Axon GenePix Autoloader 4200AL User manual

GenePix
®
Autoloader 4200AL
MICROARRAY SCANNER
User’s Guide
Part Number 2500-0165 Rev B August 2005 Printed in USA
Copyright 2005 Axon Instruments / Molecular Devices Corp.
No part of this manual may be reproduced, stored in a retrieval system, or
transmitted, in any form or by any means, electronic, mechanical, photocopying,
microfilming, recording, or otherwise, without written permission from Molecular
Devices Corp.
QUESTIONS? See Axon’s Knowledge Base: http://support.axon.com

i
P LEASE READ !!!!! SAFETY
There are important safety issues that you must take into account when using this
instrument. Please carefully read the safety warnings starting on page 45 before
you use this instrument.
VERIFICATION
This instrument is extensively tested and thoroughly calibrated before leaving the
factory. Nevertheless, researchers should independently verify the basic accuracy
of the instrument using suitable test samples.
WARNING
If this equipment is used in a manner not specified by the manufacturer, the
protection provided by the equipment may be impaired.
DISCLAIMER
This equipment is not intended to be used, and should not be used, in human
experimentation or applied to humans in any way.
Verification, Warning, Disclaimer

Table of Contents •iii
Table of Contents
Chapter 1 Introduction.......................................................................................... 1
Chapter 2 Installation............................................................................................ 3
About This User’s Guide....................................................................................... 3
Computer Requirements........................................................................................ 3
Setting Up and Moving the GenePix Scanner....................................................... 4
Preparing to Install the GenePix Scanner.............................................................. 5
Quick Overview of Hardware and Software Installation...................................... 5
Installing the SCSI Card........................................................................................ 5
Installing the GenePix Pro Software..................................................................... 7
Connecting the GenePix Scanner to the Computer............................................... 7
Windows 2000 and Windows XP Installation ...................................................... 7
Connecting the Security Key................................................................................. 8
Troubleshooting Installation ................................................................................. 8
SCSI Card Installation Problems........................................................................... 8
Chapter 3 Operation............................................................................................ 11
The Shipping-lock Slide Carrier ......................................................................... 11
Loading the Slide Carrier.................................................................................... 12
Inserting the Slide Carrier ................................................................................... 13
Single-slide Scanning.......................................................................................... 13
Batch Scanning.................................................................................................... 14
Configuring a Batch Scan ................................................................................... 14
Setting PMT Gain Automatically........................................................................ 16
Email Notification............................................................................................... 17
Batch Analysis .................................................................................................... 17
Batch Scan Log File............................................................................................ 17
Table of Contents

iv •Table of Contents
Functional Checkout............................................................................................ 17
Installing Additional Filters................................................................................. 18
GenePix Utilities ................................................................................................. 22
Park Scanner For Shipping.................................................................................. 22
Release Magazine Lock....................................................................................... 22
Open Robot Grippers........................................................................................... 23
Calibrate Focus.................................................................................................... 23
Save EEPROM Image......................................................................................... 23
Chapter 4 Imaging System Hardware................................................................ 25
Discussion of Hardware Components................................................................. 25
Optics .................................................................................................................. 25
Mechanical .......................................................................................................... 30
Electronic ............................................................................................................ 31
General Items of Interest..................................................................................... 31
Spatial Resolution................................................................................................ 31
Dynamic Range and Detection Limit.................................................................. 32
Specifications ...................................................................................................... 33
Technical Assistance.............................................................................................. 35
Warranty and Repair Service ..............................................................................37
Licensing Notice.....................................................................................................41
Declaration of Conformity.................................................................................... 43
Important Safety Information.............................................................................. 45
Index....................................................................................................................... 65
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Introduction •1
Chapter 1
Introduction
The GenePix Autoloader 4200AL is the latest microarray scanner from Axon
Instruments, Inc. It has several enhanced features for high-performance
quantitative imaging set by the benchmark GenePix 4000 series scanners. Key
features of the 4200AL are:
• Automatically loads, scans and analyzes up to 36 slides.
• Convenient all-in-one scan, stack-and-store slide carrier.
• Line-by-line dynamic autofocusing for unprecedented field uniformity.
• Up to four internally installed laser excitation sources.
• Gradient neutral density wheel permitting 5–100% laser transmission.
• Data Scan resolution from 5 µm to 100 µm.
• Fast Preview Scan at 40 µm.
• Uses 16-bit ultra-low noise digitization.
• Dynamic range of 10
4
.
• Easy-access 16-position emission filter wheel with standard filters for each
laser installed at the factory.
Chapter 1

2 •Introduction
• Full integration with GenePix Pro Microarray Analysis Software and
Acuity Microarray Informatics software.
Axon Instruments has consulted widely among the scientific pioneers of microarray
techniques to produce an instrument that fulfills all their image acquisition and
primary analysis needs.
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Installation •3
Chapter 2
Installation
About This User’s Guide
This User’s Guide focuses on the technical and theoretical aspects of the GenePix
Autoloader 4200AL scanner. We recommend that you use this Guide in
conjunction with the GenePix Pro Software User’s Guide, and the on-line Help in
GenePix Pro (press <F1>).
For information on setting up your GenePix Autoloader 4200AL scanner and
software, please refer to this chapter.
For a guided tutorial on scanning your first slide, see Chapter 3 of this manual, and
Chapter 4 of the GenePix Pro Software User’s Guide.
Computer Requirements
Please refer to the Axon Instruments web site for up-to-date information.
Should you choose to purchase your own computer, Axon recommends that due
consideration be made for the selection of a quality supplier and/or components.
Chapter 2

4 •Installation
Setting Up and Moving the GenePix Scanner
Placement
Place the GenePix Autoloader 4200AL scanner on a secure laboratory bench top or
reinforced table. The scanner weighs more than 50 kg (110 lb) and requires two
people to lift it. There are four recessed hand spaces underneath the scanner to
assist lifting. Carefully place the scanner into its final position; do not slide it into
position as this may result in internal damage or misalignment of the optics.
Moving the Scanner
The GenePix Autoloader 4200AL scanner is delivered to you in the “Park”
position, using a slide carrier modified specifically to secure the robot arm for
shipping. This shipping-lock slide carrier has a plastic slide glued into position 36.
Do not attempt to remove the plastic slide. Do not use this slide carrier for routine
scanning, but save it, as it must be in the scanner whenever the scanner is moved.
Always use the Park Scanner utility prior to moving the scanner, whether making a
short move to another location or shipping the scanner a long distance.
Open the Park Scanner utility from the GenePix Utilities program, which can be
found in the Start Menu / Axon Laboratory / GenePix Pro group.
Note: GenePix Pro must be closed before opening the GenePix Utilities program.
To park the scanner:
1. Close GenePix Pro, and start GenePix Utilities.
2. Select the Park Scanner for Shipping button.
3. When prompted by the software, insert the shipping lock slide carrier into
the scanner, and close the scanner door.
4. Wait for the status message indicating that scanner has been parked
successfully.
5. Immediately turn off scanner power. Do not reopen GenePix Pro, as this
automatically un-parks the scanner.
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.