Roche Nimblegen MS 200 User manual

Table of Contents
Prologue .......................................................................................................................i
I. Revision History.................................................................................................... i
II. Contact Addresses................................................................................................ i
III. Certificate of Conformity..................................................................................ii
IV. Warranty ............................................................................................................ii
V. Trademarks .........................................................................................................ii
VI. Intended Use...................................................................................................... ii
VII. License Statements for the Instrument ...........................................................ii
VIII. Software License Agreement ..........................................................................ii
IX. Preamble ...........................................................................................................iii
X. Use of the Instrument Operator’s Manual .......................................................iii
XI. Conventions Used in this Manual ................................................................... iv
XII. Warnings and Precautions .............................................................................. v
XIII. Disposal of the Instrument and Consumables............................................ vii
AOverview................................................................................................................. 1
1. Introduction......................................................................................................... 1
2. Specifications ....................................................................................................... 6
2.1 Specifications of the Microarray Scanner ................................................ 6
2.2 Specifications of the Control Unit............................................................ 8
2.3 Specifications for Microarray Slides......................................................... 8
B System Description............................................................................................ 11
1. System Packages................................................................................................. 11
2. System Description............................................................................................ 12
2.1 Description of the Instrument................................................................ 12
2.2 Slide Magazine......................................................................................... 13
2.3 Slide Magazine Box ................................................................................. 14
3. Installation ......................................................................................................... 19
3.1 Installation Warning and Recommendation......................................... 19
3.2 Unpacking the Instrument ..................................................................... 19
3.3 Space and Power Requirements ............................................................. 19
3.4 Environmental Requirements ................................................................ 20
3.5 Installation of the Control Unit.............................................................. 21
3.6 Installation of the Instrument Software................................................. 21
3.7 Starting the Control Unit, Microarray Scanner, and Instrument
Software ................................................................................................... 25
3.8 Performing System Verification: The Initial ILC Test .......................... 27
C Operation..............................................................................................................31
1. Introduction....................................................................................................... 31
2. Using the Instrument Software: A Typical Scanner Experiment ................... 31
3. Starting the Instrument Software ..................................................................... 32

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3.1 Understanding Sessions ..........................................................................35
3.2 Using the Help Viewer ............................................................................37
3.3 Setting Software Options.........................................................................38
4. Specifying Parameters........................................................................................39
4.1 Working with the Magazine Control .....................................................39
4.2 Specifying Scan Parameters.....................................................................41
5. Specifying Image File Settings ...........................................................................46
6. Specifying Scan, Barcode, and Autogain Areas ................................................48
7. Starting and Aborting a Scan.............................................................................58
7.1 Before You Start the Scan........................................................................58
7.2 Starting a Scan .........................................................................................58
7.3 Aborting a Scan........................................................................................60
7.4 Saving Log Files........................................................................................60
8. Reviewing Images...............................................................................................61
8.1 Displaying an Image ................................................................................61
8.2 Zooming in and out ................................................................................61
8.3 Displaying Intensity Data for a Feature..................................................62
8.4 Adjusting Image Appearance ..................................................................62
8.5 Displaying a Histogram or Line Profile..................................................63
8.6 Choosing the Channel(s) to Display ......................................................66
D Maintenance and Care ..........................................................................................67
1. ILC Test ..............................................................................................................67
2. Liquid Spill Cleanup ..........................................................................................68
3. Ozone Filter Replacement .................................................................................68
4. Instrument Relocation.......................................................................................68
5. Instrument Disinfection ....................................................................................70
EAppendix ...............................................................................................................73
1. Troubleshooting.................................................................................................73
2. Ordering Information........................................................................................79
3. Quick Start .........................................................................................................80
3.1 Starting the Scanner, Control Unit, and Instrument Software .............80
3.2 Loading Microarray Slides ......................................................................81
3.3 Specifying Parameters .............................................................................81
3.4 Scanning...................................................................................................81
3.5 Reviewing Images ....................................................................................82
3.6 Instrument Software Workspace ............................................................82
4. Index...................................................................................................................84

Prologue
I. Revision History
Version Revision Date
1.0 April 2009
© Copyright 2009, Roche NimbleGen, Inc. All rights reserved. Information
in this document is subject to change without notice. No part of this
document may be reproduced or transmitted in any form or by any means,
electronic or mechanical, for any purpose, without the express written
permission of Roche NimbleGen, Inc.
Questions or comments regarding the contents of this manual can be
directed to your Roche NimbleGen Account Manager or Roche Microarray
Technical Support. Go to www.nimblegen.com/arraysupport for contact
information.
Every effort has been made to ensure that all the information contained in
the NimbleGen MS 200 Microarray Scanner Operator’s Manual is correct at
the time of printing. However, Roche NimbleGen, Inc. reserves the right to
make any changes necessary without notice as part of ongoing product
development.
II. Contact Addresses
Manufacturer Tecan Austria GmbH
Untersbergstrasse 1A
A-5082 Grödig/Salzburg
AUSTRIA/EUROPE
Distribution Roche Diagnostics GmbH
Sandhofer Straße 116
D-68305 Mannheim
GERMANY

