ThermoFisher Scientific Continuµm User manual

Procedure: Service
Title: Installing the Continuµm IR Microscope
Installing Hardware, Software and System Configuration
Revision: 01
Procedure # Install-001-2
ECCN: EAR99
This document contains confidential or proprietary information of Thermo Fisher Scientific. Neither this
document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 1 of 32
Continuµm
Part number: 912A0572
Part description: Continuµm IR Microscope
Functional description: The Continuµm is an infrared micro-sampling
system that provides the highest available IR spatial resolution and viewing
quality.
Problems associated with this assembly:
Tools required: Refer to page 4.
Estimated time required: Approximately 5-6 hours total depending on
configuration.
Notes: Refer to notes on page 6 of this document for important information.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 2 of 32
Rev Notes
00 Release.
01 Revised to depict installation using the new camera.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
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Important: Prior to performing any replacement procedure, you must read the
Microscope Safety Guide. If you do not have the Safety Guide, it is available for
download from the PSE website. If you do not have access to the PSE website,
email international support to request access at
[email protected]
Safety Risks when performing this procedure:
None

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 4 of 32
Tools required for microscope installation
½” Crescent or socket wrench
Microscope gage block (iS10)
Medium short Phillips screwdriver
Medium Phillips screwdriver
Small Phillips screwdriver
Hex wrench set (Metric and English)
Utility knife
Small flat blade screwdriver
Flat blade jewelers screwdriver
Slide/S78 1mm/.01mm reflective light micrometer
Pinhole slide
AptCal 2010 – Available on the PSE website
2-1/16” balldrivers or hex keys
2-5/64” balldrivers
5/64” L-wrench (hex key)
3/32” Long handled balldriver
3/32” Medium length balldriver
3/16” L-wrench (hex key)
5/32” Long handled balldriver
9/64” Long handled balldriver
3/16” Long handled balldriver
Imperial set of hex keys
2 -1.5mm balldrivers or hex keys
3mm Balldriver
Needle-nose pliers
Permanent marker
Glass microscope slide
Lighter or matches
LN2 approved gloves
Face shield

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
This document contains confidential or proprietary information of Thermo Fisher Scientific. Neither this
document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 5 of 32
Notes:
1. This procedure describes the installation of the current configuration of the
Continuµm Microscope.
2. This procedure assumes that the Continuµm microscope is being installed with a
new, current model spectrometer. Performance tests should be performed and
passing specification on the spectrometer prior to performing Continuµm
performance tests.
3. This procedure assumes that the computer system meets the minimum requirements
for the configuration.
4. This procedure assumes that either a passport or external flipper mirror is installed
on the spectrometer to allow redirection of the main beam to the Continuµm.
5. The Continuµm installation procedure is broken into sections (i.e. Install-001-2) to
make downloading the file easier and faster and to allow the service rep to download
only the sections they need as reference.
6. The Continuµm install procedure assumes the person using the procedure has been
through formal Continuµm training. This is due to the many alignment and
calibration procedures that cannot be thoroughly explained and understood in a
document.
7. All configurations of the iS50 and Continuµm microscope referred to in this
procedure are assumed to be operating under OMNIC 9.0 or greater. OMNIC 9.0 is
the first version of OMNIC software to support the iS50 Spectrometer.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 6 of 32
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Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 7 of 32
Note If Atlµs is not installed substitute µView where applicable in this procedure.
1. Install the Continuum components.
1.1. Unpack the 15X and/or 32X condenser(s).
1.2. Prepare to install the 15X or the 32X condenser into the condenser rack.
If the condenser rack is not already at its lowest point, turn the condenser
rack knob counter-clockwise to completely lower the condenser rack.
Condenser rack all the way down

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
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1.3. Prepare to install the 15X or the 32X condenser. If both condensers were
ordered, use the 15X and set the 32X aside; the 32X will be installed and
tested later in this procedure. If only a 15X or 32X is available, use the
available condenser.
Note Each condenser has a notch and locator pin at the base of the
assembly. The condenser rack has a channel at the back of the condenser
rack. The locator pin will determine proper seating of the condenser in the
condenser rack when it is fully engaged in the condenser rack channel.
1.4. Install the 15X or the 32X condenser into the condenser rack. Turn the
condenser rack lock-down screw counter-clockwise so the screw does NOT
protrude through the condenser rack.
Lock-down screw protruding Lock-down screw flush (not protruding)
Holding the condenser at the bottom (black portion of assembly), carefully
slide the condenser into the condenser rack so the description (15X/32X) is
facing forward. Slowly rotate the condenser assembly clockwise until you
feel the locator pin engage with the channel. Do not rotate the silver ring.
Notch and locator pin
Channel in condenser rack

