SYSMEX CyFlow Cube 8 User manual

For Research Use Only. Not for use in diagnostic procedures.
CyFlow® Cube 8
Operating Manual
CyFlow® Software Version 1.0 RUO
Doc. No.: CY-S-3068RIFUEN | Doc. Rev.: 032 | 17-05-2018 | EN | CN 383

2 CyFlow® Cube 8 | Operating Manual | May 2018 | Revision 032
Imprint
Original Operating Manual
Sysmex Partec GmbH
Am Flugplatz 13
D-02828 Görlitz Germany
www.sysmex-partec.com
All rights reserved. No part of this manual may be reproduced, transcribed or translated in any form
or by any means electronic or otherwise, without the prior permission of Sysmex Partec GmbH.

Table of contents
CyFlow® Cube 8 | Operating Manual | May 2018 | Revision 032 3
Table of contents
1 Introduction ............................................................................................. 6
1.1 About this operating manual .................................................... 6
1.2 Typographical conventions ...................................................... 7
1.3 General conditions .................................................................... 8
1.4 CE compliance ........................................................................... 8
2 Safety ....................................................................................................... 9
2.1 Intended use............................................................................... 9
2.2 Prohibited use ............................................................................ 9
2.3 Reasonably foreseeable misuse .............................................. 9
2.4 User definition.......................................................................... 10
2.4.1 User qualification groups ........................................................... 10
2.4.2 User qualification table............................................................... 11
2.5 Environmental conditions....................................................... 11
2.6 Prohibition and warning signs on the device ....................... 12
2.7 Personal protective equipment .............................................. 12
2.8 Laser safety .............................................................................. 13
2.9 Electrical safety........................................................................ 13
2.10 Alterations to the device ......................................................... 13
3 Overview ................................................................................................ 14
3.1 Components of the device ...................................................... 17
3.2 Type plate ................................................................................. 18
3.3 Scope of delivery ..................................................................... 19
3.4 Accessories and spare parts .................................................. 21
4 Transport and storage.......................................................................... 22
5 Installation ............................................................................................. 23
5.1 Positioning the device............................................................. 23
5.2 Installation and uninstallation ................................................ 23

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6 Operation ...............................................................................................24
6.1 Inserting the Software dongle.................................................24
6.2 Start-up procedure...................................................................24
6.2.1 Switching on the device .............................................................24
6.2.2 Logging in and logging out .........................................................25
6.2.3 Performing a Prime ....................................................................26
6.3 Performing a measurement.....................................................27
6.4 Performing an intermediate cleaning.....................................28
6.5 Shutdown procedure ...............................................................29
6.5.1 Cleaning for shutdown ...............................................................29
6.5.2 Switching off the device .............................................................29
6.6 Software operation...................................................................30
6.6.1 Preparing measurements using the Worklist .............................30
6.6.2 Analysing data and creating reports using the Playlist...............37
7 Troubleshooting....................................................................................39
7.1 Performing a de-bubble procedure ........................................39
7.2 Performing a de-clog procedure.............................................39
7.3 Sheath fluid, waste and fluids.................................................40
7.4 Calibration and Count Check Beads (low, medium, high) ...41
7.5 Measurements and data acquisition ......................................41
8 Cleaning.................................................................................................42
8.1 Cleaning the device .................................................................42
8.2 Performing a cleaning procedure...........................................43
9 Maintenance ..........................................................................................44
10 Disposal .................................................................................................45
11 Technical data .......................................................................................46

