Agilent Technologies SureScan G4900DA Manuel utilisateur
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superseded.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
Table des matières
