Thermo Scientific Nicolet RaptIR User manual

Nicolet RaptIR
FTIR Microscope
USERGUIDE
269-3517 00 A Revision A February 2022

Contents
1.Introduction 4
1.1Intended use 5
1.2Disclaimer 6
1.3Conventions Used 7
1.4Warranty information 8
2.Overview 9
2.1Features and controls 10
2.2Connections and ports 12
2.3Optional Joystick 13
2.4Optional trinocular eyepiece 14
2.5Using OMNIC Paradigm software 15
3.Operation 19
3.1Prepare the microscope 20
3.2Analyze samples 23
3.3ATR measurements 29
3.4Locate, light, and mask the sample 31
3.5Verify microscope performance 36
4.Maintenance 39
4.1Clean the microscope 40
4.2Maintain the liquid nitrogen dewar 41
5.Troubleshooting 42
6.Contacting us 45
6.1Ordering parts 46

© 2022 Thermo Fisher Scientific Inc. All rights reserved.
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The contents of this document are subject to change without notice. All technical information in this document is for
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Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-free
and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might
result from any use of this document, even if the information in the document is followed properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
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shall govern all conflicting information between the two documents.
For Research Use Only. This instrument or accessory is not a medical device and is not intended to be used
for the prevention, diagnosis, treatment or cure of disease.
WARNING
Avoid an explosion or fire hazard.
This instrument or accessory is not designed for use in an explosive atmosphere.

1.Introduction
Thermo Scientific Nicolet™ RaptIR™ FTIR Microscope 4
1.Introduction

1.Introduction
1.1Intended use
The Thermo Scientific NicoletRaptIRFTIRMicroscope is a Fourier-transform (FTIR) microscope designed for use in a
controlled laboratory environment, and is intended to be used with Nicolet series spectrometers.
With the RaptIR microscope, you can quickly find your target, collect high-resolution visual images, and generate high
spatial resolution IR data for analysis.
OMNIC Paradigm software includes a full suite of analytical tools, customizable workflows to automate your routine tasks,
and simple to use tools for microparticle analysis as well as area, point, and line analysis.
With the RaptIR Microscope, you can sample thick (up to 4 cm) and heavy (up to 5 kg) samples, and with multiple
objectives and an automated nosepiece, the microscope supports a range of options for viewing samples and collecting IR
data.
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1.2Disclaimer
Do not use the microscope for anything other than its intended purpose as described in this user guide.
NOTICE
Read the site and safety information for your system before using the microscope.
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1.Introduction

1.Introduction
1.3Conventions Used
Safety precautions and other important information use the following format:
DANGER
Avoid hazard. Indicates a hazardous situation which, if not avoided, will result in serious injury or death.
WARNING
Avoid hazard. Indicates a hazardous situation which, if not avoided, could result in serious injury or death.
CAUTION
Avoid hazard. Indicates a hazardous situation which, if not avoided, could result in minor or moderate injury.
NOTICE
Follow instructions with this label to avoid damaging the system hardware or losing data.
Note Contains helpful supplementary information.
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1.4Warranty information
Thermo Fisher Scientific warrants that each product we sell is free from defects in labor and materials and shall conform to
its product specifications as defined in the product user documentation. If the product does not function as warranted during
the warranty period, we will repair or replace it without charge. If in our judgment we are unable to do so, you may return it to
us and we will refund your money.
This warranty replaces all other warranties, expressed or implied, including the implied warranties of merchantability and
fitness for a particular purpose and any other obligations or liabilities on the part of Thermo Fisher Scientific whether in
contract, warranty, negligence or otherwise. Thermo Fisher Scientific shall not be liable for and disclaims all consequential,
incidental and contingent damages.
1.4.1Warranty period
The system warranty period is 12 months in the U.S.A. and Canada. The warranty period begins on the date of installation
or 30 days from the date of invoice, whichever is sooner.
The system warranty period for products sold outside the U.S.A. and Canada is 12 months from the date of installation or 14
months from the date of shipment, whichever is sooner.
1.4.2Limit of warranty
Misuse, accident, modification, unsuitable physical or operating environment, improper maintenance, or damage caused by
a product for which we are not responsible will void the warranty.
Consumables are not covered under warranty.
Items Not Covered by Warranty
We do not warrant uninterrupted or error-free operation of a product. We provide certain non-Thermo Fisher Scientific
products on an “as is” basis. Non-Thermo Fisher Scientific manufacturers or suppliers may provide their own warranties. A
separate software warranty is provided with the software user documentation.
NOTICE
Inside the shipping box, the instrument is sealed in a plastic bag to keep the optical components dry.
You must allow 24 hours for the instrument to reach room temperature before opening the bag. If the bag is opened before the
instrument reaches room temperature, moisture could condense on the optical components and cause permanent damage.
Your warranty will not cover:
lDamage due to improper moving techniques.
lMissing or damaged parts if the shipping boxes are unpacked before our service engineer installs the system.
lDamage due to removing the sealed plastic bag before the instrument has come to room temperature.
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1.Introduction

