THORLABS CM100 User manual

Reflective Confocal Microscope
CM100
User Guide

Copyright December 16, 2016 ThorLabs, Inc.. All rights reserved.
Information in this document is subject to change without notice. The software described in this document is furnished under a license agreement or
nondisclosure agreement. The software may be used or copied only in accordance with the terms of those agreements. No part of this publication may be
reproduced, stored in a retrieval system, or transmitted in any form or any means electronic or mechanical, including photocopying and recording for any
purpose other than the purchaser's personal use without the written permission of ThorLabs, Inc..
ThorLabs, Inc.
108 Powers Court
Sterling, VA 20166
703-651-1700

Chapter 1 Warning Symbols and Definitions 1
Chapter 2 Safety 2
Chapter 3 Description 3
3.1. Features at a Glance 3
3.2. Imaging Capabilities 3
Chapter 4 Getting Started 4
4.1. Unpacking and Inspection 4
4.2. Setting up the CM100 5
4.3. Cable Connection Diagram 8
Chapter 5 Alignment 9
5.1. Widefield Imaging 18
Chapter 6 Maintaining the CM100 19
6.1. Cleaning 19
6.2. Connector Cleaning 19
6.3. Troubleshooting 19
Chapter 7 Specifications 20
Chapter 8 Mechanical Drawing 23
Chapter 9 Regulatory 24
9.1. Waste Treatment is Your Own Responsibility 24
9.2. Ecological Background 24
Chapter 10 Thorlabs Worldwide Contacts 25
Table of Contents
CM100

Chapter 1 Warning Symbols and Definitions
Below is a list of warning symbols you may encounter in this manual or on your device.
Symbol Description
Direct Current
Alternating Current
Both Direct and Alternating Current
Earth Ground Terminal
Protective Conductor Terminal
Frame or Chassis Terminal
Equipotentiality
On (Supply)
Off (Supply)
In Position of a Bi-Stable Push Control
Out Position of a Bi-Stable Push Control
Caution: Risk of Electric Shock
Caution: Hot Surface
Caution: Risk of Danger
Caution: Laser Radiation
Caution: Spinning Blades May Cause Harm
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CM100 Chapter 1: Warning Symbols and Definitions

Chapter 2 Safety
All statements regarding safety of operation and technical data in this user guide will only apply
when the unit is operated correctly. Refer to the relevant User Guide of the individual product for
safety instructions. Please read the following warnings and cautions carefully before operating the
device.
WARNING
DO NOT use the device for anything other than its intended use. If the device is used in a
manner not specified by Thorlabs, the protection provided by the equipment may be
impaired.
WARRANTYWARNING
DO NOT open the scanner block, electronics enclosure, detector module or computer.
There are no serviceable parts in these products. DONOTperform instrumentation
maintenance or service except as specifically stated. Any modification or servicing of this
system by unqualified personnel renders Thorlabs free of any liability. Only personnel
authorized by Thorlabs and trained in the maintenance of this equipment should remove
any covers or housings or attempt any repairs or adjustments.
CAUTION
The computer supplied with this system requires configuration for specific ACline voltages
of 110 VAC or 230 VAC nominal. Refer to the computer's User Guide for details.
WARNING
DONOT operate in a wet, damp, or explosive environment.
WARNING
In case of software failure, turn off the laser source.
Rev A, December 16, 2016 Page 2
CM100 Chapter 2: Safety

