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.

iv | NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0
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.

vi | NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0
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.

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | vii
Figure 1: Safety and Warning Labels on the Microarray Scanner
XIII. Disposal of the Instrument
and Consumables
Disposal of the Instrument
Because components of the Microarray Scanner could be exposed to
potentially infectious chemical samples, toxic or corrosive chemicals, or
radioactive chemicals, perform appropriate waste management to ensure
there is no risk of contamination.

viii | NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0
ALWAYS DISINFECT AND DECONTAMINATE THE
INSTRUMENT BEFORE DISPOSAL. Depending on the
experiments, components of the Microarray Scanner could have
been in contact with biohazardous material. Refer to the
“Instrument Disinfection” section in Chapter D, Maintenance and
Care, for details.
•Make sure to treat this material according to applicable safety
standards and regulations.
•Always decontaminate (i.e. clean and disinfect) all components
before disposal.
•Follow laboratory procedures for biohazardous waste disposal.
Observe all national, regional, and local regulations for waste
disposal and management.
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 from electrical and electronic equipment
separately.
Pollution degree: 2
Method of Disposal: Electronic waste, contaminated waste
(infectious waste)
Disposal of the Consumables
Biological hazards can be associated with the waste material of the
process run on the instrument.
Treat used consumables and all substances in accordance with good
laboratory practice guidelines.
Inquire about appropriate collecting points and approved methods
of disposal in your country, state, or region.

A Overview
1. Introduction
The Microarray Scanner is a laser-scanning instrument dedicated to
acquiring fluorescent images on standard microarray slides (1 x 3 inch).
High resolution combined with high sensitivity as well as uniformity,
reproducibility, auto calibration, and a dynamic range are key characteristics
of the Microarray Scanner.
A slide magazine enables the automatic processing of up to 48 slides, which
can be scanned several times using different laser, filter, and photomultiplier
tubes (PMTs) gain settings with no further user intervention in a single
batch run.
Active air filtering reduces ozone concentration so that the slide processing
and storage area is protected from external high ozone concentrations
during operation.
The Microarray Scanner produces single- or multi-image Tagged Image File
Format files (TIFF, .tif) that can be read by software packages available from
Roche NimbleGen and other vendors.
Following is a description of the instrument’s key functionality and
components:
Autofocus Procedure
Microarray slides can have a variable surface planarity, which can affect the
focusing of the scanning laser and may cause problems with measuring
fluorescence intensities.
To counter this problem, the Microarray Scanner implements a dynamic
autofocus procedure that measures the surface contour (surface modeling)
before it scans a slide. During this procedure, the Microarray Scanner
performs a multi-line scan using different positions across the entire slide to
evaluate the surface. Then the contour of the slide is interpolated to correct
for focal distance and tilt while scanning.

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This unique dynamic autofocus procedure is more reliable than single
focusing routines, which concentrate on only one point of the slide.
Moreover, this dynamic autofocus procedure is less vulnerable to
disturbances such as dust on the slide surface.
Laser Excitation
The Microarray Scanner is designed for microarray imaging using
individual solid state lasers that emit light at wavelengths suitable for
exciting fluorescent dyes used as labels.
The lasers are able to excite Cy3- and Cy5-labeled samples to measure
fluorescence intensities in microarray analysis. Laser emission for excitation
of fluorescent dyes can be chosen at these wavelengths:
Green: 532nm
Red: 635nm
Other dyes similar to Cy3 and Cy5 can also be used, such as Alexa 555 and
Alexa 647 or DY 547 and DY 647.
Excitation intensity can be varied with neutral density filters located in a
filter wheel behind the lasers so that each laser can be adjusted separately
with its own filter device.
A reference photodiode is used for detecting the laser power.
Emission Filters
The Microarray Scanner is equipped with filters that are optimized for the
emission spectrum of the fluorescent cyanine dyes Cy3 and Cy5 and the
other dyes specified earlier.
Detection
Fluorescence emission is directed through filters before reaching the
photodetector. To detect photons emitted by the tagged molecules,
photomultiplier tubes (PMTs) with very high sensitivity and low electronic
noise are used to convert the light energy into electric current that can be
measured. The resulting current is proportional to the incident emission
light at the photodetector.

