Agilent Technologies SureScan G4900DA User manual
Agilent G4900DA
SureScan Microarray Scanner System
Microarray Scan Control Software 9.1
User Guide
For Research Use Only. Not for use in diagnostic procedures.
Revision B0, September 2019
SureScan System User Guide
Notices
© Agilent Technologies, Inc. 2011-2013, 2015,
2019
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Manual Part Number
G4900-90000
Edition
Revision B0, September 2019
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051 USA
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Safety Notices
CAUTION
A CAUTION notice denotes a hazard. It
calls attention to an operating
procedure, practice, or the like that, if not
correctly performed or adhered to, could
result in damage to the product or loss
of important data. Do not proceed
beyond a CAUTION notice until the
indicated conditions are fully
understood and met.
WARNING
A WARNING notice denotes a hazard. It
calls attention to an operating
procedure, practice, or the like that, if
not correctly performed or adhered to,
could result in personal injury or death.
Do not proceed beyond a WARNING
notice until the indicated conditions are
fully understood and met.
This guide applies to the Microarray Scan
Control Software 9.1.3 or higher until
superseded.
SureScan System User Guide 3
In This Guide…
This user guide contains instructions to get started with, use, troubleshoot, and maintain your
SureScan Microarray Scanner System. The system is comprised of the SureScan microarray
scanner, computer workstation, and control and analysis programs.
1Introduction
This chapter describes the microarray scanner and preparation for its operation.
2Getting Started
In this chapter, learn how to operate the SureScan scanner safely and learn how to set up and
then scan slides with the Agilent Microarray Scan Control program.
3Using the Scan Control Program
This chapter describes how you use the Scan Control program to set up and run the scanner.
4Using Scan Control Tools
In this chapter, learn how to use commands in the Scan Control Tools menu. This chapter
includes how to set up scan protocols and scan regions, display log files, and select default
settings for the program.
5Maintaining and Troubleshooting Your System
This chapter describes maintenance procedures and tips, as well as error messages for
troubleshooting your system.
6Reference
This chapter includes descriptions of the Scan Control windows and dialog boxes. It also contains
scanner and slide specifications and regulatory compliance information.
SureScan System User Guide 4
Content
Contents
1 Introduction 8
A Powerful Tool for Microarray Analysis 9
System Description 10
Hardware and software features 10
Parts list 10
Computer system requirements 11
Scanner physical description 11
Site preparation 12
Safety guidelines 12
Principles of Operation 14
Slide positioning 14
Laser excitation 14
Scanning 14
Fluorescence detection 14
Programs Installed on the Computer Workstation 15
2 Getting Started 16
Operating the Scanner 17
Step 1. Turn on the SureScan scanner and start the Scan Control program 17
Step 2. Insert slides into slide holders 19
Step 3. Load the slide holders into the cassette 21
Step 4. Set or change protocol scan settings 23
Step 5. Add slides to the scan queue 23
Step 6. Scan your slides 24
Step 7. Remove the slides 24
About Scan Protocols 25
Offline Mode 26
Turning Off the SureScan Scanner 27
3 Using the Scan Control Program 28
Using the Slot Table 29
To change a Slide ID 29
To set or change the scan protocol 29
To change the output folder for a scan 30
SureScan System User Guide 5
To apply a selection to multiple slides 30
To add a slide to the scan queue 30
To add all slides to the queue 30
To move a slide in the queue 31
To remove a slide from the scan queue 31
To remove all slides from the scan queue 31
To open the scanner door 31
To close the scanner door 32
To start a scan 32
Changing Slide Scan Settings 33
To change settings for a single slide 33
To change settings for multiple slides 33
To add a description for the slide 34
To add a user name 34
4 Using Scan Control Tools 35
Creating and Changing Scan Protocols 36
To create a scan protocol 36
To change an existing scan protocol 36
To export a scan protocol 37
To import a scan protocol 37
To remove a scan protocol 38
Creating and Changing Scan Regions 39
To create a scan region 39
Change an existing scan region for non-Agilent slides 39
To export a scan region 40
To import a scan region 40
To remove a scan region 41
Adding a Barcode 42
To add a barcode 42
Turning on Lasers Manually 43
To turn on lasers 43
Troubleshooting Tools 44
To display recent errors 44
To display log files 44
