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.

Installation •5
Quick Overview of Hardware and Software Installation
Here is a brief outline of how to get started with your GenePix scanner. Detailed
instructions follow immediately below.
If you have purchased a GenePix scanner without the optional host computer:
1. Install the SCSI card (see below.)
2. Install GenePix Pro and attach the security key to parallel or USB port.
For all users:
3. Attach the GenePix scanner to the computer with the SCSI cable.
4. Attach the power cord to the GenePix scanner.
5. Turn on the GenePix scanner.
6. Turn on the computer.
Installing the SCSI Card
Included with your GenePix scanner is a SCSI adapter card for your host computer.
This card is used to transfer data and instructions between the host computer and
the GenePix scanner.
The SCSI card that is included with the GenePix scanner is a PCI-based
Plug’n’Play card from AdvanSys that will install easily on most computers. We
recommend that you use the included SCSI card.
To install the AdvanSys 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.
Chapter 2

6 •Installation
3. Remove the AdvanSys SCSI adapter 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 GenePix scanner yet.
5. Plug and Play operating systems such as Window 2000 and Windows XP
will automatically recognize the Advansys SCSI adapter and install the
correct driver.
6. Install GenePix Pro software (see below.)
7. Close Windows and turn off the computer. Attach the SCSI cable to the
SCSI adapter and the GenePix scanner (the scanner should also be powered
off; see below.)
8. Turn on GenePix scanner first and wait for approximately 15 seconds
before turning on computer.
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 a SCSI-2 device that
is 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. 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.
Installing the GenePix Pro Software
To install the GenePix Pro software, please consult the instructions in the GenePix
Pro manual.
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Installation •7
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 SCSI connector, please ensure that
your computer has been turned off, and that the GenePix scanner power is turned
off. Once the computer has been turned off, connect the 50-pin data cable between
the SCSI adapter of your computer and the GenePix scanner hardware. The SCSI
connector and power connector are located at the back of the GenePix scanner.
Once the SCSI connection has been made, connect the power cord to the GenePix
scanner. Turn on the power supply, and then turn on your computer.
Windows 2000 and Windows XP Installation
If the connections have been made correctly and GenePix Pro software has already
been installed, when you restart your computer Windows will show a message that
indicates that “New Hardware” has been detected. Windows 2000 will
automatically install the necessary driver for the GenePix scanner.
Windows XP requires that you manually install the driver using the Add New
Hardware Wizard. This wizard starts any time a new Plug and Play device is
detected. Working through the wizard, select the option to “Install the software
automatically (Recommended)”. Press Next and then press Finish when prompted.
Repeat the procedure seven additional times.
If you are connecting the GenePix scanner to a computer that was purchased with
the GenePix scanner, the driver is already installed.
Chapter 2

8 •Installation
Connecting the Security Key
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.
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 Professional 4200A scanner. If this
does not occur please verify the following items:
• The data 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 operational (see above).
• The GenePix SCSI ID 4 does not conflict with any other SCSI devices that
you may have already installed on your computer (e.g., a Jaz drive).
• The scanner power was turned on before booting the computer.
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Operation •9
Chapter 3
Operation
Inserting a Slide
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 slide holder to raise the top
half. With one finger, hold open the flat-spring positioner on the inside left edge of
the slide holder. Drop the slide face down into the slide holder frame. The slide
should be supported by the three sapphire balls on the frame. A slight flick of the
flat-spring positioner will ensure proper positioning of the slide. Do not push the
slide into position. Gently close the slide holder lid, 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.
Note: The slide holder is a precision component designed to ensure proper focusing
and field uniformity. Improper handling may damage the slide holder and affect
imaging performance. 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.
Chapter 3

10 •Operation
Functional Checkout
The Functional Checkout procedure is to help you confirm that your GenePix
Professional 4200A microarray scanner is performing according 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 instrument and then any time after
that if you wish to check the performance of the instrument.
The GenePix 4200A 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.
Installing Additional Filters
Your GenePix 4200A Professional scanner comes with one standard filter for each
installed laser. The standard filters are not accessible by the user. You can install
additional filters in any of the twelve remaining filter positions.
The installation process involves two steps:
1. Install the filters in the scanner;
2. Record the information for the new filters in GenePix Pro.
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Operation •11
1. Install the filter(s) in the scanner
Turn off power to the instrument before opening the filter wheel compartment.
1. Use a 5/32” hex wrench (provided with the optional filter kit) to access the
filter wheel compartment on the front of the scanner (Figure 1). Turn the
hex wrench counterclockwise to release the filter door latch. Pull the
handle to remove the filter cartridge (Figure 2).
Figure 1: Opening the filter compartment. Figure 2: Removing the filter cartridge.
2. Turn the wheel to align any open position with the hole in the top of the
filter cartridge. The number of that filter position is visible in the smaller
adjacent hole. Note the number of the filter position you will use: this
number must be recorded in GenePix Pro (see below).
3. Handle filters by the edges only. The rim of the filter is marked with an
arrow indicating the direction of light propagation through the filter. Drop
the filter into the hole with the arrow pointing down.
4. Using the cylindrical wrench, screw a lock-ring into the hole to gently
secure the filter. Do not over-tighten.
Figure 3: Tightening the lock-ring.
Chapter 3

12 •Operation
5. Repeat for any additional filters.
6. When you have installed all additional filters, insert the filter cartridge into
the instrument. Close the door and turn the hex key clockwise to secure
the latch.
2. Record the information for the new filters in GenePix Pro
1. Turn on the scanner and computer. If GenePix Pro is running, shut it down.
2. From the Windows Start menu, go to Programs / Axon Laboratory /
GenePix Pro / Filter Tool.
GenePix 4200A User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Operation •13
3. In the Filter Tool program, click the checkbox for the filter position you are
adding.
4. Enter the midpoint of the wavelength range that is transmitted by the filter.
For example, a 530DF30 filter transmits a 30 nm band of light centered at
530 nm (i.e,. it transmits 515 – 545 nm), therefore the midpoint of this filter
is entered as “530”. For a long-pass filter, enter the peak emission of the
dye you will use with that filter.
5. In GenePix Pro you can display either the filter’s Formal name (e.g.,
“530DF30”) or an Alternate name (e.g., “Alexa 488” or “Blue Filter”).
Enter both names here so that each user can choose their preferred
nomenclature in GenePix Pro.
6. After you have entered this information for each new filter, click Save.
7. Close the Filter Tool program.
When you open GenePix Pro, the new filters are listed in the Hardware Settings
dialog box.
Chapter 3