SYSMEX CyFlow Ploidy Analyser User manual

With CyView™ 1.8
Doc. No.: CY-S-3039IFUEN | Rev: 006 | Rev. date: 27-10-2021 | EN | CN 1434
CyFlow™ Ploidy Analyser
Operating Manual

Table of contents
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Table of contents
1Identification....................................................................................................7
1.1 Product information ...........................................................................................7
1.2 Manufacturer.....................................................................................................7
2Introduction .....................................................................................................8
2.1 About this Operating Manual .............................................................................8
2.2 Typographical conventions................................................................................9
2.2.1 Safety information..............................................................................................9
2.2.2 Text highlights.................................................................................................10
2.3 General conditions...........................................................................................11
2.4 CE compliance................................................................................................11
2.5 Sysmex representatives ..................................................................................12
2.6 Authorised distributors.....................................................................................12
3Safety .............................................................................................................13
3.1 Intended Use...................................................................................................13
3.2 Prohibited use .................................................................................................13
3.3 Reasonably foreseeable misuse......................................................................13
3.4 User definition .................................................................................................13
3.4.1 User qualification groups.................................................................................14
3.4.2 User Qualification Matrix..................................................................................14
3.5 Environmental conditions.................................................................................14
3.6 Prohibition and warning signs on the device....................................................15
3.7 Personal protective equipment ........................................................................15
3.8 General safety.................................................................................................16
3.9 Laser radiation hazards...................................................................................16
3.10 Electrical hazards............................................................................................16
3.11 Alterations to the device ..................................................................................16
4Overview ........................................................................................................17
4.1 Device.............................................................................................................17
4.2 Components of the device...............................................................................19
4.2.1 Control elements .............................................................................................19
4.2.2 Computer interface ports.................................................................................19
4.2.3 Sheath Fluid and Waste bottle.........................................................................19
4.2.4 Sample port with electrodes ............................................................................20
4.2.5 Type plate........................................................................................................20
4.3 Scope of delivery.............................................................................................21
4.4 Scope of operation ..........................................................................................21
4.5 Reagents.........................................................................................................22
4.6 Accessories and spare parts ...........................................................................23
5Transport and storage...................................................................................23
6Installation .....................................................................................................24
6.1 Positioning the device......................................................................................24

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6.2 Installation and uninstallation...........................................................................24
7Operation .......................................................................................................25
7.1.1 Switching on the device...................................................................................25
7.1.2 Logging in........................................................................................................26
7.1.3 Priming the device...........................................................................................26
7.2 Running a Quality Check.................................................................................27
7.3 Performing a measurement (Sample Port).......................................................27
7.4 Saving acquired data.......................................................................................28
7.5 Performing intermediate cleaning....................................................................29
7.6 Shutdown procedure .......................................................................................29
7.6.1 Shutdown cleaning..........................................................................................29
7.6.2 Switching off the device...................................................................................30
7.7 Software operation ..........................................................................................30
7.8 Fault, cause and remedy.................................................................................30
7.8.1 Sheath Fluid, waste and other fluids................................................................30
7.8.2 Calibration and Count Check Beads (low, medium, high)................................32
7.8.3 Measurements and data acquisition ................................................................32
8Maintenance...................................................................................................33
8.1 Maintenance overview.....................................................................................33
8.2 Maintenance procedures.................................................................................34
8.2.1 Sheath Fluid refilling........................................................................................34
8.2.2 Inline Filter renewal .........................................................................................34
8.3 Other maintenance..........................................................................................35
8.3.1 Device cleaning...............................................................................................35
8.4 Technical service.............................................................................................36
8.4.1 Preventive maintenance..................................................................................36
8.4.2 Defective device..............................................................................................36
9Disposal .........................................................................................................37
9.1 Disposal of device ...........................................................................................37
9.2 Disposal of components ..................................................................................37
9.3 Waste disposal................................................................................................37
9.4 Sheath Fluid disposal......................................................................................38
10 Troubleshooting............................................................................................40
10.1 Fault, cause and remedy.................................................................................40
10.1.1 Sheath Fluid, waste and other fluids................................................................40
10.1.2 Calibration and Count Check Beads (low, medium, high)................................41
10.1.3 Measurements and data acquisition ................................................................41
11 Maintenance...................................................................................................42
11.1 Maintenance overview.....................................................................................42
11.2 Maintenance procedures.................................................................................43
11.2.1 Sheath Fluid refilling........................................................................................43
11.2.2 Inline Filter renewal .........................................................................................43
11.3 Other maintenance..........................................................................................44