To create a snapshot of the instrument state 44
To reset calibration warnings 44
To run a self test 45
Setting up Scanner Defaults 46
To set the default scan data folder 46
SureScan System User Guide 6
To set the laser saver delay 46
To set the location of the Feature Extraction program 46
To select to run Feature Extraction after scanning 47
Mapping Scan Protocols to Designs 48
To map a scan protocol to a slide design 48
5 Maintaining and Troubleshooting Your System 49
Maintaining Your System 50
Scheduled software maintenance 50
Scheduled hardware maintenance 50
Tips to prevent problems 51
Troubleshooting Your System 52
Technical Support 52
Frequently Asked Questions (FAQs) 53
Hardware Troubleshooting 54
Software Troubleshooting 55
File locations 56
System error messages 56
Using the Diagnostic Display 62
Updating the Scanner Firmware and Scan Control Program 63
To check if an update is available 63
To update the Scan Control program and firmware 63
To verify the software installation 64
6 Reference 65
Scan Control Program Window Reference 66
Scan Control main window 66
Tools menu 67
Help menu 68
Slot table 69
Function buttons 71
Settings pane 72
Log tabs 73
Scan Control Program Dialog Box Reference 74
Agilent Installation Qualification Tool 74
Export Scan Protocol dialog box 75
Export Scan Region dialog box 76
Input Barcode dialog box 76
Scan Protocol Editor dialog box 77
Scan Region Editor dialog box 82
SureScan System User Guide 7
Self Test dialog box 83
Settings dialog box – General Settings 84
Settings dialog box – Design To Protocol Mapping 85
About Adding Slides 87
Performing Feature Extraction on Scanned Images 88
SureScan Scanner Specifications 89
Slide Specifications 91
Scan dimensions 91
Glass specifications 91
Barcode and barcode label specifications 91
Regulatory Information 94
SureScan System User Guide 9
A Powerful Tool for Microarray Analysis
The SureScan scanner is part of the SureScan system solution from Agilent Technologies. The
scanner is a sophisticated laser-induced fluorescence scanner designed to read microarrays
printed on standard 1 in 3 in slides.
The scanner measures the fluorescence intensity of labeled sample nucleic acid (DNA and RNA)
bound to microarrays. Its ability to measure fluorescence from two dyes simultaneously
facilitates all two-color microarray studies. This technology provides for rapid, high-quality,
automated scanning of microarrays.
Figure 1 SureScan scanner
Each slide is scanned in minutes, and the files are prepared for feature extraction analysis.
SureScan System User Guide 10
System Description
In this section you find listings of hardware and software features, parts, and computer
requirements. A physical description of the SureScan scanner and information on site preparation
and safety are also provided.
Hardware and software features
The SureScan scanner provides the following features:
•Dynamic autofocus
•Single and dual color scanning
•Automatic PMT gain calibration before each scan
•2-, 3-, 5-, or 10-micron pixel size
•Dynamic range of >104for a single scan in 16-bit scan mode, >105 for a single scan in 20-bit
scan mode, and >106for a dual scan in 16-bit scan mode (XDR)
•Uniformity specification of <5% CV (Coefficient of Variation)
•TIFF image file compression
•Flip and rotate images
•Internal and external barcode reading
The Agilent Microarray Scan Control program allows you to select the dye (fluorescence)
channels, scan regions, resolution, dynamic range, PMT gain, and output folders for each of the
slides in the cassette. You can load these settings automatically from saved application-specific
protocols, or set them manually in the slot table.
Parts list
The G4900DA SureScan microarray scanner system consists of the following components:
•G2600D SureScan scanner with integral 24-slide cassette
•24 slide holders
•Computer workstation with recovery software on CD
•Power cords and network cable
•Agilent Microarray Scan Control Software installed
•Agilent Feature Extraction Software installed
•Agilent Installation Qualification Tool Software installed
•Declaration of Conformity
SureScan System User Guide 11
Computer system requirements
The SureScan Microarray Scanner System comes with a computer that meets or exceeds the
following configuration. Agilent Technologies supports only the computer provided with the
system.
Software
•Windows 7 64-bit Professional or Windows 10 64-bit Pro operating system
Hardware
•Intel Core 2 Duo E8500 3.16 GHz or equivalent
•8 GB RAM
•Minimum 250-GB hard disk. (Proper disk maintenance is required to ensure that you always
have available disk space for data generation. See Table 11 on page 78 for estimated sizes of
scanned images.)
