Axon GenePix Professional 4200A User manual

GenePix
®
Professional 4200A
MICROARRAY SCANNER
User’s Guide
Part Number 2500-0153 Rev C 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 37 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.............................................................. 4
Quick Overview of Hardware and Software Installation...................................... 5
Installing the SCSI Card........................................................................................ 5
Installing the GenePix Pro Software..................................................................... 6
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.............................................................................................. 9
Inserting a Slide..................................................................................................... 9
Functional Checkout ........................................................................................... 10
Installing Additional Filters ................................................................................ 10
Chapter 4 Imaging System Hardware................................................................ 15
Discussion of Hardware Components................................................................. 15
Optics .................................................................................................................. 15
Mechanical.......................................................................................................... 20
Electronic ............................................................................................................ 21
General Items of Interest..................................................................................... 22
Spatial Resolution ............................................................................................... 22
Table of Contents

iv •Table of Contents
Dynamic Range and Detection Limit..................................................................25
Specifications ...................................................................................................... 25
Technical Assistance.............................................................................................. 27
Warranty and Repair Service ..............................................................................29
Licensing Notice.....................................................................................................33
Declaration of Conformity.................................................................................... 35
Important Safety Information.............................................................................. 37
Index.......................................................................................................................57
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Introduction •1
Chapter 1
Introduction
The GenePix
®
Professional 4200A is the latest microarray scanner from Axon
Instruments. It has several enhanced features for high performance quantitative
imaging set by the benchmark GenePix 4000 series scanners. Key features of the
4200A are:
• 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;
• Full integration with GenePix Pro and Acuity 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.
Chapter 1

Installation •3
Chapter 2
Installation
About This User’s Guide
This User’s Guide focuses on the technical and theoretical aspects of the GenePix
Professional 4200A hardware. We recommend that you use this Guide in
conjunction with the GenePix Pro Software User’s Guide, and the on-line Help
within GenePix Pro (press <F1>). For information on setting up your GenePix
Professional 4200A scanner and software, please refer to Chapter 1. For a guided
tutorial on scanning your first slide, see Chapter 4 of the GenePix Pro Software
User’s Guide.
Computer Requirements
Please refer to the Axon Instruments website 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 Professional 4200A scanner onto a secure laboratory bench top
or reinforced table. The scanner weighs approximately 45 kg (99 lb) and requires
two persons to lift. 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
Always use the Park Scanner utility prior to moving the scanner, whether making a
short move to another location or when shipping the scanning long distance. The
Park Scanner utility is accessed by opening the GenePix Utilities program, which
can be found in the Start Menu / GenePix Pro menu or by directly running the
GP_Utilities.exe executable file located in the GenePix Pro installation directory.
Instructions:
1. Close GenePix Pro, if open and start GenePix Utilities program.
2. Press Park Scanner button.
3. Wait for status message indicating that scanner has been successfully
parked.
4. Immediately turn off scanner power; do not reopen GenePix Pro as this will
un-park the scanner.
5. Place one or two pieces of adhesive tape to secure the door closed.
Failure to park the scanner may result in misalignment or damage of the optical system.
Preparing to Install the GenePix Scanner
If you have purchased a GenePix scanner without the optional host computer please
follow the instructions below. If you purchased a GenePix scanner with a bundled
host computer, the necessary hardware and software are already installed. If so,
skip to “Connecting the GenePix Professional 4200A to the Computer”.
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.