Thermo Scientific GeneTitan Scanner User guide

For Research Use Only. Not for use in diagnostic procedures.
GeneTitan™Scanner
USE AND MAINTENANCE GUIDE
Catalog Numbers 00-0442 and 00-0443
Publication Number MAN0018315
Revision A.0

Affymetrix Inc. | 3450 Central Expressway | Santa Clara, CA 95051 | USA
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The information in this guide is subject to change without notice.
DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,
INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,
INCLUDING YOUR USE OF IT.
Revision history: Pub. No. MAN0018315
Revision Date Description
A.0 31 December 2019 New publication.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Microsoft and Windows
are either registered trademarks or trademarks of Microsoft Corporation in the United States and/or other countries. Smart Shutter is a trademark of
Sutter Instrument Company. Cermax is registered trademark of Excelitas Technologies Corp.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 5
Instrument overview ............................................................. 5
Parts of the instrument system ................................................... 5
GeneTitan™Scanner ........................................................ 6
Workstation setup .......................................................... 8
Lambda LS light source ..................................................... 10
Lambda SC shutter control .................................................. 10
Uninterruptible power supply ............................................... 12
■CHAPTER 2 GeneTitan™Scanner operation .......................... 13
Guidelines .................................................................... 13
Lambda system operation ....................................................... 13
GeneChip™Command Console™(GCC) ............................................ 14
Start the scanner .............................................................. 15
Scan an array plate ............................................................. 15
Shut down the scanner ......................................................... 16
■CHAPTER 3 Maintain the Instrument ................................. 17
GeneTitan™Maintenance ........................................................ 17
Monthly .................................................................. 17
Every six months .......................................................... 17
Lambda LS xenon arc lamp ...................................................... 18
Replace the Lambda LS fuse ................................................ 18
Xenon lamp replacement ................................................... 19
Lambda SC Smart Shutter™Controller ............................................ 24
Replace the Lambda SC fuse ................................................ 24
■APPENDIX A Troubleshooting ......................................... 25
GeneTitan™Instrument support files for troubleshooting ............................ 25
Log files .................................................................. 25
GeneChip™Command Console™log files ...................................... 25
Other GeneChip™Command Console™files ................................... 25
GeneTitan
™
Scanner Use and Maintenance Guide
3

GCC log files for the GeneTitan™Scanner ..................................... 26
GeneTitan™Scanner ....................................................... 26
■APPENDIX B Parts and materials ..................................... 28
Replacement parts ............................................................. 28
■APPENDIX C Instrument specifications .............................. 29
Environmental requirements .................................................... 29
Electrical requirements ......................................................... 30
Component clearances required for installation and maintenance .................... 31
Lambda LS xenon arc lamp specifications ......................................... 31
Lambda SC controller cables .................................................... 32
■APPENDIX D Safety ..................................................... 33
Symbols on this instrument ..................................................... 33
Standard safety symbols .................................................... 33
Additional safety symbols ................................................... 34
Location of safety labels .................................................... 35
Conformity symbols ........................................................ 36
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 36
Instrument safety .............................................................. 36
General .................................................................. 36
Physical injury ............................................................ 37
Electrical safety ........................................................... 38
Cleaning and decontamination ............................................... 39
Instrument component and accessory disposal ................................ 39
Laser safety ............................................................... 40
Safety and electromagnetic compatibility (EMC) standards .......................... 40
Safety standards ........................................................... 41
EMC standards ............................................................ 41
Environmental design standards ............................................. 41
Chemical safety ................................................................ 42
Biological hazard safety ......................................................... 43
■APPENDIX E Documentation and support ............................ 44
Related documentation ......................................................... 44
Customer and technical support ................................................. 44
When to call technical support ................................................... 45
Limited product warranty ....................................................... 45
Contents
4
GeneTitan
™
Scanner Use and Maintenance Guide

Product information
Instrument overview
The Applied Biosystems™ GeneTitan™ Scanner is a high-throughput imaging device
with multi-axis robotic handling capability for imaging 24-, 96-, mini 96, and 384HT-
array plate formats. The scanner is designed to measure the uorescence signals of
labeled DNA targets that are hybridized to the array plates. The illumination source
of the GeneTitan™ Scanner is an external, high-intensity xenon arc lamp. The
GeneTitan™ Scanner is also equipped with a lter slider that allows up to 2 optical
lters sets to detect uorescence intensity of samples in array plate layouts for
downstream analysis.
Parts of the instrument system
The GeneTitan™ Scanner System consists of:
• GeneTitan™ Scanner
• Computer workstation and monitor—Windows™ 10 IoT operating system with
GeneChip™ Command Console™ software (GCC) and Microsoft™ Oce 2016
preinstalled
• Lambda LS— Stand-alone xenon arc lamp and power supply that is equipped
with a stand-alone SmartShuer™ system
• Lambda SC—SmartShuer™ Controller
• Uninterruptible power supply (UPS)
1
GeneTitan
™
Scanner Use and Maintenance Guide
5