Scanner physical description
Scanner front view
Figure 2 SureScan scanner, front view
Power On/Off
Door
Status indicator light
Removable front panel
SureScan System User Guide 12
Scanner rear view
Figure 3 SureScan scanner, rear view
Site preparation
Make sure that the environment meets the “SureScan Scanner Specifications” on page 89 of
Chapter 6. If you have any questions, contact your local Agilent sales and support center or
www.agilent.com.
Safety guidelines
The SureScan scanner is designed for safety and ease of use. Be sure that you understand and
observe all the warnings and cautions before operating the SureScan scanner.
Power fuse
Power plug
LAN connector
Laser cooling
air outlet
Laser cooling
air inlet
Main cooling
air outlet
Main cooling
air inlet
Power supply
air outlet
WARNING Do not attempt to repair or gain access to SureScan scanner internal components. You
risk exposure to high voltage and harmful laser radiation. Removing the main cover
voids the warranty
WARNING Connect the SureScan scanner to a grounded power outlet. It relies on a protective earth
ground for safety.
CAUTION In order to minimize vibration due to the rapid scanning of the laser excitation across the
microarray, install the scanner on a sturdy lab bench or table. Do not install the scanner in
proximity to other lab equipment that might cause vibration.
SureScan System User Guide 14
Principles of Operation
This section describes the operating features of the SureScan scanner.
Slide positioning
The SureScan scanner holds up to 24 1 in 3 in slides in a nonremovable cassette. During
scanning, the slides are sequentially transported into scanning position, scanned, and then
returned to the cassette. Slides can be added to and removed from the scanner queue
dynamically without stopping the scanner.
Laser excitation
The SureScan scanner uses two lasers; a green diode-pumped solid-state laser (532 nm) and a
red diode laser (640 nm). The lasers excite Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5) labeled RNA or
DNA to measure fluorescence after hybridization of the target nucleic acid to the microarray
probes. Dyes similar to Cy-3 and Cy-5, such as Alexa 647, 555, and 660 dyes, can also be used.
The SureScan scanner is optimized for high signal-to-noise performance in the Cy-3
(550 – 610 nm) and Cy-5 (650 — 750 nm) emission bands. It has a wide dynamic range and low
spectral crosstalk, allowing for measurement of a broad range of target concentrations and for
higher data confidence at lower signal levels.
Scanning
The laser excitation is scanned rapidly up and down across the microarray. The dynamic
autofocus ensures that the microarray is always positioned in the focal plane of the scan lens,
resulting in a uniform and calibrated-intensity scan.
Fluorescence detection
Fluorescence from the labeled samples is converted to an electrical signal by a high-performance
PMT. Very low noise amplifiers and digital integrators process the PMT signal into a digital
measurement that is recorded in the TIFF file.
SureScan System User Guide 15
Programs Installed on the Computer Workstation
The computer that is included with your SureScan Microarray Scanner System has the following
software programs preinstalled.
Agilent Microarray Scan Control program – used to set up and operate the scanner.
Agilent Feature Extraction program – automatically performs feature extraction using scanned
image files created by the scanner. You can also run the Feature Extraction program manually to
examine images and set up feature extraction options.
Agilent Installation Qualification Tool program – verifies that the Scan Control program was
installed correctly and was not corrupted after installation. Produces an Installation Qualification
Report for your records.
SureScan Microarray Scanner System
User Guide
16
2 Getting Started
Operating the Scanner 17
Step 1. Turn on the SureScan scanner and start the Scan Control program 17
Step 2. Insert slides into slide holders 19
Step 3. Load the slide holders into the cassette 21
Step 4. Set or change protocol scan settings 23
Step 5. Add slides to the scan queue 23
Step 6. Scan your slides 24
Step 7. Remove the slides 24
About Scan Protocols 25
Offline Mode 26
Turning Off the SureScan Scanner 27
This chapter describes how to operate the scanner, including how to set up and scan your slides
quickly and easily.
If you have any problems, see Chapter 5 for troubleshooting information.
SureScan System User Guide 17
Operating the Scanner
The following steps explain how to operate the scanner. For more information on how to use the
Scan Control program, see Chapter 3, “Using the Scan Control Program,”.