ii | NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0
III. Certificate of Conformity
Provided with the NimbleGen MS 200 Microarray Scanner.
IV. Warranty
For warranty and service information, contact your Roche NimbleGen
Account Manager. Go to www.nimblegen.com/arraysupport for contact
information.
V. Trademarks
NIMBLEGEN is a trademark of Roche. Other brands or product names are
trademarks of their respective holders.
VI. Intended Use
The NimbleGen MS 200 Microarray Scanner is designed to read
fluorescently labeled DNA microarrays on 1 x 3 inch standard glass
laboratory slides for experiments in research laboratories. This Microarray
Scanner is intended for life science research only.
VII. License Statements for the
Instrument
Any patents or patent applications are owned by the original equipment
manufacturer.
VIII. Software License Agreement
An envelope containing all license and end user agreements is packaged with
the NimbleGen MS 200 Microarray Scanner. Please observe all statements
made in these documents.

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | iii
IX. Preamble
Read this entire manual before operating the NimbleGen MS 200
Microarray Scanner. This document is intended as instructions for use for
the Microarray Scanner. It provides information about:
Installation
Operation
Maintenance and care
Troubleshooting
X. Use of the Instrument Operator’s
Manual
This Operator’s Manual describes the operation of the NimbleGen MS 200
Microarray Scanner and contains the following chapters:
Chapter A, Overview, provides an introduction to the instrument’s
capabilities and specifications for the instrument, control unit, and
microarray slides.
Chapter B, System Description, contains a description of the instrument’s
components and consumables and instructions on the installation of the
instrument and software.
Chapter C, Operation, describes the operating procedures for the
instrument.
Chapter D, Maintenance and Care, describes the maintenance procedures
that are required for the instrument.
Chapter E, Appendix, contains troubleshooting and ordering information of
the instrument and its accessories and consumables. It also provides a quick
start guide to help you get started using the Microarray Scanner quickly.

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XI. Conventions Used in this Manual
Text Conventions
To impart information that is consistent and memorable, the following text
conventions are used in this Operator’s Manual:
Convention Description
Numbered listing Steps in a procedure that must be performed in the order listed.
Italic type, blue Points to a different chapter in this Operator’s Manual to consult or
to a web site.
Italic type
Identifies the names of controls (checkboxes, option buttons, etc.)
in dialog boxes, windows, or message boxes in the instrument
software.
Bold type Identifies buttons and menu names when operating the instrument
software.
Underscore and
brackets
A placeholder for information such as in the actual name of a
directory in a path is enclosed in brackets, e.g. <install path>.
Placeholders (for file names, numbers, dates, etc.) are separated by
an underscore ( _ ), e.g. <Barcode>_<User Text>_<Laser WL>.
Symbols
The following types of notices may be used in this manual to highlight
important information or to warn the operator of a potentially dangerous
situation:
Symbol Description
Note. Gives helpful information.
STOP
Caution: Possibility of instrument damage or data loss if instructions are not
followed.
Warning – Risk of Danger. Risk of personal injury to the operator or a safety
hazard to the instrument or surrounding area.

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | v
Biohazard. Precautions must be taken when working with potentially
infectious material.
Laser. Do not stare into the beam!
Flammable Materials and Risk of Fire. Proper laboratory safety precautions
must be observed.
Proper disposal. Directive 2002/96/EC on waste electrical and electronic
equipment (WEEE). Negative environmental impacts associated with the
treatment of electrical and electronic equipment waste.
Do not treat electrical and electronic equipment as unsorted municipal
waste.
Collect waste electrical and electronic equipment separately.
It is important to understand and follow all laws regarding the safe and
proper disposal of electrical instrumentation. Contact Roche Microarray
Technical Support for information on proper disposal. Follow your
institutional requirements for disposal of the accessories.
XII. Warnings and Precautions
Handling Requirements
The Microarray Scanner must be used by only trained and skilled personnel.
It is essential that the following safety information required for installation
and operation of the Microarray Scanner is carefully read and observed.
Ensure that this safety information is accessible for every employee working
with the Microarray Scanner.
Always follow basic safety precautions during use to reduce the risk of
injury, laser radiation, or electrical shock.
Read and understand all information in this document. Failure to read,
understand, and follow its instructions could result in damage to the
instrument, injury to operating personnel, or poor instrument
performance.
Observe all (Warning) and STOP (Caution) statements in this
document.

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The Microarray Scanner is rated as a Class 1 (no hazard during normal
use) laser product and contains two Class 3b lasers.
Never force a slide or other accessory into the slide magazine or any
component of the instrument.
Observe proper laboratory safety precautions, such as wearing
protective clothing and using approved laboratory safety procedures.
It is assumed that instrument operators, due to their vocational experience,
are familiar with the necessary safety precautions for handling chemicals
and biohazardous substances. Adhere to the following laws and guidelines:
National industrial protection law
Accident prevention regulations
Safety data sheets of the reagent manufacturers
Safety and Information Labels
Safety and information labels found on the rear of the Microarray Scanner
warn of potential hazard or highlight important information. These labels
refer to issues that must be taken into account when using this instrument.