2
1
1Yellow LED light
2Green LED light
GeneChip™ Command Console™ software controls the power to the GeneTitan™
Scanner. Power the instrument on or o using the software.
Instrument status indicator
The two indicator lights in the lower left front of the instrument display various
paerns of light and color indicating dierent instrument conditions. The following
table denes the meaning for the status light paerns.
Light indicator Instrument status
Solid green Ready or idle state
Solid yellow Initializing/homing the instrument
Blinking green Imaging in progress
Blinking yellow Hardware or software error state
GeneTitan™
Scanner
Chapter 1 Product information
Parts of the instrument system
1
6
GeneTitan
™
Scanner Use and Maintenance Guide

GeneTitan™Scanner drawer door
The GeneTitan™ Scanner drawer door is on the left side of the scanner. The drawer
door is controlled by the GCC software, and opens during operation to receive or
expel the array plate and scan tray combination.
1
2
1Scanner drawer door
2Scanner drawer extended
WARNING! Crushing Injury Hazard. Do not place hands or face near the load
tray when loading plates into or ejecting plates from the instrument.
Chapter 1 Product information
Parts of the instrument system
1
GeneTitan
™
Scanner Use and Maintenance Guide
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Connections
8
1
2
3 4
7
65
Figure 1 GeneTitan™Scanner back connections
1Power receptacle—connect to the Lambda LS
2Power cable and circuit breaker button
3BNC port for CCD camera cable to control the external shutter—connect to the Lambda
SC TTL IN receptacle
4Kvaser USB port for motion controller communication cable—connect to the computer
5Power receptacle for the GeneTitan™Scanner—connect to the UPS
6USB port for the internal devices communication cable—connect to the computer
7FireWire port for CCD camera communication cable—connect to the computer
8Light guide—connects to the Lambda LS
CAUTION! FireWire (IEEE 1394 High-Speed Serial Bus) and USB cables are not
locking connectors. Ensure that the FireWire and USB cables are plugged
securely and in the correct orientation in both the scanner and the workstation.
Avoid snagging or pulling cable during scanner operation.
The instrument workstation consists of a separate computer, keyboard, mouse, and
monitor connected to the GeneTitan™ Scanner through its rear utility panel. The
workstation includes the following pre-installed software:
• Windows™ 10 Enterprise 2016 LTSB operating system
• Microsoft™ Oce 2016
• GeneChip™ Command Console™ software (scanner control)
Workstation setup
Chapter 1 Product information
Parts of the instrument system
1
8
GeneTitan
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Scanner Use and Maintenance Guide

Computer back panel connections
1
5
2
7
3
10
8
9
6
4
1Serial port—connect to Lambda LS
2USB 2.0 port (2)—connect to the keyboard and mouse
3USB 3.0 port—connect to scanner
4USB 3.0 port—spare
5Ethernet port—connect to local network
6USB 3.0 port—connect to Kvaser USB cable from scanner
7USB 2.0 port (1)—spare
8DVI and HDMI video ports—connect to monitor
9FireWire ports (2)—connect one to scanner
10 Power cable connector—connect to the UPS
Note: Three additional USB 2.0 ports, and 1 additional USB 3.0 port are in the front of the
computer.
Chapter 1 Product information
Parts of the instrument system
1
GeneTitan
™
Scanner Use and Maintenance Guide
9

The Lambda LS is a stand-alone xenon arc lamp and power supply system that is
equipped with a SmartShuer™ component.
The system consists of a xenon-arc lamp, lamp housing, cold mirror, SmartShuer™,
and power supply. The Lambda LS is designed for use with a liquid light guide that
transmits at, intense illumination to the optical train of the GeneTitan™ Scanner.
The Lambda LS xenon arc lamp illuminator system is installed by a qualied eld
service engineer and placed near the scanner. The lamp system must not be placed on
the oor. Do not move the lamp system after installation.
Lambda LS light source connections
4
3
1
2
1Light guide connection
2Lens tube
3Liquid light guide—connect to the back panel of the scanner (see the following caution
note)
4Serial connection—connect to the Lambda SC
CAUTION! The liquid light guide is a fragile ber optic cable. Do not kink or
bend the cable to less than 6 inches (15.25 cm) radius. Do not place objects on
the light guide.
The Lambda SC is a microprocessor-controlled shuer driver for the SmartShuer™
device in the Lambda LS. It oers enhanced performance that allows programmable
control over the exposure time, the delay between exposures, the number of
exposures, the mode of triggering, and the mode of shuer opening.
IMPORTANT! Always keep the Manual Shuer Control switch in the AUTO position.
Lambda LS light
source
Lambda SC
shutter control
Chapter 1 Product information
Parts of the instrument system
1
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GeneTitan
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Scanner Use and Maintenance Guide