Step 1. Turn on the SureScan scanner and start the Scan Control
program
1Turn on the scanner using the power switch on the front of the instrument. After you turn on
the scanner, the scanner loads and initializes its firmware.
When the scanner is ready (about two minutes), the status indicator light turns off.
2Turn on the computer workstation and wait for it to boot up.
3Double-click the Agilent Microarray Scan Control icon to start the Scan Control program.
Or
Click Start > All Programs > Agilent > Agilent Microarray Scan Control.
Figure 4 Agilent Microarray Scan Control icon
When the program starts, the Agilent Microarray Scan Control program main window opens
and the scanner performs its initialization sequence. See “Scan Control main window” on
page 66.
•The Scan Control program communicates with the scanner via the LAN cable, sending
commands and parameters, and receiving status and data.
•The lasers turn on and start to warm up.
•The autoloader initializes and performs a slide eject cycle (to make sure that no slide is
loaded).
•The scanning system is initialized and the data acquisition system is calibrated.
After the initialization sequence finishes, the Open Door button is enabled and you can load
slides.
NOTE To learn how to set up the lasers to turn off automatically when not in use, see
“To set the laser saver delay” on page 46.
NOTE If the scanner has 24 slides loaded when you turn it on, the initialization will fail
because it cannot perform the slide eject cycle.
SureScan System User Guide 18
For more information on the Scan Control program window, see “Scan Control Program
Window Reference” on page 66.
Figure 5 Agilent Microarray Scan Control program window – ready to add slides
The status of the scanner is indicated at the lower right corner of the Scan Control window, in
the status bar.
Initialize The scanner is initializing. When the initialization is finished, the Open Door button is enabled,
and the lasers continue to warm up.
WarmUp The lasers typically take less than 30 seconds to warm up. During warm-up, you can load
slides, set protocols, and add slides to the queue. Once the lasers are warmed up, you can start
scanning.
LasersOff Indicates that the lasers are turned off.
Ready You can load slides or begin a scan.
Error Indicates that the scanner has encountered an error. Close the Scan Control program then
shut off the scanner. Restart the scanner and the Scan Control program. If the error continues,
contact Agilent technical support.
SureScan System User Guide 19
Step 2. Insert slides into slide holders
A slide is inserted into a slide holder before loading it into the scanner.
1Before you insert the slide, place the slide holder on a flat surface, with the clear cover facing
up, and the tab on the right. This helps to ensure that you have the slide aligned properly when
you insert it into the slide holder.
2Gently push in and pull up on the tabbed end of the clear plastic cover to open it.
Figure 6 Opening the slide holder
Figure 7 Inserting slide into the slide holder
3Insert the slide into the holder, as follows:
aHold the slide at the barcode end.
bMake sure that the active microarray surface faces up, toward the slide cover, with the
barcode on the left.
NOTE You cannot start scanning until both lasers are warmed up, at least one slide is
in the queue, and the scanner status is Ready.
NOTE Fingerprints cause errors in the fluorescence detection. For accurate readings,
touch only the edges of the slide and always use gloves when handling slides.
Also, do not write on the slides with markers or place any labels on the slide
other than an appropriate barcode.
Slide ledge
SureScan System User Guide 20
cCarefully place the end of the slide without the barcode label onto the slide ledge. See
Figure 7.
dGently lower the slide into the slide holder. See Figure 8.
eClose the plastic slide cover, pushing on the tab end until you hear it “click”. This moves the
slide into position in the holder.
fGently push in and pull up on the tabbed end of the clear plastic cover to open it again and
verify that the slide is correctly positioned.
Once inserted, the slide lies flat and matches up with the alignment points on the slide
holder.
gClose the plastic slide cover, pushing on the tab end until you hear it “click”. See Figure 9.
Figure 8 Slide inserted in slide holder
Figure 9 Slide holder – closed with slide
For instructions on removing the slides, see “Step 7. Remove the slides” on page 24.
Agilent slides have two barcodes, one on each side of the glass. See Figure 10. Typically,
non-Agilent slides have only one barcode. For both Agilent and non-Agilent slides, place the active
microarray side of the slide facing toward the slide holder cover.
If you have a slide whose active surface is on the side opposite to the barcode, the scanner
cannot read the barcode.
NOTE See “Barcode and barcode label specifications” on page 91 to apply a second
readable barcode.
CAUTION An improperly inserted slide can damage the scanner.
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