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 9 of 32
Using your fingers on one hand, gently push against the condenser to hold it
in place and using your other hand; snug the lock-down screw to lock the
condenser in place.
Gently push back on the condenser and then snug the lock-down screw
2. Unpack the XL motorized X-Y stage and stage controller (optional). If a
motorized stage was not ordered, continue with step 3.
Note The XL motorized stage is an independent accessory. It interfaces to the stage
controller which is directly connected to the computer.
2.1. Remove and unwrap the X-Y stage.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
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2.2. Remove the stage cable, sample holder and stage tool set. Remove the
X-Y stage cable, universal sample holder, and stage tool set from the
shipping container and remove the packaging; set all three aside.
2.3. Invert the X-Y stage and record the stage parameters located on the
bottom of the stage for future reference.
2.4. Install the X-Y stage on to the z stage dove mount. Tilt and then slide the
back of the stage on to the dove mount so the “tabs” on the bottom of the
stage [ring] hook under the dove mount.
Important If the tabs do not “grab” the dove mount properly, the stage will
rock and may shift during data collection.
Tabs should hook
under the z stage
dove mount to
secure the stage.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
This document contains confidential or proprietary information of Thermo Fisher Scientific. Neither this
document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 11 of 32
2.5. Square the X-Y stage and secure to the z stage dove mount. Using one
hand, hold the X-Y stage flat and square to the front of the microscope and
then using the 1.5mm balldriver from the stage tool set, slowly turn the
balldriver clockwise while slightly rotating the stage left to right to engage the
setscrew with the notch in the z stage dovemount. When engaged, continue
to tighten the setscrew until snug.
Note The dove-tail mount is keyed to automatically square the stage to the
microscope. This is achieved by the setscrew being tightened into the notch
of the z stage dove tail.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 12 of 32
2.6. Unpack and set the stage controller on the tabletop. Remove the
controller power supply, power cable, USB cable, driver DVD, and controller
from the shipping container. Set the controller on the tabletop near enough to
the microscope to attach the cables and joystick.
2.7. Connect the motorized stage cable between the stage and stage
controller. The cable has a locking mechanism on the stage end. Slide the
mechanism to the left to unlock, attach the cable, and then slide the
mechanism to the right to lock.
Slide to left to unlock Slide to right to lock
2.8. Unpack and connect the joystick to the connector on the rear of the
stage controller.
2.9. Connect the USB cable to the controller; do not connect the USB cable
to the computer until instructed to later in this procedure.
Joystick
Power
Stage cable
From the stage
USB communications
cable to computer

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 13 of 32
2.10. Confirm the on/off switch located on the front of the controller is off.
The switch will be in the “0” position.
2.11. Connect the power cable to the rear of the controller and the power
cord to the power supply.
2.12. Connect the external power supply to a power outlet.
2.13. Install the universal sample holder. Insert the sample holder into the X-Y
stage. Rotate the holder until the groves engage firmly with the plunger
screws.
Note The sample holder should rotate smoothly but still engage firmly with
the plunger screws. If the sample holder is too loose or too tight in the mount:
a) Using a 5/64” L-wrench, remove the 3 lock-down screws from the
rectangular stage insert and set the screws aside.
b) Carefully remove the insert from the stage being careful not to
displace or lose the washers as depicted below.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 14 of 32
c) Use a small flat-blade screwdriver to adjust the plunger screws as
necessary.
d) Reinstall the rectangular insert and sample holder on to the
motorized stage. Assure the washers are aligned with the holes,
then reinstall and tighten the lock-down screws.
2.14. Continue with step 4.
3. Unpack the manual X-Y stage. Unwrap the manual X-Y stage and the universal
sample holder; set the sample holder aside.
3.1. Back out the thumbscrew. Invert the manual stage and then using your
fingers, turn the thumbscrew on the front of the stage so the tip of the plunger
screw is flush with the mount.
Plunger screw protruding Plunger screw flush
Plunger screws