Lambda SC back panel
2 3 54 7
6
8
1
1Fuse Label—Information found here includes the instrument model number, appropriate
supply voltage, and the type of fuse required for the supply voltage.
2Power Switch—Used with power socket to turn power on and off to the Lambda SC and the
attached Lambda LS light source.
3Fuse—Fuse compartment contains the supply voltage fuse and an extra fuse. Replace
blown fuses with a fuse of the appropriate value as given on the fuse label. Mains fuse: 5 x
20-mm glass tube, T1.0A 250 V IEC 60127-2 Sheet III.
4Line Power—Power socket is used to connect the supplied power cord to the Lambda SC.
5
Smart Shutter™port—9-pin DSUB male connector used to link the Lambda SC with the
Lambda LS Smart Shutter™light source.
6TTL Input and Output—Two BNC receptacles for TTL control of the connected Lambda LS
Smart Shutter™light source. TTL IN is connected to the back panel of the GeneTitan™
Scanner. TTL OUT is not used in the GeneTitan™Scanner System configuration.
7Serial port—9-pin DSUB female receptacle that establishes an RS-232 serial interface
between the Lambda SC and a host computer using the provided cable.
8USB port—USB B-type port. The GeneTitan™Scanner System does not use this port.
Lambda SC front panel
2
13
1Shutter Light—This lamp is lit while the
Smart Shutter™is in the open state.
2Power Light—This lamp is lit while the controller is powered on.
3Manual Shutter Control Switch (Open Auto Closed)—This 3-position switch manually
opens or closes the Smart Shutter™, overriding programmed operation or external control
(TTL signaling and/or remote host computer connected via RS-232 Serial or USB).
The manual shutter control switch middle position (labeled AUTO) places the Lambda SC
controller into control of its programming under TTL control or under the control of an
externally connected host computer.
Chapter 1 Product information
Parts of the instrument system
1
GeneTitan
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Scanner Use and Maintenance Guide
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The GeneTitan™ Scanner has an external uninterruptible power supply (UPS). The
UPS provides and maintains power to the scanner, workstation, and external light
source with shuer.
5
1
2
7
8
4
3
6
1Chassis ground connection screw
2Outlets
3USB B‑type port
4UPS monitoring port
5Battery connector
6Input circuit breaker
7Controlled outlet group
8UPS input
Uninterruptible
power supply
Chapter 1 Product information
Parts of the instrument system
1
12
GeneTitan
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Scanner Use and Maintenance Guide

GeneTitan™Scanner operation
This chapter describes the basic scanner operations. For detailed information see the
GeneChip™ Command Console™ User Guide, Pub. No. 702569.
Guidelines
Review and understand the following guidelines regarding the use and safe operation
of the scanner. Also, it is important to read and be familiar with the safety guidelines
that are presented in Appendix D, “Safety“.
IMPORTANT! To protect your warranty and ensure safe operation, a Thermo Fisher
Scientic Field Service Engineer (FSE) must service the instrument. If the instrument
is not working correctly, contact Thermo Fisher Scientic Technical Support.
• Do not install any unapproved third-party software on the GeneTitan™ Scanner
computer workstation.
• When running the GeneTitan™ Scanner System, do not:
– run anti-virus scans.
– run disk defragmentation.
– run backup software.
Instead, schedule these activities for those times when you are not imaging
arrays.
• Never push an object into the instrument ventilation slots as it can cause
equipment damage or personal injury.
• Do not set any liquids or containers holding liquids on top of the instrument, or
near the electrical systems.
WARNING! Do not place hands or face near load tray when loading or ejecting
a plate.
Lambda system operation
Conrm that the power switches for both the Lambda LS xenon arc lamp and the
Lambda SC shuer controller are in the "On" position before you launch the GCC
Standalone Scanner Control application. The application initializes the system,
including the lamp. The aached SmartShuer™ automatically opens and closes. The
Lambda SC defaults to online when power is on or after a reset. If the unit is
connected to a serial port with properly installed software, the serial port is selected
as the default remote control interface. The Lambda SC is online when power is on,
ready for serial port commands.
2
GeneTitan
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Scanner Use and Maintenance Guide
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Never manually switch the lamp and the shuer controller on or o using the power
switch on the back panel of the units. The power switch on both of the Lambda units
must always be "On". The GeneTitan™ Scanner control software manages the lamp
activity and switches the lamp and shuer controller on and o, as required.
CAUTION! Due to the draw of current during lamp ignition, the Lambda LS
must be powered on before other electronic and computer equipment,
especially when they are powered from or grounded to the same circuit. Failure
to do so can reset microprocessor-based equipment and/or destroy sensitive
operational amplier-based instrumentation. Allow the GCC Standalone
Scanner Control to manage power to system components.
It takes 10 minutes to warm up the lamp. In standby mode, the lamp remains on for
1 hour before it is automatically switched o. The automatic shutdown of the lamp is
by design and is intended behavior. Do not try to save the lamp life by using the
power switch on the lamp. The lamp provides approximately 500 hours of service.
The GeneChip™ Command Console™ software application tracks and displays
remaining lamp life.
IMPORTANT! Always keep the Lambda SC Manual Shuer Control switch in the
AUTO position.
GeneChip™Command Console™(GCC)
The GeneTitan™ Scanner is operated via GeneChip™ Command Console™ software,
v6.0 or later, preinstalled on the GeneTitan™ Scanner System workstation. The GCC
Launcher component of GeneChip™ Command Console™ provides fast access to open
the GCC Standalone Scanner Control application.
1
1GCC Standalone Scanner Control
Chapter 2 GeneTitan™Scanner operation
GeneChip
™
Command Console
™
(GCC)
2
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GeneTitan
™
Scanner Use and Maintenance Guide