Chapter 3 Description
Thorlabs' Entry-Level Upright Reflective Confocal Microscope is a complete single-channel system.
By eliminating signals that originate from outside the focal plane, confocal microscopy provides the
ability to acquire high resolution, optically sectioned images from within a thick sample. The CM100
supports reflected-light confocal imaging for viewing the surface structure of biological samples or
for inspection applications.
The CM100 has a 35 mm x 52 mm x 3 mm silver-coated mirror at the front of the scan path that
directs light from the scanners to the objective. In order to use this microscope for widefield as well
as confocal imaging, you can replace this mirror with a beamsplitter. The CM100 is designed to
provide a cost effective entry point to owning a modular confocal microscope that can be upgraded
to an advanced confocal microscope.
3.1. Features at a Glance
● Upright Microscope Based on the Cerna DIY Microscopy Platform
♦95 mm Dovetail on Rail Accepts Cerna Accessories
♦D1N Dovetail on Top of Scan Path for Cerna Widefield Imaging Modules
● Confocal Scan Path with Galvo-Galvo Scanners
● One Benchtop Excitation Laser (660 nm SMLaser)
● One Multialkali PMT (Photomultiplier Tube)
● Filter Set for Reflected-Light: One Beamsplitter, One Quarter-Wave Plate, and Two
Polarizers
● Rigid Stand Slide Holder on Manual XYStage, 1/2" Travel
● 20X Olympus Objective
● PC with DAQ and ThorImageLS®Software
3.2. Imaging Capabilities
● Full frame 4096 x 4096 Pixel Images (Uni-Directional Scan)
● 2 FPSfor 512 x 512 Pixel Bi-Directional Scans
● Galvo/Galvo Scan Head with 1.0 to 10 µs Pixel Dwell Times
● 796 µm x 796 µm Field of View (FN25)
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CM100 Chapter 3: Description

Chapter 4 Getting Started
This section is provided for those interested in getting the Reflective Confocal Microscope up and
running quickly.
4.1. Unpacking and Inspection
Open the package, and carefully remove the CM100 and its accessories. Unpack the laser, Galvo-
Galvo Controller, PMT, computer, and monitor from their respective packages. The table lists the
standard accessories shipped with the device.
Name Quantity
Reflective Confocal Microscope 1
Rigid Stand on XY Translation Stage 1
20X Microscope Objective (RMS20X) 1
NIBreakout Box 1
K-Cube Stepper Driver (KST101) 1
K-Cube Power Supply (KPS101) 1
Laser (S1FC660) 1
Galvo/Galvo Controller (LSK-GG) 1
PMT (PMT1001/M) 1
Computer with Monitor, Keyboard, and Mouse 1
Clamping Fork (CF175) 1
Post Holder (PH082E) 1
Optical Post (TR20/M) 1
NI SHC68-68-EPM Cable 1
NI SH6868 Cable 1
Polarization-Maintaining Patch Cable (P1-630PM-FC-2) 1
Armored Fiber Patch Cable 1
Beamsplitter1(BSW10R) 1
Polarizers1(LPVISE100-A) 2
Quarter-Wave Plate (WPQ10E-670) 1
K-Cube USB Cable 1
SMA to BNC Cable 1
Alignment Tool 1
Rev A, December 16, 2016 Page 4
CM100 Chapter 4: Getting Started

Name Quantity
Grid Slide (R1L3S3P) 1
M6x16 mm Socket Head Cap Screw 12
1/4-20x5/8" Socket Head Cap Screw 12
M6 Flat Washer 6
2 mm Hex Wrench 1
2.5 mm Hex Wrench 1
3/32" Hex L-Key 1
3/16" Hex L-Key 1
1.5 mm Hex Wrench 1
5 mm Hex L-Key 1
2 mm Hex L-Key 1
1) The filter set comes pre-installed on the microscope.
Inspect the device and its accessories for any missing parts or damage. If there is any problem,
please contact our nearest office (see Thorlabs Worldwide Contacts Chapter on Page 25 for details).
4.2. Setting up the CM100
CAUTION
DO NOT place the SMA to BNC cable or DB-25 Connector cable near any electrical noise
sources such as a power cable.This may cause poor quality images.
A. Microscope
1. Use four screws (M6 for metric/1/4-20x5/8" for imperial) to mount the CM100 onto the optical
table.
See the Mechanical Drawing Chapter on Page 23 for mounting holes.
2. Use the 2 mm hex wrench to remove the shipping plate on the objective arm.
3. Use two screws and washers to mount the K-Cube Stepper Motor Controller onto the optical
table.
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CM100 Chapter 4: Getting Started

