Thermo Scientific Nicolet Continuum User manual

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269-239701, Rev A

Contents
Nicolet Continuµm Microscopes.............................................................1
Questions and concerns .....................................................................2
About this manual..............................................................................3
Microscope components ....................................................................4
Preparing the Microscope ........................................................................7
Turning on power...............................................................................7
Cooling the detector.........................................................................11
Installing the purge baffle ................................................................13
Initializing the stage.........................................................................14
Z-axis .........................................................................................15
XY-axes .....................................................................................18
Limiting stage travel ..................................................................22
Controlling stage movement.....................................................25
Preparing the optical components....................................................28
Adjusting the eyepieces .............................................................29
Reticle focus and diopter adjustments .......................................36
Condenser focus and alignment.................................................38
Initializing the Reflex aperture ........................................................43
Analyzing Samples ................................................................................49
Performing a reflection experiment .................................................49
Performing a transmission experiment ............................................63
Advanced Techniques............................................................................77
Polarization options .........................................................................77
Visible polarization....................................................................77
Nomarski differential interference contrast ...............................81
Infrared polarization ..................................................................89
Optical filters ...................................................................................90
Attenuated total reflection ...............................................................91
Setting up the internal Contact Alert System.............................92
Using the internal Contact Alert System .................................100
Setting up the external quantitative Contact Alert System.....108
Grazing angle reflection.................................................................116

More about the Hardware ................................................................... 123
Selecting a detector ....................................................................... 123
Using objectives and condensers .................................................. 127
Specifications and typical uses ............................................... 128
Refractive index compensation............................................... 130
Adjusting field of view and image contrast ................................ 132
Transmission irises.................................................................. 133
Reflection irises ...................................................................... 133
Masking off areas of interest......................................................... 134
Adjusting the aperture size, shape and orientation ................. 135
Using the software to adjust the aperture................................ 136
Using the manual controls to adjust the aperture.................... 138
Using autofocus ............................................................................ 141
Using auto ATR contact................................................................ 145
Troubleshooting .................................................................................. 151
Symptoms and solutions ............................................................... 151
Testing microscope performance.................................................. 168
In reflection mode ................................................................... 168
In transmission mode .............................................................. 176
Upgrading the computer, recovering from viral attacks, and
reinstalling software................................................................ 184
Index ................................................................................................... 187

Continuµm User Guide
1
Nicolet Continuµm Microscopes
Congratulations on your purchase of a Thermo Scientific Nicolet
Continuµm microscope! The Continuµm™ microscope is an
infrared microsampling system that provides the highest available IR
spatial resolution. The Continuµm design enables unlimited
sampling and mapping capability, and incorporates unprecedented
ease of use.
The on-axis infinity corrected optical design of the Continuµm
microscope provides exceptional sample viewing quality and
exceptional infrared sampling.

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The microscope features the TruView™ illumination system, which
allows continuous optical-quality viewing of the sample. The
Reflex™ aperture minimizes diffraction by using a single aperture to
provide aperturing before and after the sample.
You should be familiar with the operation of your spectrometer and
system software before using the microscope. The microscope was
designed to be used with either OMNIC™ Atlµs™ or OMNIC
software. µView™ software is also available for video management
during visible and discrete point microanalysis. For complete
information on using these packages, see the on-line Help system or
other documentation that came with the software. In this manual, we
will refer to OMNIC Atlµs commands. If your system is not
equipped with OMNIC Atlµs, see the instructions for collecting data
that came with your spectrometer.
The Continuµm microscope must be installed as part of a Thermo
Scientific spectrometer system and can be used only after it is
properly connected to the spectrometer.
The Microscope Safety Guide that came with your microscope
contains important safety information. This guide is available in
several languages. Contact our local office for information about the
languages that are available. To prevent personal injury and damage
to equipment, read the guide and follow the safety precautions
contained in it whenever you use the system.
Questions
and concerns
In case of emergency, follow the procedures established by your
facility. If you have questions or concerns about safety or need
assistance with operation, repairs or replacement parts, you can
contact our sales or service representative in your area or use the
information at the beginning of this document to contact us.

Continuµm User Guide
3
About
this manual
This manual explains how to use the system to collect and process
FT-IR spectra after a Nicolet™ Series spectrometer and Nicolet
Continuµm microscope are installed. Included is basic information
about using OMNIC Atlµs software, as well as chapters on how to
operate the microscope. (If you did not purchase OMNIC Atlµs
software, see the documentation that came with your spectrometer
for information about using OMNIC to collect data.)
A Continuµm microscope is used for illustration purposes. The
following conventions are used in this manual to draw your attention
to important information:
This symbol tells you that you can find more information in the
on-line help and tutorials. To access help or a tutorial, click the Help
menu in OMNIC.
This symbol tells you that you can find more information in this
manual or other printed documentation that came with your
instrument.
Note Notes contain helpful supplementary information. 
Notice Follow instructions labeled “Notice” to avoid damaging the system
hardware or losing data. 
Caution Indicates a potentially hazardous situation which, if not avoided,
may result in minor or moderate injury. It may also be used to alert
against unsafe practices. 
Warning Indicates a potentially hazardous situation which, if not avoided,
could result in death or serious injury. 
Danger Indicates an imminently hazardous situation which, if not avoided,
will result in death or serious injury. 

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Microscope
components
The following illustrations identify the microscope controls and
components.

Continuµm User Guide
5
Front panel

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Control panel (on left side)