Start the scanner
1. Power on the workstation.
2. Sign in to your user account.
3. Click the GCC Standalone Scanner Control icon on the Launcher window.
The following operations occur:
• The GeneTitan™ Scanner control window opens.
• The GeneTitan™ Scanner Servo is powered on.
• All subsystem components in the GeneTitan™ Scanner initialize to their default
state to ensure that each component in the instrument is functioning properly.
• The GeneTitan™ Scanner performs a homing routine.
Scan an array plate
An array plate that has completed hybridization and uidics processing is required
for this procedure. The array plate must be in a GeneTitan™ scan tray with the
appropriate volume of Array Holding Buer.
Note: You can scan only 1 array plate at a time.
The following icons are present on the toolbar, depending on the status of the scan
workow.
1 2 3 4 5 6
1Start
2Load
3Unload Plate
4Stop
5Email Settings
6Help
1. Check the remaining lamp life under System Status in the upper left of the
GeneTitan Scanner window. If needed, change the xenon lamp. (See “Replace
the xenon lamp“ on page 22.)
Note: There is a lamp life threshold of 10 hours. When this value is reached, the
software prevents plate imaging and the lamp must be replaced. Replace the
lamp before this threshold is reached.
2. Click Start .
The scanner drawer door opens and the drawer extends on the left side of the
scanner.
3. Place the array plate-scan tray combination on the drawer. Ensure that it is
loaded in correct orientation and that it is seated snugly and securely on the
drawer tabs.
IMPORTANT! When loading the array plate-scan tray combination onto the
scanner drawer, be careful not to spill the Array Holding Buer.
Chapter 2 GeneTitan™Scanner operation
Start the scanner
2
GeneTitan
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Scanner Use and Maintenance Guide
15

IMPORTANT! Note that barcode faces the rear of the scanner.
4. Click Load .
The array plate-scan tray combination is retracted into the scanner, the array
plate barcode is read, and the software determines the pate format. An array
graphic is displayed with all of the arrays on the plate selected by default.
5. (Optional) If you only want to scan a subset of arrays on the plate, select the
arrays to scan in the array graphic.
• Click and drag to select contiguous arrays in a row, column, or block.
• Control-click to select noncontiguous arrays.
Note: If needed, click Stop to retract the drawer and stop the current process.
6. Click Start .
7. Click OK in the Start Processing conrmation window to continue.
Scanning proceeds. When the scan is complete, color-coded results are displayed
in the array graphic in the System Status section of the GeneTitan Scanner
window. See the GeneChip™ Command Console™ User Guide (Pub. No. 702569) for
more information.
8. Click Unload Plate to open the drawer.
9. Remove the array plate-scan tray combination, then press Load to retract the
drawer and to close the scanner door.
Shut down the scanner
Click File4Exit to exit the GCC Standalone Scanner Control application.
Note: Do not remove the power cord from the back of the GeneTitan™ Scanner. The
power cord is removed only if the scanner requires service.
Chapter 2 GeneTitan™Scanner operation
Shut down the scanner
2
16
GeneTitan
™
Scanner Use and Maintenance Guide