4. Connect the cable from the Motorized Objective Arm to the Motor port of the K-Cube
Stepper Motor Controller.
5. Connect the K-Cube Power Supply to a standard power outlet.
6. Connect one end of the USB cable to the K-Cube Stepper Driver Controller and the other
end to the computer.
B. Computer
1. Setup the computer, monitor, keyboard, and mouse.
2. Connect one end (silver) of the NI SHC68-68-EPM cable to the computer (Connector 0) and
the other end (blue) to the rear panel of NI Breakout Box.
3. Connect one end of NI SH6868 cable to the NI Breakout Box and other end to the DAQ port
of Galvo/Galvo Controller.
C. Galvo-Galvo Controller
1. Connect the DB-25 Connector cable to the Scanner port of the Controller and the other end
to the Scanner Controller port of CM100.
2. Connect the power cord to a standard power outlet.
D. Laser
Read the Laser User Guide included along with the unit before setting up the laser.
WARNING
DO NOTswitch on the laser while installing the Confocal system. This may cause injury due
to laser radiation. Make sure the laser source is off.
1. Remove the red cap from the CM100 back panel.
2. Connect one end of the PM (Polarization-Maintaining) Patch cable to the laser and the other
end to the CM100 back panel.
Rev A, December 16, 2016 Page 6
CM100 Chapter 4: Getting Started

Make sure to align the key on the Patch cable connector with the key slot on the fiber
bulkhead before connecting the cable.
3. Connect the power cord to a standard power outlet.
E. PMT
1. Use the post holder and clamping fork to mount the PMT onto the optical table.
2. Connect the USB port to the computer.
3. Connect the SMAto BNC cable from the OUTport of the PMT to the AI1 port on the NI
Breakout Box.
4. Connect one end of the Armored Fiber Patch cable to the PMT and the other end to the
Pinhole port in the CM100.
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CM100 Chapter 4: Getting Started

4.3. Cable Connection Diagram
NI Breakout Box - Rear Panel
NI Breakout Box - Front Panel
PM Patch Cable
SMA to BNC Cable
NATIONAL
INSTRUMENTS
BNC-2090A
SE
DIFF
SE
DIFF
SE
DIFF
SE
DIFF
SE
DIFF
SE
DIFF
SE
DIFF
SE
DIFF
RSE
NRSE
USB Cable
NI SHC68-68-EPM Cable
NI SHC6868 Cable
K-Cube USB Cable
DB-25 Connector Cable
PMT
Galvo/Galvo Controller
Laser
CM100
K-Cube
Computer
Armored Fiber Patch Cable
Motorized Objective Arm Cable
Rev A, December 16, 2016 Page 8
CM100 Chapter 4: Getting Started

Chapter 5 Alignment
You must align the microscope before imaging. There are two Alignment procedures: Illumination
Alignment and Grid Slide Alignment.
A. Illumination Alignment
Perform the Illumination Alignment procedure prior to Grid Slide Alignment.
1. Use the 2.5 mm hex wrench to remove the red front and back cover of the microscope.
There are six M4 screws on the back cover and one M4 screw on the front cover of the
microscope. To use the microscope for widefield imaging, see Widefield Imaging on Page
18
2. Use the 2 mm hex key to remove the dovetail cover on top of the microscope.
3. Use the slider on the objective holder to move it to its rear position, and then attach the
Alignment tool to the front port of the objective arm.
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CM100 Chapter 5: Alignment

4. Turn on all devices.
For the laser, turn the POWER key switch clockwise. The unit is ON when the display lights
up. DONOT activate the laser at this step.
5. Use the PWRADJUST knob on the laser to set it to maximum power.
6. Open ThorImageLS application, and select the hardware components you have setup in the
Hardware Setup window.
The Hardware Setup window appears when you open the ThorImageLS application.
Alternately, you can access it from the main screen of the application. Click on the
icon on the Menu panel to open the Hardware Setup window.
Make sure that a green dot appears next to the components that are relevant to your
hardware setup. A red dot appears if the device is not present or unable to communicate.
Rev A, December 16, 2016 Page 10
CM100 Chapter 5: Alignment

