLyric™ System Instructions For Use

notifications on QC reports  60 reports  175

PMTV  116, 166
O about  36
operating system  24, 266 adjusting  77, 79, 94, 105
operating temperature range  267 worklist  162
operator  210 population  88, 92
operator permissions  216 port, manual tube  50, 52
optical positive population  116
configuration  57 power
optical configuration  117 button  27-28, 48, 50
optical filter  61-62 specification  63
power specifications  267
P preferences
administration  219-220
panels  43
BD FACSLink  227
parameters  79
cytometer schedule  221
password  210, 214
dot plot  225
PDF  111, 181
ERP export  228
percent robust coefficient of
experiment  226
variation  61-62, 238
expiration  223
performance QC  54, 166
FCS export  229
photomultiplier tube voltage See
file locations  224
PMTV  36
general  220
physical specifications  267
Levey-Jennings  240
physician reports  191
overview  218
plate
result export  230
layout  147
schedule  221
type  202
Setup and QC  222
plot
Setup and QC report  224
creating  89-90
system  220
cytometer settings  88, 95
worklist  226
gates  90, 92
worklist printing  231
previewing  106
printing options  226
 Index    275

private  67 reports
assay setup  58
Q lab  188
QC physician  191
characterization  237 QC  59
performance  54 supplemental  193
reports  58-59 restoring backup  260
tracking  58, 239 reviewing reports  176
Qr  61, 63 run all  141, 158, 160
qualified tubes  32 run pointer  75, 106, 135, 160
Quick Start  39-40 running a worklist  157

R S

rack safety symbol definitions  14

imaging system  200 sample
layout  205 carrier  139
loading  203 ID  137, 155
type  201 sample ID  98
re-acquire specific entries or sample injection tube  74, 137
tubes  165 scheduled maintenance  246
re-acquiring entries  164 search  67
ready  138 selecting entries  135
ready status  77, 151, 158 serial number  60
reagents Setup and QC  36, 41, 55, 57, 236
single-color  101 Setup and QC preferences  222
real-time status  58, 151 Setup and QC tab  57
reference settings  121, 126-127 Setup and QC workspace  57
Reference System  44 setup beads See CS&T beads  48
relative fluorescence detection setup tasks  58
share  67, 69
efficiency  61, 63
share, assay  113
replacing sheath filter  256
report  111
276      BD FACSLyric™ System Instructions For Use

sheath shutdown  49, 51, 137, 247

filter  253, 256, 258 startup  48, 221
fluid  35 status  39
tank  49, 248 system preferences  220
shutdown  49, 51, 221, 247
single-color reagents  101 T
SIT  74, 137 tank
slider, PMTV  95 sheath  49, 248
slope  62 waste  48-49, 250
software specifications  266 tasks  137, 150, 155
SOV  96, 116 technical support  15
spillover values, See SOV  96 threshold  79
startup  48, 221 title bar  43
statistics  175-176 transportation and storage  268
status Trucount  33
bar  43 tube ID  98
connected icon  49 tube parameters  93
indicator  26, 28, 199 tube properties  70, 121
real-time  58, 151 tube settings  98, 116, 126
system  39 tubes
worklist  138 acquiring  76
stop timer  142, 159, 162 adapter  33
subfolders  67, 83 deleting  76
supervisors  220 ID  135
supplemental reports  193 new  76
system next  76
components  25, 200 pausing  76
configuration  29 previewing  76
health report  219 rack  147, 151
imaging  200 restarting  76
information  60 resuming  76
options  34 stopping  76
reference  44
 Index    277

type  32 worklist
worklist  76 about  38
acquiring  158, 164
U analysis  174, 183-184
unscheduled maintenance  246 approving  178
user-defined assay  84, 113, 175 controls  140, 158
user account  210, 213-214 creating  132, 155
user management deleting  134
details panel  210 entries  134, 136
master panel  210 exporting  134
overview  210 importing  133
tasks  211 re-acquiring entries  164
run options  161
V skipping  163
stopping  164
vent line  256
tab  132
W worklist entry controls  143
worklist workspace  130
warnings on QC reports  60 worklists icon  130
waste tank  24, 48-49, 250 worksheet
water  158 gates  90, 92
water, DI plots  89, 106
daily clean  247 workstation  20, 24
monthly clean  255
shutdown  49 X
system startup  48
x-axis  239, 241
width, voltage pulse  79
x-axis parameter label  90
window extension  64
workflow Y
acquisition  82
analysis  174 y-axis parameter label  90
daily  45
experiment  82
 Becton, Dickinson and Company
BD Biosciences
  2350 Qume Drive
  San Jose, CA 95131 USA
   
Benex Limited
EC REP
Pottery Road, Dun Laoghaire
Co. Dublin, Ireland
Tel +353.1.202.5222
Fax +353.1.202.5388
 
BD Biosciences
European Customer Support
Tel +32.53.720.600
[email protected]
 
Australian and New Zealand Distributors:
 
Becton Dickinson Pty Ltd.
66 Waterloo Rd
Macquarie Park NSW 2113
Australia
 
Becton Dickinson Limited
14B George Bourke Drive
Mt Wellington, Auckland 1060
New Zealand
 
 
bdbiosciences.com
[email protected]

   

eifu.bd.com