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11.3.1 Device cleaning...............................................................................................44
11.4 Technical service.............................................................................................45
11.4.1 Preventive maintenance..................................................................................45
11.4.2 Defective device..............................................................................................45
12 Disposal .........................................................................................................46
12.1 Disposal of device ...........................................................................................46
12.2 Disposal of components ..................................................................................46
12.3 Waste disposal................................................................................................46
12.4 Sheath Fluid disposal......................................................................................47
13 Software.........................................................................................................48
13.1 User Management...........................................................................................48
13.1.1 Login ...............................................................................................................48
13.1.2 User Administration.........................................................................................48
13.2 Overview .........................................................................................................50
13.2.1 Title bar...........................................................................................................50
13.2.2 Drop down menu.............................................................................................50
13.2.3 Main window....................................................................................................51
13.2.4 Controls...........................................................................................................51
13.3 Data management...........................................................................................52
13.3.1 Open (.fcs).......................................................................................................53
13.3.2 Save (.fcs).......................................................................................................53
13.3.3 Open Configuration .........................................................................................53
13.3.4 Save Configuration..........................................................................................53
13.4 Data acquisition controls..................................................................................54
13.4.1 Acquisition controls..........................................................................................54
13.4.2 Device realtime display....................................................................................55
13.4.3 Settings...........................................................................................................56
13.4.4 Compensation.................................................................................................57
13.4.5 Plots................................................................................................................58
13.4.6 Results............................................................................................................59
13.4.7 Regions...........................................................................................................61
13.4.8 General ...........................................................................................................67
13.4.9 Acquisition.......................................................................................................68
13.4.10 Measure (Sample Port)..............................................................................69
14 Technical data ...............................................................................................72
14.1.1 Device specifications.......................................................................................72
14.2 Environmental conditions.................................................................................74
14.3 Optical specifications.......................................................................................74
14.4 Fluidic specifications........................................................................................75

Table of figures
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Table of figures
Figure 1: Front and left side of the device .......................................................................17
Figure 2: Ports for external devices.................................................................................18
Figure 3: Rear side of the device.....................................................................................18
Figure 4: Sample port at the right side of the device .......................................................19
Figure 5: Type plate........................................................................................................20
Figure 6: Selecting Prime Mode......................................................................................26
Figure 7: Selecting Work Mode.......................................................................................28
Figure 8: Selecting FCS-File Storage..............................................................................28
Figure 9: Intermediate Cleaning......................................................................................29
Figure 10: Selecting Shutdown .......................................................................................30
Figure 11: Login and system check window....................................................................48
Figure 12: User administration window (exemplary)........................................................49
Figure 13: Main window (DNA-DAPI_C.cvc85 configuration active)................................51
Figure 14: File operations ...............................................................................................51
Figure 15: Device realtime display..................................................................................52
Figure 16: Acquisition controls........................................................................................52
Figure 17: Intermediate Cleaning....................................................................................52
Figure 18: Compensation tab..........................................................................................57
Figure 19: Plots register (Histogram)...............................................................................58
Figure 20: Plots register (Dot plot)...................................................................................58
Figure 21: Results register..............................................................................................59
Figure 22: Creating a quadrant region.............................................................................61
Figure 23: Creating a vertical Region..............................................................................61
Figure 24: Create a polygonal region..............................................................................62
Figure 25: Display options...............................................................................................63
Figure 26: Show Regions (density colored).....................................................................63
Figure 27: Show Regions (unicolored)............................................................................63
Figure 28: Show all events + Regions (unicolored) .........................................................63
Figure 29: Analysis options.............................................................................................64
Figure 30: Peak Analysis Result Table............................................................................65
Figure 31: Region properties...........................................................................................66
Figure 32: General register .............................................................................................67
Figure 33: Acquisition register.........................................................................................68
Figure 34: Measure register............................................................................................69
Figure 35: Acquisition process for all Sample Port Measure Modes................................70
Figure 36: Workstep register...........................................................................................71

