THORLABS CM201 User manual

CM201
Green Fluorescent Protein
Confocal Microscope
User Guide

Copyright January 28, 2022, Thorlabs, Inc . All rights reserved.
Information inthis document is subject to change without notice. The software described in this document is furnished under alicense
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 aretrieval 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

CM201
Table of C on te n ts
Chapter 1 Warning Symbol 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 CM201 ................................................................................................... 5
4.3. Cable Connection Diagram.......................................................................................... 8
4.3.1. Electronic Control Unit (ECU) Connections..........................................................................9
4.3.2. Galvo-Galvo Scanning Pair.................................................................................................10
Chapter 5 Alignment..........................................................................................................................12
Chapter 6 Maintaining the CM201....................................................................................................23
6.1. Cleaning...................................................................................................................... 23
6.2. Connector Cleaning.................................................................................................... 23
6.3. Troubleshooting ......................................................................................................... 23
Chapter 7 Specifications...................................................................................................................24
Chapter 8 Mechanical Drawing........................................................................................................26
Chapter 9 Regulatory ........................................................................................................................27
Chapter 10 Thorlabs Worldwide Contacts........................................................................................28

CM201 Chapter 1: Warning Symbol Definitions
Rev G, January 28, 2022 Page 1
Chapter 1 Warning Symbol Def ini t ion s
Belowis 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
Warning: Laser Radiation
Caution: Spinning Blades May Cause Harm

CM201 Chapter 2: Safety
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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.

CM201 Chapter 3: Description
Rev G, January 28, 2022 Page 3
Chapter 3 Description
Thorlabs' Entry-Level Upright GFP (Green Fluorescent Protein) Confocal Microscope (CM201) 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 CM201 is optimized for
imaging fluorescence produced by GFP. The upright GFP confocal microscope system includes a laser, PMT
detector,objective, and motorized Z-axis control.
The CM201 features a movable silver-coated mirror on a manual slider at the front of the scan path that allows users
to select between confocal and widefield imaging modalities without replacing the optic. The confocal microscope is
designed so that imaging capabilities can be added to accommodate new experimental needs as your research
requirements grow.
3.1. Features at a Glance
•Upright Microscope Based on the Cerna DIY Microscopy Platform
o95 mm Dovetail on Rail Accepts Cerna Accessories
oD1N Dovetail on Top of Scan Path for Cerna Widefield Imaging Modules
•Confocal Scan Path with Galvo-Galvo Scanners
•One Benchtop Excitation Laser (488 nm SM Laser)
•One Multialkali PMT (Photomultiplier Tube)
•Optics Set for Fluorescence Imaging: Dichroic and Emission Filters
•Rigid Stand Slide Holder on Manual XY Stage, 1/2" Travel
•20X Nikon Objective
•PC with DAQ and ThorImage®LS 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 s Pixel Dwell Times
•884 m x 884 m Field of View

CM201 Chapter 4: Getting Started
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Chapter 4 Getting Started
This section is provided for those interested in getting the GFP Confocal Microscope up and running quickly.
4.1. Unpacking and Inspection
Open the package, and carefully remove the CM201 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
GFP Confocal Microscope
1
Rigid Stand on XY Translation Stage
1
20X Microscope Objective (N20X-PF)
1
NI Breakout Box
1
K-Cube Stepper Driver (KST101)
1
K-Cube Power Supply
1
Laser (S4FC488)
1
Galvo-Galvo Controller (LSKGG4(/M))
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
Dichroic Filtera(MD498)
1
Emission Filtera(MF525-39)
1
NI SHC68-68-EPM Cable
1
NI SH6868 Cable
1
Single Mode Fiber Patch Cable (P1-405B-FC-2)
1
Armored Fiber Patch Cable
1
K-Cube USB Cable
1
SMA to BNC Cable
1
Alignment Tool
1
Fluorescence Slide
1
Fluorescent Bead Slide
1
M6 x 16 mm Socket Head Cap Screw
12
1/4"-20 x 5/8" Socket Head Cap Screw
12
M6 Flat Washer
6
2 mm Hex Wrench
1
2.5 mm Hex Wrench
1
5 mm Hex L-Key
1
2 mm Hex L-Key
1
1.5 mm Hex Wrench
1
3/32" Hex L-Key
1
3/16" Hex L-Key
1
a.The filtersetcomes pre-installedon 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 28 for details).

