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.

Installation •5
Installing the SCSI Card
Included with your GenePix scanner is a SCSI card for your host computer. This
card is used to transfer data and instructions between the host computer and the
GenePix hardware.
The SCSI card that is included with your GenePix scanner is a PCI-based Plug-n-
Play card that will install easily on most computers. We recommend that you use
the included SCSI card.
To install the SCSI card:
1. The computer must have an available PCI slot.
2. Turn off computer and unplug the power cord. Remove the computer cover
according to the computer manufacturer’s instructions.
3. Remove the AdvanSys SCSI card from bag; do not touch the metal traces or
contacts, and carefully insert into the open PCI slot. Do not force into place, it
should go in with a gentle push. Screw the endplate to the chassis.
4. Replace computer cover, plug in power cord and turn on the computer. Do not
connect your GenePix scanner yet.
5. Plug-n-Play operating systems such as Window 2000 and Windows XP will
automatically recognize the Advansys SCSI card and install the correct driver.
For additional information, please refer to the manufacturer’s instructions included
with the card.
If you already have a SCSI card installed on your host computer and do not want to
replace it with the included SCSI card, you must verify that it is SCSI-2 and Win-
ASPI compliant. You must also ensure that you have the proper cabling to connect
the SCSI card to the GenePix scanner. While it is possible that an existing SCSI
card may work with the GenePix scanner, technical support is provided only for the
SCSI card that is bundled with the GenePix scanner.
Chapter 2

6 •Installation
If you are using the GenePix scanner on a computer with multiple SCSI devices
please ensure that there are no SCSI ID conflicts. At the factory, the GenePix
scanner SCSI ID is set to 4, permanently. If there is more than one SCSI device
attached on the same SCSI bus, either the ID of the conflicting device must be
changed or the device must be removed.
Installing the GenePix Pro Software
First, to be able to install GenePix Pro under Windows 2000 or Windows XP, a user
must be logged on as the Administrator.
The latest version of the GenePix Pro software is on the included CD-ROM.
Simply insert the CD-ROM into your computer and the installation program
automatically starts. If the installation program does not start automatically,
perhaps because you have the autorun feature of Windows disabled, you can
manually start the installation by running the Setup.exe program file on the
CD-ROM. This file is found in the GenePix subdirectory on the CD-ROM.
When the installer has finished, you will be given the choice of restarting or
shutting down your computer. Select the “Yes, I want to shut down my computer
now and install the hardware” option. Once your computer has shut down, proceed
below to “Connecting the GenePix scanner to the Computer”.
Connecting the GenePix Scanner to the Computer
Caution: Failure to follow these instructions in the correct order can lead to
damage to your instrument.
Before connecting the GenePix scanner to your computer, please ensure that both
your computer and GenePix scanner are turned off. Once the computer has been
turned off, connect the 50-pin SCSI cable between the SCSI card of your computer
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.

Installation •7
and the GenePix hardware. The SCSI connector and power connector are located at
the back of the GenePix scanner.
Once the SCSI connection has been made, check that the power is turned off, and
then connect the power cord to your GenePix scanner. First turn on your GenePix
scanner, and then turn on your computer.
Windows 2000 and Windows XP
If the connections have been made correctly, when you restart your computer
Windows will show a message that indicates that “New Hardware” has been
detected. Windows will automatically install the necessary driver for the GenePix
scanner.
If Windows does not automatically find the driver, you can manually select the
driver using the Add New Hardware Wizard. This wizard starts any time a new
Plug-n-Play device is detected. Working through the wizard, select the option to
“Search for the best driver for your device”. Press Next. Select the CD-ROM as
one of the locations to search for the driver. Press Next. Windows will now find
the correct driver for the GenePix scanner.
If you are connecting the GenePix scanner to a computer that was purchased with
the GenePix scanner, the driver is already installed.
Connecting the Security Key (Dongle)
The GenePix Pro software requires a security key to operate. If the key is absent
you will be able to open images in GenePix Pro, but you will not be able to save
your settings files or save your analysis results. In addition, you can analyze only
1000 features without a key.
To install the GenePix Pro key, please consult the instructions in the GenePix Pro
manual.
Chapter 2