1 Identification
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1 Identification
1.1 Product information
Name
CyFlow™ Ploidy Analyser
Software
CyView™ 1.8
REF
CY-S-3039
Versions
CY-S-3039_V1
CY-S-3039_V2
CY-S-3039_V3
1.2 Manufacturer
Sysmex Partec GmbH
Arndtstraße 11 a-b,
02826 Görlitz,
Germany
Phone [phone]
Fax [phone]
[e-mail]
www.sysmex-partec.com

2 Introduction
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2 Introduction
2.1 About this Operating Manual
This Operating Manual will help you to operate your CyFlow™ Ploidy Analyser 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 scientific 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 to 10, 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 7, this chapter also is suitable to get to know the functioning of
your device.
In the second part, chapter 11, you will find a description of all software functions and a
detailed description of the user interface. This chapter is for reference. Chapter 12 lists the
technical data of the device.
There are product data sheets and assay manuals for the reagent kits and general
application notes and quality check manuals available. Please also refer to these
documents.
If you have any questions about the content of this manual or the use of the device, contact
your local Sysmex representative.

2 Introduction
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2.2 Typographical conventions
2.2.1 Safety information
Safety information and warnings are marked by symbols and signal words. Hazards are
categorised into four levels. 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. If applicable a hazard symbol is portrayed, to indicate the kind of hazard.
DANGER
Names the source of the hazard
Describes the consequences of the hazard. This will result in death or
severe personal injury.
•Specifies the steps that must be taken to eliminate the hazard.
WARNING
Names the source of the hazard
Describes the consequences of the hazard. This could result in death or
severe personal injury.
•Specifies the steps that must be taken to eliminate the hazard.
CAUTION
Names the source of the hazard
Describes the consequences of the hazard. This could result in minor
injury.
•Specifies the steps that must be taken to eliminate the hazard.
NOTICE
Names the source of the hazard
Describes the consequences of the hazard. This could result in material
damage.
•Specifies the steps that must be taken to eliminate the hazard.
INFORMATION
Gives further information about the device or procedure.

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2.2.2 Text highlights
To ease the reading flow, the following kinds of text highlights are used in this manual.
Table 1: Text highlights
Style
Meaning
[Brackets]
Describes an interactive element of
software. This includes paths, buttons and
tabs.
Example: Press the [Start] button.
Italic 11 pt
References instances for interaction
(names thereof) in instructions.
Example: Push the On switch on the top of
the device.
It may also be used as chapter reference.
Example: For more information, please
refer to chapter 11.1 User Management.
Italic 8 pt
Used for captions of figures (figures,
tables).
Example: Figure 20: General overview, Table 2:
Safety information
It may also be used for additional
descriptive text.
Example: Electrical hazards Beware of
electrical currents and electrical shocks
“Quotes”
Describes reference sources.
Example: Please consider our “General
Terms and Conditions of Sale and
Delivery” […]
Bold
Describes headlines of subtopics, which
need no independent chapter.
Example: Qualified personnel
Describes also specially highlighted
keywords.
Example: Names the source of the
hazard
Underlined
References external hyperlinks.
Example: www.sysmex-partec.com

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2.3 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:
•Unauthorised modifications or manipulation of the device;
•Improper use;
•Use of non-approved accessories;
•Improper handling;
•Non-compliance with this Operating Manual.
Not following these conditions will impair the safe use of the device, its components and
the safety of the user.
Sysmex Partec GmbH regulates the intended purpose of its products in the instructions
for use. The manufacturer assumes no responsibility for any application deviating from
the instructions for use stated in the product documentation (Off Label Use). We
expressly emphasize that in the event of use contrary to the intended purpose the liability
rests solely with the user.
2.4 CE compliance
The device is marked with a CE mark of conformity, which confirms the
compliance with the essential requirements of the following European Council
Directives:
•2014/35/EU on electrical equipment designed for use within certain
voltage limits;
•2014/30/EU on electromagnetic compatibility;
•2011/65/EU restriction of the use of certain hazardous substances in
electrical and electronical equipment