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | 3
The amplification of the photon signal can be controlled by the voltage
applied to the tube. PMT voltages are adjustable in the PMT gain settings
for different channels to equalize intensity values on each slide.
To optimize and increase the dynamics of scanning, adjust the PMT setting
using the histogram mode to balance channel intensity. Balance the
histogram at all points above background across signal intensity. For more
information on histograms, refer to Chapter C, Operation.
Histogram mode is not available for 2μm scans during the run but is
available post run.
Repeated use of high power settings for the lasers causes
photobleaching of the dye molecules and thus detrimentally affects
fluorescence intensity.
Read Speed
The Microarray Scanner can measure two fluorescent dyes simultaneously
(parallel mode) at increased overall scan speed. Alternatively, the dyes can
be read one at a time (sequential mode). In addition, two scanning velocities
are available: 16 lines per second (8Hz) and 24 lines per second (12Hz).
The overall processing time includes loading and unloading of a slide,
reading the barcode, performing the autofocus, autogain, and scanning
processes, and saving the image file. The file size of an image depends on the
resolution and size of the scanned area. Increasing the spatial pixel size is
accompanied with an increasing scan speed and decreasing amount of data.
The following table shows approximate file sizes and processing times for
the NimbleGen HD2 family of arrays (2.1M, 3x720K, and 12x135K probe
formats) using a speed of 24 lines per second, parallel mode, autogain
turned off, and scan length of 62mm. File size and processing time will vary
if a different scan speed or scan length is specified.

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File Size (MB)
Resolution (µm) Single Channel Dual Channel
Processing Time
(min)
2 630 1260 25
5 100 200 12
10 25 50 8
20 6 12 6
40 2 3 5
ILC Module
For periodic testing of the Microarray Scanner’s performance, the
Microarray Scanner includes an internal Integrated LaserCheck (ILC)
module. The ILC slide, which is used by this module, is provided with the
Microarray Scanner (refer to page 27 for information on how to load the
ILC slide and run the ILC module). The ILC module is designed for
durability, contains no degradable parts, and requires no consumables.
The ILC module checks whether the Microarray Scanner is operating
according to determined parameters within defined limits. The ILC module
should be run on a regular basis. Roche NimbleGen recommends a period
of time of 2 weeks.
Once you initiate the ILC run, the ILC module runs fully automated with no
user intervention. The instrument software will automatically load and
unload the ILC slide as required and perform and evaluate all tests. The
following tests are performed, and results are reported (refer to page 29 for
information on how to save the results):
Actuators Test. Performs a step-loss check for each actuator (e.g. slide
transport, filter wheels).
Barcode Reader Test. Verifies the functionality of the barcode reader.
Oscillator Test. Checks the functionality of the oscillator subsystem and
measures the following: (1) the frequency of the oscillator subsystem and
the presence of the encoder signal at medium and accelerated frequency,
(2) the maximum magnitude of the pixel jitter, and (3) the deviation
perpendicular to the scanning direction (stagger).
Electronics Test.Measures the electronic noise and determines the integrity
of the detection electronics (analog integration, connections, A/D
conversion). Data acquisition is performed with closed detector and gain set
to zero.

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | 5
Detector(s) Test. Evaluates the detector’s noise. Data are acquired with closed
detector and gain set to defined values listed in the report.
Laser(s) Test. Reviews the integrity of the laser light sources. For each laser,
the excitation light is reflected on the ILC slide, and the noise is measured
with the detector. Additionally, the laser light intensity is measured with a
reference photodiode.
Optical Alignment Test. Verifies the alignment and stability of the optical
system. For this test, Z scans on a blank glass area are performed.
Autofocus Test. Checks the reliability of the autofocus and the slide transport
subsystem while performing several Z scans using different parameters on
the ILC slide.
Optical Resolution Test. Scans defined test structures (i.e. line gratings with
high-low reflectivity parallel to the X and Y axes) on the ILC slide to provide
information on optical resolution.
Sensitivity Tests. Check the overall performance of components that are
relevant for sensitivity: electronics, detectors, lasers, alignment, and filter
blocking.
Positioning Test. Verifies and, if necessary, recalibrates the position of the
slide transport (X and Y axes) relative to the measurement optics. Defined
position marks on the ILC slide are scanned.
Geometric Linearity Test. Checks for X and Y axes and if necessary,
recalibrates (Y axis only) the image linearity within scanned images. Defined
straight line patterns on the ILC slide are scanned to evaluate the image
linearity in the X and Y directions.