2.Overview

2.Overview
2.1Features and controls
Figure 2-1: The main features of the microscope
ATrinocular video
eyepiece
The optional trinocular eyepiece provides a visual and a video image in OMNICParadigm software.
The monocular eyepiece (not shown)provides only a video.
BRotating object-
ive turret
The turret supports 1 IRobjective and 1 visual objectives. Typically, you will use a 15x IRobjective
and a 4x visual objective. The microscope also supports optional 32x IRobjective and 10x or 40x
visual objectives.
CMotorized stage The stage supports a 40 mm working distance and samples up to 5 kg. Control the stage through
OMNICParadigm software or with the optional joystick. Never attempt to move the stage by hand.
DTransmission
illumination iris
Use the field of view iris to adjust the size of the illuminated field of view. It opens and closes
concentrically.
Typically, the iris is fully opened so that it is out of the full field of view. If a sample surface is uneven,
you may find it easier to focus on the edges of the iris blades to find the best focus.
EPower indicator
and button
Press to turn the microscope on or off. The blue power indicator blinks while the microscope is start-
ing up and stays a steady blue when the microscope is ready for use.
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FReflection
Illumination iris
Use the field of view iris to adjust the size of the illuminated field of view. It opens and closes
concentrically with respect to the reticle cross hairs.
Typically, the iris is fully opened so that it is out of the full field of view. If a sample surface is uneven,
you may find it easier to focus on the area of interest if you first partially close the iris and focus on the
edges of the iris blades.
G1-Liter Liquid
Nitrogen Dewar
The liquid nitrogen dewar holds 1 liter of liquid nitrogen. Once cooled, the detector will remain cool for
about 18 hours. See "Cooling the detector" for more information.
Figure 2-2: Close up of the stage
AATRsensor The ATRsensor detects whether the slide-in ATRattachment is installed.
BSample slide
alignment indicator
Align the red indicator dots on the stage and the sample slide.
CControl stage
orientation
Used to rotate the stage during installation. Do not adjust after installation.
DSlide-in
ATRattachment
The optional slide-in ATRattachment is used for ATRmeasurements.
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2.Overview

2.Overview
2.2Connections and ports
AUSB 3.0 connection to computer's USB3.0 port
BConnection to the optional joystick
CConnect to Auxiliary Signals port on the spectrometer
DConnect to "Accessory"port on the spectrometer
EConnection to power supply cable
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2.3Optional Joystick
You can use the optional joystick to control the stage position and sample illumination. The stage and illumination can also
be controlled in the software.
To connect the joystick, plug the data cable into the "Joystick"port on the back of the microscope.
ATransmittance illumination
control
Rotate to manually dim or brighten transmittance illumination.
BReflectance illumination
control
Rotate to manually dim or brighten reflectance illumination.
CJoystick for stage control Push the joystick forward, backward, left, or right to move the stage along the sample plane.
Rotate to move the stage up or down.
DSpeed control Controls the speed of the stage for precise, slow movement or fast movement.
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2.Overview

2.Overview
2.4Optional trinocular eyepiece
Your microscope may have either a monocular eyepiece with only the camera or it may have the trinocular eyepiece with
the camera and visual eyepieces.
AVisual eyepieces Adjustable eyepieces for looking at the sample. Best used with the optional joystick.
BThree-position view selector Controls the light path for the eyepieces.
lIn:Eyepiece only, no camera
lMiddle:Eyepiece and camera
lOut:Camera only, no eyepieces
CCamera The USB camera is operated with OMNICParadigm software.
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2.5Using OMNIC Paradigm software
Run your microscope and analyze your samples using OMNICParadigm software, Thermo Scientific's streamlined material
analysis software. The user-friendly dashboard screen helps you view instrument status and recent work, process your
spectra, conduct multi-component searching, and create new libraries. Designed with lab managers and science educators
in mind, this software helps automate workflows using an intuitive drag-and-drop workflow creator. Work remotely and
collaborate with colleagues around the globe when you upload OMNIC Paradigm data to the cloud using the Thermo
Scientific OMNIC Anywhere Application.
2.5.1Interface
When working in microscopy, you will primarily work in the dashboard and the map views.
The dashboard
Begin a new session, edit measurement settings, view recent measurements, reports, and maps, and view workflows on the
dashboard.
Figure 2-1: The dashboard showing tools for microscopy
AToolbar The toolbar includes buttons for features and tools you will need use often and is used to navigate
between the Dashboard, Map, and Spectral views.
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2.Overview

