Axon GenePix Personal 4100A User manual

GenePix
®
Personal 4100A
MICROARRAY SCANNER
User’s Guide
Part Number 2500-0142 Rev E 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 Axon
Instruments / Molecular Devices Corp.
QUESTIONS? See Axon's Knowledge Base: http://support.axon.com

i
Please 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 29 before
you use this instrument.
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.
COPYRIGHT
The information in this Guide is copyrighted and must not be reproduced in any
form whatsoever without written permission from Axon Instruments / Molecular
Devices Corp.
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, Disclaimer, Copyright, Verification

Table of Contents •iii
Table of Contents
Chapter 1 Introduction............................................................................................... 1
Chapter 2 Installation................................................................................................ 3
Computer Requirements........................................................................................ 3
Preparing to Install your GenePix Scanner ........................................................... 3
Quick Overview of Hardware and Software Installation ...................................... 4
Installing the SCSI Card........................................................................................ 5
Installing the GenePix Pro Software ..................................................................... 6
Connecting the GenePix Scanner to the Computer............................................... 6
Windows 2000 and Windows XP ..................................................................... 7
Connecting the Security Key (Dongle) ................................................................. 7
Starting GenePix Pro............................................................................................. 8
Troubleshooting Installation.................................................................................. 9
SCSI Card Installation Problems....................................................................... 9
Chapter 3 Operation ............................................................................................... 11
Inserting a Slide................................................................................................... 11
Proper Use of Slide Holder ............................................................................. 11
Functional Checkout............................................................................................ 12
Moving or Shipping the Scanner......................................................................... 13
Chapter 4 Imaging System Hardware...................................................................... 17
Discussion of Hardware Components................................................................. 17
Optics .............................................................................................................. 17
Mechanical ...................................................................................................... 21
Table of Contents

iv •Table of Contents
Electronic......................................................................................................... 21
Performance Factors............................................................................................ 22
Spatial Resolution............................................................................................ 22
Dynamic Range and Detection Limit.............................................................. 25
Specifications .................................................................................................. 26
Technical Assistance................................................................................................ 27
Important Safety Information.................................................................................... 29
Declaration of Conformity......................................................................................... 49
Warranty and Service............................................................................................... 51
Licensing Notice....................................................................................................... 53
Index ........................................................................................................................ 55
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.

Introduction •1
Chapter 1
Introduction
About This User’s Guide
This User’s Guide focuses on the technical and theoretical aspects of the GenePix
®
Personal 4100A 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>).
Chapter 1

2 •Introduction
GenePix Personal 4100A Features
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.
The GenePix Personal 4100A scanner has the same high-performance quantitative
imaging as the benchmark GenePix 4000B scanner. Key features of the 4100A are:
• Scans microarray slides sequentially at up to two wavelengths.
• Has precisely controlled laser temperature and pixel-by-pixel laser
correction to compensate for normal variation in laser intensity.
• Uses 16-bit digitization.
• Has a dynamic detection range of four orders of magnitude.
• Has two standard filters, and capacity for up to six custom filters.
• Includes line-averaging mode for enhanced signal-to-noise ratio.
• Offers two scanning modes: Preview Scan at 40-µm resolution and Data
Scan at 5, 10, 20, 40, 60, 80, and 100-µm resolutions.
• Full integration with GenePix Pro software.
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.

Installation •3
Chapter 2
Installation
Computer Requirements
Please refer to the Axon Instruments website (www.axon.com) 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.
Preparing to Install your GenePix Scanner
If you have purchased a GenePix Personal 4100A scanner without the optional host
computer please follow all of the instructions below. If you purchased your
GenePix scanner with a bundled host computer, the necessary hardware and
software are already installed. If so, skip to “Connecting the GenePix scanner to
the Computer” on page 6.
Chapter 2

4 •Installation
Quick Overview of Hardware and Software Installation
For users who require a minimal level of detail, the following outlines the steps
necessary to install GenePix hardware and software. Detailed instructions follow
immediately after.
Caution: If you do not follow the instructions in the order specified below you
may damage your instrument.
Important: Initially, do not attach the GenePix scanner to your computer.
If you have purchased a GenePix scanner without the optional host computer:
1. Install the SCSI card.
2. Turn on the computer.
3. Install GenePix Pro.
For all users:
4. Shut down the computer.
5. Attach the GenePix scanner to the computer with the SCSI cable.
6. Attach the power cord to the GenePix scanner.
7. Turn on the GenePix scanner.
8. Attach the security key (dongle) to the USB or parallel port of your computer.
9. Turn on the computer.
10. Windows will automatically find the scanner and install the appropriate driver.
11. Start GenePix Pro using the GenePix Pro icon on the desktop.
12. Start scanning!
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.