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2. Specifications
2.1 Specifications of the Microarray Scanner
Specification Description
Performance
Sensitivity <0.04 Fluorescein equivalent/µm2(Cy5)
Dynamic range 5 orders of magnitude
Pixel resolution 2, 5, 10, 20, or 40µm
Reading speed 16/24 lines per second (8/12Hz)
Optical
Light sources Two solid-state lasers (532 and 635nm)
Fluorescence
detector(s)
Two low dark current photomultiplier tubes
Gain adjustment 0.01 - 1000%
Optics High-aperture collection optics (NA 0.7)
Emission filters One predefined filter per laser
Dichroic beam splitter Two different beam splitters
Pinholes Two pinholes of fixed size
Reference detector Monitors laser power
Autofocus Automatic, user-selectable slide types
Barcode reader Capable of reading NimbleGen, Code 39, and Code 128
barcode formats
Mechanical
Scanner Linear movement with cone-rod principle
Slide holder 3-axis high-precision module for scanning and automatic
alignment of exact focus position
Stacker cover Opens upon pressing of the insert/eject magazine button

NimbleGen MS 200 Microarray Scanner Operator’s Manual v1.0 | 7
Electrical
Power supply Auto-sensing: 100 - 120V / 220 - 240V, 50/60Hz
Power consumption 150VA
Approvals EN 61010-1:2001, 61010-2-081/A1:2003, 60825-1/A1:2002,
UL 61010-1:2004, IEC 61010-2-081/A1:2003, CAN/CSA-C22.2
No. 61010-1:2004, CAN/CSA-C22.2 No. 61010-2-081:2004,
CAN/CSA-E60825-1:2003
Processing
Control Software-controlled by external PC
PC operating system Windows Vista Business (64-bit)
Interface Ethernet RJ45
Data acquisition High-speed 16-bit A/D conversion
Samples to be
measured
Fluorescent features on microscope slides within the
specified slide dimensions
Slide magazine Holds up to 48 slides and allows automatic loading
Environmental
Ambient temperature Operation: 18 - 28°C (64 - 82°F)
Non-operation: -20 - 60°C (-4 - 140°F)
Relative humidity Operation: 20 - 80% non-condensing
Storage: 10 - 80% non-condensing
Overvoltage category II
Pollution degree 2
Method of disposal Electronic waste (infectious waste)
Physical
Outer dimensions Width: 60cm (23.6in)
Height: 46.6cm (18.5in)
Depth: 61.8cm (24.4in)
Weight Approximately 38kg (84.0lb)

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2.2 Specifications of the Control Unit
Component Specification
Computer HP dc7800 CMT with Dual Core 2 3GHz (gigahertz)
Memory: 8GB (gigabytes)
Disk 1: 160GB for system and applications
Disk 2: 160GB for use by users
Disk 3: 1TB (terabyte) Data storage
CD/DVD: DVD-RW
Ethernet RJ45: 1 x to connect to the Microarray Scanner (on
the computer’s PCI card)
1 x to connect to the lab’s network (on the
computer’s main board)
Monitor 19 inch LC display with sound (1280 x 1024 resolution)
Keyboard US layout
Mouse 2-button optical scroll mouse
Operating system Microsoft Vista Business 64-bit
2.3 Specifications for Microarray Slides
Slide Formats
Microarray slides to be processed using the Microarray Scanner should meet
the nominal specifications of 25.4 x 76.2mm (1 x 3in) for standard glass
laboratory slides or following dimensions:
Width: 24.6 - 26.0mm
Length: 75.0 - 76.5mm
Thickness: 0.8 - 1.2mm
Scan Area, Resolution, and Barcode Specifications
The maximum scan area on a slide is set to 22 x 75mm (Figure 2). Pixel
resolution is selectable at 2, 5, 10, 20, and 40μm.
The scan and barcode dimensions could vary due to experimental and/or
manufacturer settings. If a barcode area is designated on the slide, the
effective scan area is smaller.