THORLABS CM100 User manual

Reflective Confocal Microscope
CM100
User Guide

Copyright June 7, 2021 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 19
Chapter 6 Maintaining the CM100 20
6.1. Cleaning 20
6.2. Connector Cleaning 20
6.3. Troubleshooting 20
Chapter 7 Specifications 21
Chapter 8 Mechanical Drawing 24
Chapter 9 Regulatory 25
9.1. Waste Treatment is Your Own Responsibility 25
9.2. Ecological Background 25
Chapter 10 Thorlabs Worldwide Contacts 26
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
CM100 Chapter 1: Warning Symbols and Definitions
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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.
CM100 Chapter 2: Safety
Rev D, June 7, 2021 Page 2

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)
CM100 Chapter 3: Description
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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
Grid Slide (R1L3S3P) 1
M6x16 mm Socket Head Cap Screw 12
CM100 Chapter 4: Getting Started
Rev D, June 7, 2021 Page 4

Name Quantity
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 26 for details).
4.2. Setting up the CM100
CAUTION
DO NOT update the NI software. The newer version of the software may not be
compatible with ThorImageLS software.
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 24 for mounting holes.
2. Use the 2 mm hex wrench to remove the shipping plate on the objective arm.
CM100 Chapter 4: Getting Started
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3. Use two screws and washers to mount the K-Cube Stepper Motor Controller onto
the optical table.
4. Place the K-Cube Stepper Motor Controlled on the two dowels in the baseplate.
Secure it using the two clips on the baseplate.
5. Connect the cable from the Motorized Objective Arm to the Motor port of the K-
Cube Stepper Motor Controller.
6. Connect the K-Cube Power Supply to a standard power outlet.
7. 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.
CM100 Chapter 4: Getting Started
Rev D, June 7, 2021 Page 6

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.
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.
CM100 Chapter 4: Getting Started
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