2.Overview
BStart Session After you've loaded your sample and selected a mosaic capture location, click Start Session to
switch to the Map view and to automatically collect a mosaic image of the sample. Select Auto-
focus before capture to automatically bring the sample into the best focus.
CEject Stage Ejecting the stage is optional. Ejecting lowers the stage and moves it forward so that you have
more room to load your sample. After the sample is loaded, click Start Session to move the stage
back into position.
DMeasurements,
Maps, and Reports
Displays your Measurements, Maps, and Reports. Choose a category from the list to switch views.
EWorkflows and
Packages
Displays qualification and performance verification workflows as well as your custom workflows.
For more on creating and using workflows, see OMNICParadigm software guides and tutorials.
FSettings Create, select, save, or delete collections of settings.
GMore Click More to expand any of the main sections of the dashboard and to view additional settings or
details.
HCollection settings The most commonly used settings are shown here, in the New Measurement pane. Click More to
view additional advanced settings, including settings for background measurements.
IPreview Shows a preview image of the selected measurement, map, or report.
JWorkflow or pack-
age preview
Shows a preview image of the selected workflow or package. Locked workflows display a logo
instead of the preview of the workflow.
The map view
Analyze your sample using the map view. Here you can view your sample, define areas of interest for your analysis, and
measure sample data.
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Figure 2-2: The map view in OMNICParadigm software
AToolbar View additional microscope settings and open the live camera view, capture a new mosaic, measure a
spectrum, or navigate back to the dashboard.
BCamera
view
Open the camera view to see the live visual image of the sample. Use the View Tools to adjust the
illumination, focus, and aperture and to take a quick, snapshot mosaic, change objectives, or view a live
interferogram signal.
Use the arrows around the live image to move the stage without a joystick.
CMosaic view Shows the mosaic image and is the primary workspace where you define your background point and areas
for analysis.
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2.Overview

2.Overview
DFloating
toolbar
Analysis and navigation tools for interacting with the mosaic image.
lCursor:select regions, points, and spectra
lPan:Use to move the viewable portion of the mosaic
lMosaic:Use to draw a region for a high-magnification mosaic
lAnalysis tools
lBackground point:Select a point at which you will measure the background spectrum
lArea:Draw an area for region analysis
lPoint:Select a point to measure a spectrum
lLine:Measure a line map
lParticle analysis:Draw a region for particle analysis. This tool is only available when particle
analysis is selected on the dashboard.
lRuler:Use the ruler to measure objects in the mosaic view
lStage:Click a point on the mosaic to move the stage to that position
lRegion queue:View all of the regions and points that are currently selected for your analysis. These
are the positions that will be measured when you click Sample.
EAnalysis
panel
View your mosaics, background spectra, profiles, and history in the analysis panel.
FMosaic sky
view
The sky view shows a high-level view of the mosaic. When you zoom in, the sky view shows you what part
of the mosaic you are viewing. You can use the sky view to navigate around the whole mosaic.
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3.Operation

3.Operation
3.1Prepare the microscope
To start your analysis, prepare the microscope by turning it on, cooling the detector, and starting OMNICParadigm
software.
3.1.1Turn the microscope on
If the microscope is off, press the power button. The blue indicator light blinks during initialization and shows a continuous
blue glow when the microscope is ready to use.
3.1.2Cool the detector
Your microscope uses a liquid nitrogen cooled detector. Before using the microscope, always ensure there is enough liquid
nitrogen in the dewar.
The liquid nitrogen dewar holds 1 liter of liquid nitrogen. When cooled according to the following procedure, the detector
should remain cool for approximately 18 hours.
WARNING
Avoid freeze burns.
Liquid nitrogen is extremely cold and therefore hazardous.
lWear protective clothing and eyewear and follow standard laboratory safety practices to prevent injury.
lPour the liquid nitrogen slowly. If you pour too quickly, the nitrogen may splash.
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