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.

Installation •5
Failure to park the scanner before moving it may cause misalignment or damage to
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 Scanner to the Computer”.
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.
Chapter 2

6 •Installation
The SCSI card that is included with the GenePix scanner is a PCI-based
Plug’n’Play card from Iomega that installs easily on most computers. You must
use the included SCSI card for your GenePix Autoloader 4200AL.
To install the Iomega SCSI card:
1. The computer must have an available PCI slot.
2. Turn off computer and unplug the power cord.
3. Remove the computer cover according to the computer manufacturer’s
instructions.
4. Remove the Iomega 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.
5. Replace computer cover, plug in power cord and turn on the computer. Do
not connect GenePix scanner yet.
6. Plug and Play operating systems such as Window 2000 and Windows XP
will automatically recognize the Iomega SCSI adapter and install the
correct driver.
7. Install GenePix Pro software (see below.)
8. 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.)
9. 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
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Installation •7
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.
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.
Chapter 2

8 •Installation
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.
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.
GenePix Pro automatically detects the GenePix Autoloader 4200AL 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).
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Installation •9
• 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.
Chapter 2

Operation •11
Chapter 3
Operation
The Shipping-lock Slide Carrier
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.
See “Setting Up and Moving the GenePix Scanner” in Chapter 2.
To begin scanning you must first remove the shipping-lock slide carrier. Open
GenePix Pro and wait for the scanner to initialize. When the Status Bar reads
‘Ready’, click the Eject Slide Carrier button:
After the Status Bar has reported ‘Ejecting Slide Carrier’ and once again shows
‘Ready’, push the door and gently remove the slide carrier.
Chapter 3

12 •Operation
Loading the Slide Carrier
The slide carrier is numbered front to back from 1 to 36.
Insert slides with the arrayed surface facing towards position 1, and the bottom of
the slide pointing towards the left of the carrier (Fig.1):
Figure 1. GenePix Autoloader 4200AL Slide Carrier.
After loading all slides in the carrier, align the slides to the carrier's right-hand side.
This will make the position of the scan area consistent across all slides.
The slide carrier can accommodate slides that are between 0.9 mm and 1.1 mm
thick, including any labels. Thicker slides will get stuck in the slide carrier and will
cause slide handling failures due to the excessive force required to extract the slide
from the carrier. When in doubt, check to make sure that the slides move freely in
the slide carrier when they are seated.
Note: You can scan a single slide (using the Single scan type in GenePix Pro) from
any position, even with multiple slides in the carrier. However, the quickest
position for single slide scanning is position 36.
After scanning, multiple slide carriers can be stacked for easy storage of each batch.
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.

Operation •13
Note: Over time the sharp edges of glass slides may etch the inside surfaces of the
plastic slide carrier. If you begin to see handling failures in specific slide positions,
you should replace the slide carrier. We recommend replacing slide carriers after
approximately 30 batches.
Inserting the Slide Carrier
• Push gently on the top edge of the left-hand front door panel of the scanner
to open it.
• Insert the slide carrier back-end (i.e., position 36) first, with the front end
(i.e., position 1) towards you.
• Gently push the slide carrier until you feel a firm stop. The carrier should
be all the way inside the instrument. Do not force it.
• Close the door.
• The status bar will read “Mapping Slide Carrier” as GenePix Pro
automatically maps the positions of the slides in the carrier. A map of the
slides in the carrier is displayed. Before a scan, the slide positions are
colored as follows:
• Blue: slide is present and will be scanned.
• White: no slide is present.
• Gray: slide is present, but will not be scanned (see Single-
slideScanning or Configuring a Batch Scan below).
Single-slide Scanning
In Single scan mode, the Autoloader robot does not return the slide to the carrier
until you select Eject Slide Carrier, so the GenePix Autoloader scanner operates
very much like a manual GenePix scanner, such as the GenePix 4200A
Chapter 3

14 •Operation
Professional. You can perform Preview Scans, Data Scans, adjust scanner settings
from the Hardware Settings dialog box and stop and start scans as you like.
You can scan a single slide from any position in the slide carrier, even with
multiple slides in the carrier. However, the quickest position for single slide
scanning is position 36.
To do a Single Scan:
• Select Single from the Scan Type group on the right-hand side of the Batch
Scan tab.
• One slide position is selected (blue) on the slide carrier map. All other
mapped slides are gray. Select a slide to scan by clicking its position on the
Batch Scan tab.
• Set laser, filter and PMT parameters in the Hardware Settings dialog box.
• Click Preview Scan or Data Scan to scan the slide.
• When you are finished scanning, click the Eject Slide Carrier button on the
right-hand side of the GenePix Pro main window.
To begin a Batch Scan after using Single Scan mode, you must first Eject and
reinsert the slide carrier.
Batch Scanning
When doing a Batch Scan, the autoloader scanner scans all slides in the slide
carrier, without any user intervention. Because the scanner maps the slide carrier, it
scans only those positions containing slides.
Configuring a Batch Scan
There are two types of settings that you can make on the Batch Scan tab:
GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.