7. In the Galvo/Galvo Area Control panel, select Advanced and click .
WARNING
DONOTstare into the laser beam. Avoid direct eye exposure. Wear protective laser
eyewear. Use proper laser safety procedures. Consult with your organization's laser
safety officer for recommendations.
8. Press and release the ENABLE switch to activate the laser.
The LASER ON indicator lights up and after a delay of approximately 5 seconds, the source
begins to emit light.
9. Use the 2 mm hex wrench to adjust the tip and tilt of the Mirror Mount to center the beam on
the IR Disk of the Alignment tool.
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CM100 Chapter 5: Alignment

Use the iris on the Alignment tool to resize the beam on the center of the IR Disk. If the
beam on the IR disk appears clipped (not circular), please contact Thorlabs for assistance.
10. Press and release the ENABLEswitch to turn off the laser.
11. Remove the Alignment tool.
12. Place a piece of paper at the base of the microscope to visualize the beam.
13. Press and release the ENABLE switch to activate the laser.
14. Use the 2 mm hex key to adjust the XY Mount inside the microscope (the PM Patch cable is
connected to a XY Mount) in X and Y directions to center the hot spot (maximum beam
intensity at the center of the beam).
Note: A cell phone camera can help to visualize the hot spot of the beam on the paper.
Rev A, December 16, 2016 Page 12
CM100 Chapter 5: Alignment

Beam that Requires Adjustment Adjusted Beam
When you view the beam on the paper, the edges of the scanner mirrors give the beam a
non-circular profile.
The illumination alignment procedure is now complete.
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CM100 Chapter 5: Alignment

B. Grid Slide Alignment
Make sure to perform the Illumination Alignment procedure prior to Grid Slide Alignment.
1. Mount the objective onto the microscope.
2. Use four screws and washers to mount the Rigid Stand Slide Holder on the optical table.
Place the grid slide on the holder.
3. In the ThorImageLS application, set the parameters in the Galvo/Galvo Scanner Control
panel as shown in the image below.
4. In the Galvo/Galvo Area Control panel, set the parameters as shown in the image below.
5. Use the k-Cube Stepper Motor Controller to focus the objective onto the slide.
Rev A, December 16, 2016 Page 14
CM100 Chapter 5: Alignment

6. Use the 2 mm hex key to adjust the pinhole position in the X and Y directions to get
maximum beam intensity (a XYMount is attached to the pinhole inside the microscope).
7. In the Z Control panel, set the Slider Step Size to 1µm. Click Set next to the Start field to
store the Start location.
8. In the Z Control panel, use the ± button to gradually move the objective up (20µm distance
from the Start position). Observe if the image intensity decreases or increases.
If the intensity passes through a maximum, record the position of the objective.
9. Click Go next to the Start field to move the objective back to its original Start position.
10. In the Z Control panel, use the ± button to gradually move the objective down (20µm
distance from the Start position). Observe if the image intensity decreases or increases.
If the intensity passes through a maximum, record the position of the objective.
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CM100 Chapter 5: Alignment

11. Follow one of the below procedures based on your observation.
.If there is only one maximum intensity for the image, move the objective to the maximum point and adjust the
pinhole's X and Y position to maximize the intensity.
One Maximum Intensity
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CM100 Chapter 5: Alignment

.If there are two maximum intensities for the image, move the objective to the mid point of the two maximum
intensities. Then adjust the pinhole's X and Y position to maximize the intensity.
After the adjustment, you can see only one maximum intensity for the image.
Two Maximum Intensities
The grid slide alignment procedure is now complete and the system is ready for imaging.
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CM100 Chapter 5: Alignment