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 15 of 32
3.2. Install the manual stage on to the z stage dove mount. Tilt and then slide
the back of the stage on to the dove mount so the “tabs” on the bottom of the
stage hook under the dove mount
Important If the tabs do not “grab” the dove mount properly, the stage will
rock and may shift during data collection.
3.3. Square the manual stage and secure to the z stage dove mount. Using
one hand, hold the manual stage flat and square to the front of the
microscope and then using your fingers, slowly turn the thumbscrew
clockwise while slightly rotating the stage left to right to engage the
thumbscrew with the notch in the z stage dovemount. When engaged,
continue to tighten the thumbscrew until snug.
Note The dove-tail mount is keyed to automatically square the stage to the
microscope. This is achieved by the thumbscrew being tightened into the notch
of the z stage dove tail.
Tabs should hook
under the z stage
dove mount to
secure the stage.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
This document contains confidential or proprietary information of Thermo Fisher Scientific. Neither this
document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 16 of 32
3.4. Install the universal sample holder. Insert the sample holder into the
manual stage. Rotate the holder until the grove engages firmly with the
plunger screw.
Note If the sample holder is too loose or too tight in the mount, use a small
flat-blade screwdriver to adjust the plunger screw on the right-side of the
manual stage as necessary. The sample holder should rotate smoothly but
still firmly engage with the plunger screw.
4. Connect the AC power cord between the I/O panel on the left-side of the
Continuµm Microscope and the power outlet.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 17 of 32
4.1. Turn the power “on” to the microscope.
4.2. Using the z stage control knob on the lower right-side of the
microscope, turn the knob “Down” to completely lower the z stage.
5. Turn the power “off” to the microscope.
6. Unpack the nosepiece. Carefully remove the nosepiece and objective adjustment
screws from the shipping container and remove the packaging. Refer to the following
page.
Note The nosepiece is shipped with pre-aligned objectives. Care should be used
when unpacking the nosepiece for installation as well as with routine handling during
removal from and installation onto the microscope. Do not touch any of the
objectives when handling the nosepiece, as this could change the optical alignment
and cause the microscope to fail.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
7/18/2016 Page 18 of 32
6.1. Back out the nosepiece set-screw. Using a 3/32” balldriver, turn the handle
1 to 1-1/2 turns counter-clockwise to slightly back-out the setscrew and allow
for installation of the nosepiece. Do not remove the set-screw from the
optical pod.
6.2. Slide the nosepiece into position.
6.2.1. Hold the nosepiece by the black nosepiece ring and gently slide the dove
mount located on the nosepiece into the rails of upper optical pod until it
is stopped by the locator pin.
Rails
Locator pin
Dovemount

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
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6.2.2. Apply a gentle pressure against the front of the nosepiece assembly to
hold the nosepiece against the locator pin and then turn the 3/32”
balldriver clock-wise to secure the nosepiece in the mount. Do not over-
tighten the set-screw.
6.3. Grasp the nosepiece at the black ring with your fingers and rotate the
nosepiece either left or right so the 10X glass objective is in the beam.
7. Unpack and unwrap the trinocular viewer.

Installing the Continuµm IR Microscope - Installing Hardware, Software and System Configuration
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document nor the information therein is to be reproduced, distributed, used or disclosed, either in whole or
in part, except as specifically authorized by Thermo Fisher Scientific.
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7.1. Remove the dust cap from the trinocular mount on the top of the upper
optical pod. Using a 3/32” balldriver, turn the handle counter-clockwise and
remove the dust cap. Continue turning the balldriver until the trinocular
viewer setscrew is flush in the mount. Store the dust cap as appropriate.
7.2. Install the trinocular viewer. Lower the trinocular viewer into the trinocular
mount. Rotate the trinocular viewer so it is square with the front of the
microscope and use the 3/32” balldriver to snug the setscrew.
Note The setscrew should be snug enough so the viewer does not move
when adjusted. Do not over tighten the setscrew or you may create an indent
in the trinocular dovemount which may affect the alignment later in this
procedure.
7.3. Remove the dust caps from the eyepiece ports. Store the dust caps as
appropriate.