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2.5 Sysmex representatives
Find address and contact data of your local Sysmex representative also at
www.sysmex-partec.com.
Table 2: Representatives contacts
Europe, Middle East and Africa
Sysmex Europe GmbH
Bornbarch 1,
22848 Norderstedt,
Germany
Phone: [phone]
Web: www.sysmex-europe.com
Americas
Sysmex America, Inc.
577 Aptakisic Road,
Lincolnshire,
IL 60069,
U.S.A.
Phone: [phone]
Web: www.sysmex.com
Asia Pacific
Sysmex Asia Pacific Pte Ltd.
9 Tampines Grande #06-18,
Singapore 528735
Phone: [phone]
Web: www.sysmex-ap.com
China
Sysmex Shanghai Ltd.
9th Floor, AZIA Center 1233, Lijuazui Ring Road,
Shanghai 200120, PRC
Phone: [phone]
Web: www.sysmex.com.cn
Japan
Sysmex Corporation
1-5-1 Wakinohama-kaigandori, Chuo-ku, Kobe, Hyogo
651-0073, Japan
Phone: [phone]
Web: www.sysmex.co.jp
2.6 Authorised distributors
To receive an overview of authorised distributors nearby, please contact your local
Sysmex representative.

3 Safety
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3 Safety
3.1 Intended Use
The CyFlow Ploidy Analyser is equipped with a UV LED 365 nm emission wavelength
and/or a Nd-YAG green laser 532 nm emission line. For fluorescence detection of DAPI
(DAPI-DNA) a blue sensitive PMT is used which analyses fluorescent light between
435 nm and 560 nm. The same detector is used to monitor 532 nm side scattered light
from green laser excitation. Propidium iodide fluorescence (PI-DNA) is detected by a red
sensitive PMT at fluorescence wavelengths above 590 nm. The following versions are
distinguished:
•DAPI (REF No.: CY-S-3039_V1)
Particle and cell analysis equipment (flow cytometry system). Electronical device
with a UV LED 365 nm 3 W and one optical parameter for DNA measurements.
•PI (REF No.: CY-S-3039_V2)
Particle and cell analysis equipment (flow cytometry system). Electronical device
with a green laser 532 nm 30 mW and two optical parameters for DNA
measurements.
•DAPI/PI (REF No.: CY-S-3039_V3)
Particle and cell analysis equipment (flow cytometry system). Electronical device
with a UV LED 365 nm and a green laser 532 nm 30 mW. With two optical
parameters for DNA measurements.
3.2 Prohibited use
Never use the system with organic solvents as this can destroy the fluidic system. Only
use particles with a diameter < 100 μm. It is recommended to use Sysmex Partec
accessories and consumables only.
Do not use in diagnostic procedures. Not for use with biohazardous substances.
3.3 Reasonably foreseeable misuse
Only use this device as a sensitive measuring device.
•Do not use as personal computer.
•Do not use with chemicals harmful to the device (household sanitisers etc.).
•Do not place any objects on top of the device.
3.4 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 at 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.
Only adequately trained personnel must be allowed to operate the instrument.

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3.4.1 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.
3.4.2 User Qualification Matrix
The User Qualification Matrix represents an overview for activities associated with the
device during its life cycle.
Table 3: User Qualification Matrix
Activity
Instructed
personnel
Qualified
personnel
Authorised service
personnel
Transport
✓
✓
Installation
✓
Operation
✓
✓
✓
Cleaning
✓
✓
✓
Decontamination
✓
✓
Maintenance
✓
✓
✓
Technical
Service
✓
Uninstalling
✓
✓
Packing
✓
✓
Disposal
✓
✓
3.5 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 sunlight should be avoided.
•Operating temperature range: 15 °C to 30 °C
•Relative humidity: between 20 % and 85 %, non-condensing.

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3.6 Prohibition and warning signs on the device
The following prohibition and warning signs have been affixed to the device.
Table 4: Safety signs on the device
Symbol
Description
General hazards
Laser radiation
(Only for CY-S-3039_V2 and CY-S-3039_V3)
Laser radiation
(Only for CY-S-3039_V2 and CY-S-3039_V3)
Additional laser labelling
(Only for CY-S-3039_V2 and CY-S-3039_V3)
Laser compliance labelling
(Only for CY-S-3039_V2 and CY-S-3039_V3)
3.7 Personal protective equipment
The following personal protective equipment is recommended to operate the device.
Table 5: Personal protective equipment (PPE)
Item
Description
Gloves must be worn at all times.
Lab coat must be worn at all times.