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12 Software description ............................................................................ 50
12.1 Overview ................................................................................... 50
12.2 Views of the software window ................................................ 52
12.3 Quick Access Toolbar ............................................................. 56
12.4 Ribbon....................................................................................... 58
12.4.1 File tab ....................................................................................... 58
12.4.2 Home tab ................................................................................... 65
12.4.3 Analyze tab ................................................................................ 68
12.4.4 Preview tab ................................................................................74
12.4.5 Parameters tab .......................................................................... 76
12.4.6 Compensation tab...................................................................... 84
12.4.7 Statistics tab...............................................................................92
12.4.8 Worklist tab ................................................................................ 97
12.4.9 Playlist tab................................................................................ 100
12.4.10 Cytometer tab .......................................................................... 105
12.4.11 Overlay tab............................................................................... 109
12.4.12 Report tab ................................................................................ 114
12.4.13 Views tab ................................................................................. 123
12.4.14 Plot Format tab ........................................................................ 124
12.4.15 Region Format tab ................................................................... 128
12.4.16 Overlay Format tab .................................................................. 131
12.5 Panes ...................................................................................... 136
12.5.1 FCS File Information pane....................................................... 137
12.5.2 Results Hierarchy pane............................................................ 138
12.5.3 Settings pane........................................................................... 139
12.5.4 Acquire pane............................................................................ 140
12.5.5 Setup pane...............................................................................143
12.5.6 Stops pane............................................................................... 144
12.6 Worklist pane ......................................................................... 146
12.7 Playlist pane ........................................................................... 154
12.8 Workspace.............................................................................. 160
12.8.1 Plots tab of the Workspace......................................................160
12.8.2 Results tab of the Workspace.................................................. 171
12.8.3 Overlays tab of the Workspace................................................ 174
12.8.4 Reports tab of the Workspace ................................................. 179
12.9 Status bar ............................................................................... 184
12.10 CyFlow Options...................................................................... 187
Index..................................................................................................... 195

1Introduction
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1 Introduction
1.1 About this operating manual
This operating manual will help you to operate your CyFlow® Cube device.
Emphasis is placed on the installation, start-up and safe operation of the
device.
The basic principles of flow cytometry can be found in the medical literature
(e.g. Howard M. Shapiro, Practical Flow Cytometry, Wiley 2003).
This operating manual comes with the device. Read this operating manual
thoroughly before using the device. Please keep this operating manual for
future reference.
This operating manual is divided in two parts. The first part, chapter 1–11,
gives the user all necessary information for safe handling, scope of delivery,
to set up the device and how to operate the device properly. The general use
of the software and the typical workflows are described in chapter 6.5. This
chapter also is suitable to get to know the functioning of your device.
In the second part, chapter 12, you will find a description of all software
functions and a detailed description of the user interface. This chapter is for
reference.
There are product data sheets for the reagent kits and application notes
available. Please also refer to these documents.
If you have any questions about the content of this operating manual or the
use of the device, contact your local Sysmex representative.

1Introduction
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1.2 Typographical conventions
In this operating manual, warnings are indicated by a signal word. Hazards
are categorised into hazard levels with consequences of differing severity.
Type of hazard
This will result in death or have a serious impact on health.
Information about avoiding the hazard.
Type of hazard
This could result in death or have a serious impact on health.
Information about avoiding the hazard.
Type of hazard
This may have a minor impact on health.
Information about avoiding the hazard.
Type of hazard
This could result in material damage.
Information about avoiding the hazard.
All warnings are structured according to the same model. The type of hazard
is stated after the signal word. Then the consequences that may result from
the hazardous situation are described. And finally, how the hazardous
situation can be avoided.

1Introduction
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1.3 General conditions
Ensure that the following conditions are met when working with the device:
This operating manual must be read prior to using the device.
Report any recurring faults or problems to your local Sysmex
representative.
Sysmex Partec GmbH does not accept liability for any damage or personal
injury arising from:
Modifications or manipulation of the device;
Improper use;
Use of non-approved accessories;
Improper handling;
Non-compliance with this operating manual.
1.4 CE compliance
The device is marked with a CE mark of conformity, which confirms the
compliance with the essential requirements of the following European
Directives:
 2014/35/EC on electrical equipment designed for use within certain
voltage limits;
2014/30/EC on electromagnetic compatibility;
2011/65/EC on the restriction of the use of certain hazardous substances
in electrical and electronic equipment.
1.5

2 Safety
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2 Safety
2.1 Intended use
For Research Use Only. Not for use in diagnostic procedures.
The device is a flow cytometer, it offers automation for routine use and
flexibility for research use in the field of flow cytometric applications.
The applications cover:
Multi-colour analysis of immune cells for research purposes;
Leukocyte counting/rare event analysis for research purposes;
Microbiological analysis;
Fermentation control;
Bead-based assays for research purposes;
Particle and cell concentration analysis based on True Volumetric
Absolute Counting;
Particle size and fluorescence distribution analysis.
2.2 Prohibited use
Never use the device with organic solvents as this can destroy the fluidic
system. Only use particles with a diameter < 100 µm. Only use Sysmex
approved fluids for sheath, cleaning and decontamination.
Never for use in diagnostic procedures.
2.3 Reasonably foreseeable misuse
Only use this device as a sensitive measuring device. It should:
NOT be used as personal computer.
NOT be used with chemicals harmful to the device (household sanitisers
etc.).