8 •Installation
Starting GenePix Pro
After the successful installation of the software, you will find the entry “Axon
Laboratory / GenePix Pro” in your list of Programs in the Start menu, containing a
variety of GenePix Pro program icons. There are “GenePix Pro”, and “GenePix Pro
(Analysis Only)” entries in your Axon Laboratory group, and a shortcut icon to
GenePix Pro on your desktop. Both the “GenePix Pro” and “GenePix Pro
(Analysis Only)” icons will start GenePix Pro. The only difference between the two
is that the ‘Analysis Only’ version does not interact with the scanner hardware in
any way. All the image and data analysis functionality is fully usable in both
versions. Even if you are connected to a scanner, if you are just analyzing data and
are not doing any image acquisition then you should typically use the Analysis
Only version, as the instrument is inactive in this mode and hence laser lifetime will
be extended. For image acquisition, select “GenePix Pro”.
After the software has completed loading and the scanner has successfully
initialized, you will see a message in the bottom left corner of the software that
indicates “Eject position – the slide may be removed”. This message indicates that
the GenePix scanner has been initialized and you can insert your first slide!
Note: A user must belong to the Administrator or Power User group (also known
as “Standard user”) in order to run Internet Explorer (IE) scripts from the Reports
Tab in GenePix Pro. If a user does not have Standard user access, i.e., if they have
“guest” or “restricted user” access, the Windows environment does not allow such
users access to the scripting library required by IE, and therefore will encounter a
‘Library not registered’ error when running scripts in GenePix Pro.
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.

Installation •9
Troubleshooting Installation
SCSI Card Installation Problems
If you followed the above instructions and still require further assistance on
installation of the included SCSI card, contact Technical Support. If you are using
a SCSI card that was not provided with your GenePix scanner, you should contact
the supplier of that SCSI card for technical support.
GenePix Pro automatically detects the GenePix Personal 4100A scanner. If this
does not occur please verify the following items:
• The scanner power was turned on before booting the computer.
• The SCSI cable between the computer and the scanner is securely
connected.
• The GenePix scanner has power (the green power light at the front of the
scanner will be glowing).
• The SCSI card is properly seated in the computer.
• The GenePix SCSI ID 4 does not conflict with any other SCSI devices that
you may have connected to the same SCSI bus.
Chapter 2

Operation •11
Chapter 3
Operation
Inserting a Slide
Standard microscope slides (1" ×3"; 26 ×76 mm) can be used in GenePix scanners.
To scan a slide, first lift the door. The slide holder will move to its forward-most
position for loading. Gently lift the tab on the front of the slide holder to raise the
top half. With one finger, hold open the adjustment arm on the inside left edge of
the slide holder. Insert the slide face down into the slide holder frame with the top
edge towards the hinge of the slide holder. The slide should be supported by the
three sapphire balls on the frame. A slight flick of the adjustment arm will ensure
proper positioning of the slide. Do not push the slide into position. Gently close
the slide holder lid until it snaps shut, and close the door. You are now ready to
scan your sample. See “Image Acquisition” in the Tutorial section of the GenePix
Pro User’s Guide for scanning instructions.
Proper Use of Slide Holder
The slide holder retracts into the scanner when the scanner door is closed. Opening
the door will return the slide holder to the loading position. It takes a few moments
to fully eject the slide holder; do not open the slide holder before it has come to a
Chapter 3

12 •Operation
complete stop as this can cause misalignment. This type of misuse is evident when
scrapes or even paint from the scanner enclosure are found on the slide holder.
Misalignment of the slide holder caused by prematurely opening the slide holder
while the stage is still in motion can result in deterioration of scanner performance
and may require servicing.
The slide holder is a precision component designed to ensure proper focusing and
field uniformity. Never touch the slide holder while it is moving. Never force the
slide holder closed, or apply significant pressure to it for any reason. Do not rub or
scratch the sapphire balls.
Functional Checkout
The Functional Checkout procedure is to help you confirm that your GenePix
Personal 4100A microarray scanner is performing according to the specifications
set by Axon Instruments, Inc. A similar, but much more detailed procedure was
performed at the factory prior to shipping this unit to you. We recommend that you
follow the procedure once upon receiving the scanner and then again any time you
wish to check the performance of the scanner.
The GenePix 4100A microarray scanner has been designed to provide robust, long-
lived microarray scanning for years of normal use. However, if the images you
acquire on the GenePix scanner do not appear correct and if you believe there is a
problem with the scanner, it is important to follow these instructions before
contacting Technical Support:
1. Start the GenePix Pro software and click the Report tab.
2. Click the Functional Checkout link.
3. Follow the Functional Checkout procedure.
GenePix Pro automatically logs hardware performance into the Hardware
Diagnostics Report every two hours during operation.
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.

Operation •13
Moving or Shipping the Scanner
The scanning mechanism must be secured to protect it from damage prior to
moving or shipping the scanner. To “park” the scanner, follow these instructions:
a) Go to the Start/Programs/Axon Laboratory/GenePix Pro folder and select
GenePix Utilities as shown.
b) When it opens you will see the following screen:
Select “Park Scanner for Shipping”
Chapter 3

14 •Operation
c) A new pane will pop up that says “Parking the scanner, please wait” while
the slide holder is being parked:
d) When the slide holder is parked, a new window will appear stating that the
scanner has been parked.
Click “OK”
GenePix 4100A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices, Corp.