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3.8 General safety
The system operates with the reagents stated in the scope of operation,
such as Hypochlorite Solution and Decontamination Solution. For further
information please see chapter 4.3 Scope of delivery.
The waste bottle collects all used substances, its contents are not able to
re-enter the fluidic system by design.
Important information regarding the safe handling, transport and disposal
of reagents is contained in the related Safety Data Sheets.
Always meet the national and international guidelines and regulatory
standards for PPE (personal protective equipment).
Find Safety Data Sheets for our products at www.sysmex-partec.com.
3.9 Laser radiation hazards
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).
The device complices with 21 CFR 1040.10 and 1040.11 except for
deviations pursuant to Laser Notice No. 50, dated June 24, 2007.
Only authorised service personnel is allowed to 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 could results from emission by laser light of class IIIb lasers.
3.10 Electrical hazards
The main electrical source used must be grounded or earthed due to local
specifications. The mains cable carries out the protective earthing. Please
place the device in such a way that the electrical power cord can easily be
unplugged. Removable power cords should be replaced by adequate
power cords only.
Beware of possible voltage when changing the fuse (T 3.15 A 250 V).
3.11 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.

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4 Overview
4.1 Device
NOTICE
Glass parts are fragile
Objects put on the glass top or display of the device may damage or
break the glass and do not scratch glass surfaces.
•Do not place any objects on the glass top or display of the device.
Your CyFlow™ Ploidy Analyser is a fully equipped desktop flow cytometer. The CyFlow™
Ploidy Analyser is equipped with a UV LED 365 nm emission wavelength and/or a Nd-YAG
green laser 532 nm emission line.
The CyFlow™Ploidy Analyser is equipped with one (CY-S-3039_V1) or two (CY-S-
3039_V2 / CY-S-3039_V3) optical detectors for the detection of DAPI fluorescence (CY-S-
3039_V1) and/or Propidium Iodide fluorescence and side scattered light (CY-S-3039_V2 /
CY-S-3039_V3). The fluorescence and side scattered light is collected by a microscope
lens in an angle of 90°. The light is subdivided into two different wavelength bands by optical
filter glasses.
The device runs with an integrated computer. Data acquisition, device control, and data
analysis are controlled and performed by the software.
Figure 1: Front and left side of the device
#
Item
#
Item
1
Sample port
3
On switch
2
Ports for external devices
4
Display

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Figure 2: Ports for external devices
#
Item
#
Item
#
Item
1
USB port
2
HDMI port
3
Serial 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
Keyboard port
14
Mouse port
Figure 3: Rear side of the device
#
Item
#
Item
1
Waste tubing connection Waste
bottle
5
Air tubing connection Waste bottle
2
Sensor cable connection Waste
bottle
6
Connector socket power cord
3
Sensor cable connection Sheath
Fluid bottle
7
Power switch
4
Sheath tubing connection Sheath
Fluid bottle
8
Fuse insert (T 3.15 A 250 V)

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Figure 4: Sample port at the right side of the device
#
Item
#
Item
1
Start electrode
4
Sample holder
2
Stop electrode
5
Sample port injection needle
3
Sample tube
4.2 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:
4.2.1 Control elements
The device is operated via keyboard and mouse. The On switch is located on the top
lefthand corner, when the display of the device is lifted up. The power switch is located on
the rear side of the device.
4.2.2 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.
4.2.3 Sheath Fluid and Waste bottle
The Sheath Fluid transports the sample flow during the measurement. The connecting
ports for the tubing of the Sheath Fluid bottle and Waste bottle are located on the rear
side of the device. The Sheath Fluid bottle and Waste bottle are located next to the
device.

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4.2.4 Sample port with electrodes
The Sample port is located on the right side of the device.
It holds the Sample tube during the measurement. The start and stop electrodes of the
Sample port allow the independent determination of exactly 200 μl volume for each
sample. The method of True Volumetric Absolute Counting (TVAC) supported by
CyFlow™ Ploidy Analyser systems is based on the precise measurement of a fixed
sample volume.
4.2.5 Type plate
The type plate is attached to the rear side of the device.
The shows information on the type plate varie according to the system configuration. The
system configuration is represented by the REF number (e.g. CY-S-3039_V1).
Figure 5: Type plate
Table 6: Type plate symbols
#
Item
Manufacturer
Manufacturer name and address
Manufacturing Date
Serial Number
Reference Number
CE mark
Waste of Electrical and Electronic Equipment