2 Safety
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2.4 User definition
The device may only be used by personnel properly instructed in its
handling. The manufacturer, authorised distributor or a person authorised by
the operator (and trained by either the manufacturer or an authorised
distributor) must provide instruction in handling the device with the help of
this operating manual.
The device is aimed for a large spectrum of users, from beginners to
experts. In the best case an expert is around – so, if you are a beginner, let
her/him help you.
Access to the device is not permitted to insufficiently qualified personnel.
2.4.1 User qualification groups
Instructed personnel
Instructed personnel have to be trained by qualified personnel or personnel
authorised by Sysmex to operate the device within the scope of the intended
use. They have to be able to assess if the device can be safely used and are
proficient in handling hazardous substances.
Qualified personnel
Qualified personnel have in-depth knowledge of the device and the
applications. They have been trained by personnel authorised by Sysmex to
operate the device, to perform cleaning and certain maintenance operations.
Qualified personnel have a scientific or technical education and several
years of experience in flow cytometry and are proficient in handling
hazardous substances.
Authorised service personnel
Personnel conducting technical service must be authorised by Sysmex.
Please contact the service department of your local Sysmex representative.

2 Safety
CyFlow® Cube 8 | Operating Manual | May 2018 | Revision 032 11
2.4.2 User qualification table
× = activity can be performed by the user
¹ = please refer to the maintenance table for detailed instructions (see
chapter 9 Maintenance on page 44).
2.5 Environmental conditions
The device may only be used in laboratories. The specified ambient
temperature and relative humidity conditions must be maintained at all times.
The laboratory environment must be clean. Direct sun light should be
avoided.
Relative humidity: between 20 % and 85 %, non-condensing.
Activity Instructed
personnel
Qualified
personnel
Authorised
service
personnel
Transport × ×
Installation ×
Operation × × ×
Cleaning × × ×
Decontamination × ×
Maintenance ×¹ ×¹ ×
Technical service ×
Uninstalling × ×
Packing × ×
Disposal × ×
CyFlow® Cube 8
Configuration
Operating temperature range
V1, V2, V4, V5, V6,
V7, V8, V9, V10,
V11
15 °C to 30 °C
N1 15 °C to 30 °C

2 Safety
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2.6 Prohibition and warning signs on the device
The following prohibition and warning signs have been affixed to the device.
2.7 Personal protective equipment
The following personal protective equipment is recommended to operate the
device.
Warning sticker Meaning
Laser radiation
Electrical hazards
Beware of electrical currents and electrical shocks
Additional laser labelling
Gloves must be worn at all times.
Lab coat must be worn at all times.

2 Safety
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2.8 Laser safety
The device is equipped with a class IIIb laser unit. If the housing of the
device is closed, the laser class of the laser unit is classified as a laser
class I (EN 60825-1:2015).
Never open the housing of the device.
Laser light of laser class IIIb can be emitted if the housing of the device is
damaged or the laser protection is removed. Serious injuries of the eyes and
the skin are the results of emission of laser light of laser class IIIb.
2.9 Electrical safety
The main electrical source used must be grounded or earthed due to local
specifications.
Please place the device in such a way that the electrical power cord can
easily be unplugged. Removable power cords should not be replaced by
inadequate wiring.
Beware of possible voltage when changing the fuse (T 4.0 A 250 V).
2.10 Alterations to the device
Unauthorised alterations to the device can result in risks and hazards.
Therefore, unless expressly permitted by the manufacturer, no alterations
may be made to the device.
If the device is altered, appropriate tests and trials must be performed to
ensure the continued safe use of the device.
2.11