CM201 Chapter 4: Getting Started
Rev G, January 28, 2022 Page 5
4.2. Setting up the CM201
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" forimperial) tomount the CM201 onto the optical table.
See the Mechanical Drawing Chapter on Page 26 for mounting holes.
2. Use the 2 mm hex wrench to remove the shipping plate on the objective arm.
3. Use the 3/32" hex key to remove the locking screw and move the slider to the front of the microscope.
4. Use two screws and washers to mount the K-Cube Stepper Motor Controller onto the optical table.
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.

CM201 Chapter 4: Getting Started
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B. Computer
1. Setup the computer, monitor, keyboard, and mouse.
2. Connect one end (silver) of the NI SHC68-68-EPMcable tothe computer (Connector 0) and the other end
(blue) to the rear panel of theNI BreakoutBox.
3. Connect one end of NI SH6868 cable to theNI Breakout Box and other end tothe DAQ port of the
Galvo/GalvoController.
C. Galvo/Galvo Controller
1. Connect the DB-25 Connector cable tothe Scanner port ofthe Controller and the other end to the Scanner
Controller port of theCM201.
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 CM201 back panel.
2. Connect one end of the SM (Single Mode) Fiber Patch cable to the laser and the other end to the CM201
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.

CM201 Chapter 4: Getting Started
Rev G, January 28, 2022 Page 7
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 of
the CM201.

CM201 Chapter 4: Getting Started
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4.3. Cable Connection Diagram

CM201 Chapter 4: Getting Started
Rev G, January 28, 2022 Page 9
4.3.1. Electronic Control Unit (ECU) Connections
Figure 1 Electronic Control Unit (ECU), Rear View
l X IN: This is the command signal for the X galvanometer. It is not used in Thorlabs complete imaging systems
setups.It may be monitored without interrupting thesystem, solong as the impedance is 1 kΩ.
| Y IN: This is the command signal for the Y galvanometer. It may be monitored without interrupting the system, so
long as the impedance is 1 kΩ.
| X OUT: This is the monitor signal that indicates the location of the X galvanometer. It may be monitored without
interrupting the system, so long as the impedance is 1 kΩ.
| Y OUT: This is the monitor signal that indicates the location of the Y galvanometer. It may be monitored without
interrupting the system, so long as the impedance is 1 kΩ.
To access scanning IO signals, a BNC2090A pass-through box is placed between the galvo-resonant controller
and the computer. The IO is shown below:
Figure 2 Description of Input/Output Signals from the Electronic Control Unit

CM201 Chapter 4: Getting Started
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4.3.2. Galvo-Galvo Scanning Pair
With Galvo-Galvo systems there are two galvos, a fast (X axis) galvo, and a slow (Y axis) galvo. The fast Galvo
moves across the image linearly, with even velocity. It takes 200 µs to turnaround at the edges of the image.
There is a turnaround at each side of the image. The slow Galvo (Y axis) controls line movement, and there is a
flyback between images.
The Line trigger is synchronized to the fast X galvo, triggering on the acquisition, and going to zero during the
turnarounds. This line trigger synchronization is true for both bidirectional/two-way and unidirectional/one-way
acquisition.

CM201 Chapter 4: Getting Started
Rev G, January 28, 2022 Page 11
The slow galvo (Y axis) moves once per image frame. During each sweep of the Y galvo scanner the ECU is
signaling a frame trigger (FRAME TRIGGER OUT or vertical line sync) for acquisition synchronization.

CM201 Chapter 5: Alignment
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Chapter 5 Alignment
You must align the microscope before imaging. There are two Alignment procedures: Fluorescence Slide
Alignment and Bead Slide Alignment.
A. Fluorescence Slide Alignment
Perform theFluorescence Slide Alignment procedure prior to Bead 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.
2. Use a 2 mm hex key to remove the dovetail cover on top of the microscope.

CM201 Chapter 5: Alignment
Rev G, January 28, 2022 Page 13
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.
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 the ThorImageLS Application and select the hardware components you have set up 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.

CM201 Chapter 5: Alignment
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7. In the Galvo/Galvo Area Control panel, select Advanced and click

CM201 Chapter 5: Alignment
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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 a 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.
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.

CM201 Chapter 5: Alignment
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12. Mount the objective onto the microscope.
13. Use four screws and washers to mount the Rigid Stand Slide Holder on the optical table.
Place the fluorescence slide on the holder.
14. Press and release the ENABLE switch to activate the laser.