Maintain the Instrument
GeneTitan™Maintenance
The GeneTitan™ family of instruments requires lile in the way of customer
maintenance. The instruments must be kept clean and free of dust. Dust buildup can
degrade performance. Wipe the exterior surfaces clean using a mild dish detergent
solution in water. Do not use ammonia-based cleaners or organic solvents such as
alcohol or acetone to clean the system because they can damage the exterior surfaces.
IMPORTANT! Only the xenon bulb, fuse, and fan lter are replaceable by the
customer. Only qualied eld service engineers are allowed to open and service the
GeneTitan™ Scanner. There are no customer serviceable parts inside the scanner
housing. Contact Thermo Fisher Scientic to schedule qualied eld service personnel
to replace all internal parts.
CAUTION! Do not aempt to service the instrument. Unauthorized service can
result in injury, damage the instrument, and/or void the warranty.
The following tasks must be performed regularly to ensure that the imaging device
remains in working order.
Wipe down the outer surface of the imaging device with a dry cloth.
Replace the cooling fan air filter
A new Cooling Fan Filter (Cat. No. 01-078501-0785) is required for this procedure.
1. Shut down the scanner using the GeneChip™ Command Console™ Standalone
Scanner software application, then shut down the Windows™ operating system.
2. Remove the power cord from the back of the scanner.
3
Monthly
Every six months
GeneTitan
™
Scanner Use and Maintenance Guide
17

3. Pull the lter cartridge from the right rear underside of the scanner.
4. Remove the old lter from the cartridge, then replace with a new lter.
5. Return the lter cartridge to the right rear underside of the scanner, then
reconnect the power cord.
6. Power on the workstation when ready to resume use of the scanner.
Lambda LS xenon arc lamp
If the lamp does not power on when the power is turned on, check the line power fuse
to see if it has blown. The fuse is in a pry-out holder on the power input module on
the back of the lamp. A spare fuse is also provided in the power input module.
WARNING! Replace fuse with the same type and rating: 5 Amp, 250 V, 5 x
20 mm, time delay fuse (EIC 60127-2).
1. Unplug power cord from the back of the Lambda LS.
The slot is visible just under the edge of the fuse holder.
2. Use a small screwdriver, then pry the holder straight out of the power entry
module.
The fuse that is readily visible in the fuse holder when you take it out is the one
that is "active" when the holder is installed. A spare fuse is also stored within the
fuse holder, as shown in the following diagram.
Replace the
Lambda LS fuse
Chapter 3 Maintain the Instrument
Lambda LS xenon arc lamp
3
18
GeneTitan
™
Scanner Use and Maintenance Guide

3
4
1
2
5
6
1Power switch
2Pry here to remove the fuse holder
3Top view of the fuse holder
4Side view of the fuse holder
5Active fuse
6Press here for spare fuse
3. Press down on compartment end, then push it out of the other end. You can use
the old fuse to push out the spare fuse compartment.
4. Replace the active fuse with the spare, then reinstall the fuse holder and power
cord.
If the lamp fails to power on with the new fuse installed, call Technical Support.
After the normal life expectancy of the lamp has expired, the software application
alerts you to the requirement to replace the lamp. The lamp replacement procedure is
simple, but good health and safety precautions must be followed.
CAUTION! Do not try to replace the lamp when the scanner is in use or
powered on.
Lamp life/imaging device status notices
The System Setup pane displays lamp life and imaging device status notices for the
GeneTitan™ Scanner.
In normal operation, the pane displays the hours of life that is left in the lamp.
A red or yellow notice is displayed when the lamp life is geing short.
A red notice is also displayed when the imaging device is oine.
Xenon lamp
replacement
Chapter 3 Maintain the Instrument
Lambda LS xenon arc lamp
3
GeneTitan
™
Scanner Use and Maintenance Guide
19

Note: The 300-wa xenon lamp in the GeneTitan™ Scanner is warranted for 500
hours. The instructions to remove and replace the lamp are found in “Remove the
xenon lamp“ on page 20, and “Replace the xenon lamp“ on page 22. After changing
the lamp, you must manually reset the lamp life clock.
Remove the xenon lamp
WARNING! Power o the lamp using the switch in the rear of the unit and
then disconnect the power cord. Allow to cool before aempting to replace the
lamp.
1. Unscrew the 4 retaining bolts with your ngers.
1
1Remove these 4 bolts.
Chapter 3 Maintain the Instrument
Lambda LS xenon arc lamp
3
20
GeneTitan
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Scanner Use and Maintenance Guide