3Overview
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3Overview
Your CyFlow® Cube device is a fully equipped desktop Flow Cytometer
(FCM). Which features a modular optical concept. This allows different
lasers with different wavelength ranges be used as light sources and the
detection of up to 8 optical channels (parameters).
The device allows the optics to be optimised for any application simply by
exchanging optical filters and mirrors. The device runs with an internal PC.
Data acquisition, device control, and data analysis are controlled and
performed by the software.
Fig. 3.1 Front and left side of the device
1On switch
2 Sample port
3 Ports for external devices
4 Sliding compartment
5 Display
5
1
2
3
4

3Overview
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Fig. 3.2 Ports for external devices
Fig. 3.3 Rear side of the device
1 USB port
2 HDMI port
3 VGA port
4 Ethernet port
5 USB port
6 Ethernet port
7 Audio port
8 Audio port
9 USB port
10 USB port
11 USB port
12 DVI port
13 USB port
14 Keyboard port
15 Mouse port
1 Fuse insert (T 4.0 A 250 V)
2 Power switch
3 Connector socket for the power cord
15 7
1 3
1213 91011
2 4 5 6
8
14
2
1
3

3Overview
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Fig. 3.4 Sample port at the right side of the device
1 Start electrode
2 Stop electrode
3 Sample tube
4 Sample holder
5 Sample port injection needle
5
1
2
4
3

3Overview
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3.1 Components of the device
The device contains the flow cuvette, the optics, the fluidics, the computer
unit and data acquisition electronics. No work steps inside the device are
necessary.
The main components of the device are:
Control elements
The device is operated via keyboard and mouse. The On switch is located
on the top, when the display of the device is lifted up. The power switch is
located on the rear side of the device.
Computer interface ports
The computer interface ports connect the device with additional optional
electronic devices. They are located on the left side of the device.
Sheath fluid bottle and waste bottle
The sheath fluid transports the sample flow during the measurement.
The connecting ports for the tubings of the sheath fluid bottle and waste
bottle are located inside the device. The tubings are preinstalled. The sheath
fluid bottle and waste bottle are located in the sliding compartment at the
rear side of the device.
Sample port with electrodes
The sample port is located on the right side of the device.
The sample port holds the sample tube during the measurement. The start
and stop electrodes of the sample port allow the independent determination
of exact 200 μL volume for each sample. The method of True Volumetric
Absolute Counting (TVAC) supported by CyFlow® Cube systems is based on
the precise measurement of a fixed sample volume.

3Overview
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3.2 Type plate
The type plate is attached to the rear side of the device.
The content of the type plate varies according to the system configuration.
The system configuration is represented by an addition to the REF number
(e.g. CY-S-3068R_N1).
The following signs are part of the type plate which has been affixed to the device.
Symbol Meaning
For Research Use Only
Manufacturer
Certification mark
Reference Number
Serial Number
Manufacturing date
Waste of Electrical and Electronic Equipment
Operating manual
Indicates the temperature limits to which the device can be
safely exposed
No direct sunlight at the installation location
Indicates the range of relative humidity to which the device
can be safely exposed
Caution
RUO

3Overview
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3.3 Scope of delivery
Fig. 3.5 Scope of operation
The scope of delivery includes:
1 CyFlow® Cube device;
1 Power cord;
1 Software dongle;
1 Operating manual;
1 Laboratory bottle, 1 litre, labeled with sheath;
1 Laboratory bottle, 1 litre, labeled with waste;
1 CyFlow® Cube device
2 Keyboard and mouse
3 Waste bottle
4 Sheath fluid bottle with inline filter for
sheath fluid
2
1
4 3

3Overview
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1 Blue cap with electrodes, cabling and tubing for sheath including inline
filter;
1 Red cap with electrodes, cabling and tubing for waste.
The scope of operation includes:
1 CyFlow® Cube device;
1 Power cord;
1 Software dongle;
1 Operating manual;
1 Keyboard and 1 mouse;
1 Laboratory bottle, 1 liter, labeled with sheath;
1 Laboratory bottle, 1 liter, labeled with waste;
1 Blue cap with electrodes, cabling and tubing for sheath;
1 Red cap with electrodes, cabling and tubing for waste.