THORLABS CM401 User manual

CM401
Hyperspectral Imaging
System
User Guide

Copyright © February 11, 2022 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

CM401 Hyperspectral Imaging System
Table of Contents
Chapter 1 Warning Symbol Definitions.............................................................................................1
Chapter 2 Safety...................................................................................................................................2
Chapter 3 Description .........................................................................................................................3
3.1. Features at a Glance..................................................................................................... 3
3.2. Specifications Overview............................................................................................... 4
Chapter 4 Getting Started...................................................................................................................5
4.1. Unpacking and Inspection ........................................................................................... 5
4.2. Setting up the CM401 ................................................................................................... 6
4.2.1. General Setup.......................................................................................................................6
4.2.2. System Installation................................................................................................................6
Chapter 5 Capturing an Image ...........................................................................................................9
Chapter 6 Maintaining the CM401....................................................................................................14
6.1. Cleaning...................................................................................................................... 14
Chapter 7 Specifications...................................................................................................................15
7.1. Microscope Body Specifications............................................................................... 15
7.2. Sample Holder Specifications.................................................................................... 15
7.3. XY Translation Stage Specifications......................................................................... 15
7.4. Objective Specifications ............................................................................................ 16
7.5. Condenser Specifications.......................................................................................... 16
7.6. Tunable Bandpass Filter Specifications................................................................... 17
7.7. Camera Port Specifications ....................................................................................... 17
7.8. Camera Specifications ............................................................................................... 18
7.9. Motorized Controller Specifications.......................................................................... 19
7.10. Plasma Light Source Specifications ......................................................................... 20
Chapter 8 Mechanical Drawing........................................................................................................21
8.1. Microscope without Sample Holder .......................................................................... 21
8.2. Microscope with Sample Holder................................................................................ 22
Chapter 9 Regulatory ........................................................................................................................23
Chapter 10 Thorlabs Worldwide Contacts........................................................................................24

CM401 Hyperspectral Imaging System Chapter 1: Warning Symbol Definitions
Rev C, July 15, 2022 Page 1
Chapter 1 Warning Symbol 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
Warning: Laser Radiation
Caution: Spinning Blades May Cause Harm

CM401 Hyperspectral Imaging System Chapter 2: Safety
Page 2 TTN131444-D02
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. 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 operated in a manner
not specified by Thorlabs, the protection provided by the equipment may be impaired.
WARRANTY WARNING
DO NOT open the controller, 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 housing or attempt any repairs or adjustments.
WARNING
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 wet, damp, or explosive conditions.

CM401 Hyperspectral Imaging System Chapter 3: Description
Rev C, July 15, 2022 Page 3
Chapter 3 Description
Thorlabs’ Hyperspectral Imaging System provides a platform to study a sample with co-located features. In
hyperspectral imaging, a stack of spectrally separated, two-dimensional images is acquired. This allows quick
sample identification and analysis.
The Hyperspectral Imaging System consists of Thorlabs’ flexible Cerna®microscope, Kurios® tunable filter, and
scientific-grade camera. The tunable bandpass filter allows narrow spectral regions to be individually imaged with
a monochrome camera. It helps to acquire images with quantitative spectral data for each pixel. Since the filter is
not moved or exchanged during measurement, the data is not subject to pixel shift image registration issues. In
addition, the Kurios filter includes a benchtop controller with external triggers.
3.1. Features at a Glance
•General Microscope Features
oMicroscope Body with 7.74" Throat Depth
o10X Magnification Plan Fluor Objective
oNosepiece with 1" of Fine Z Travel
o0.9 NA Condenser Suitable for Brightfield, Phase Contrast, Darkfield, and DIC (Differential
Interference Contrast)
oCondenser Holder with 1" of Fine Z Travel
oTwo 3-Axis Controllers and Knob Boxes
•Sample Holder
oAdjustable-Height Slide Holder
oXY Translation Stage with 1" Motorized Travel
•Image Collection
oLow-Noise 12.3 MP Scientific Camera
oMonochrome CMOS with High Quantum Efficiency
•Computer
oHigh Performance Computer for Rapid Image Acquisition and Data Transfer
oAutomated Wavelength Switching and Image Capture using DAQ and ThorImage®LS Software
•Illumination
oHigh-Power Plasma Light Source
oLiquid Crystal Tunable Bandpass Filter for Vibrationless Wavelength Switching from 420 to
730 nm

CM401 Hyperspectral Imaging System Chapter 3: Description
Page 4 TTN131444-D02
3.2. Specifications Overview
The following table provides an overview of the CM401 specifications. For detailed specifications on individual
devices, see the Specifications Chapter on page 15.
Specification
Value
Microscope
Cerna Series Modular Microscope
Objective
Nikon 10X Plan Fluorite Objective
(N10X-PF)
Condenser
0.9 NA Air Condenser (CSC1002)
Tunable Filter Specifications
Item #
KURIOS-VB1
Wavelength Range
420 –730 nm
Bandwidth, CWL = 550 nma
Narrow: 10 nm FWHM
Medium: 18 nm FWHM
Wide: 32 nm FWHM
Minimum Incremental Step Size
1 nm
Tuning Accuracy
±FWHM/10
Switching Speedb
Narrow: <230 ms
Medium: <150 ms
Wide: <100 ms
Scientific Camera Specifications
Item #
CS126MU
Sensor Type
CMOS Monochrome
Number of Active Pixels
4096 (H) x 3000 (V) (~12.3 MP)
Pixel Size
3.45 µm x 3.45 µm
Host PC Interface
Gigabit Ethernet
Vertical Hardware Binning
Continuous Integer Values from 1 to 16
Horizontal Hardware Binning
Continuous Integer Values from 1 to 16
Exposure Time
0.028 to 14700.9 ms
in ~0.014 ms Increments
ROI
Frame Ratec
Full Sensor (4096 x 3000)
21.7 fps
Half Sensor (2048 x 1500)
46.1 fps
~1/10th Sensor (410 x 300)
206.1 fps
Min ROI (260 x 4)
914.4 fps
Light Source Specifications
Item #
HPLS343
Type
High-Power Plasma Light Source and Ø3 mm LLG
(Liquid Light Guide)
Wavelength Range
350 –800 nm
Optical Output Powerd
4.0 W (Typical), 3.5 W (Minimum)
Automated Stage Specifications
1" (25.4 mm) Motorized Travel Nosepiece and Condenser Holder
1" (25.4 mm) Motorized Travel Sample Holder
Bidirectional Repeatability
1 µm
Backlash
1 µm
Minimum Achievable Incremental Movement
100 nm
Minimum Repeatable Incremental Movement
200 nm
Included Software
ThorImage®LS 3.1 with Lifetime Support
a. The bandpass width increases linearly with wavelength.
b. The switching speed depends upon the bandpass width setting and the initial and final wavelength.
c. Camera Frame Rate is impacted by the Vertical Hardware Binning parameter.
d. Measured at the output of the liquid light guide, when bulb and LLG are at start-of-life.

CM401 Hyperspectral Imaging System Chapter 4: Getting Started
Rev C, July 15, 2022 Page 5
Chapter 4 Getting Started
This section is provided for those interested in getting the Hyperspectral Imaging System up and running quickly.
4.1. Unpacking and Inspection
Open the package and carefully remove the CM401 and its accessories. The table below lists the standard
accessories shipped with the device.
Name
Quantity
Microscope Body
1
Monochrome Scientific Camera (CS126MU)
1
I/O Breakout Board for Scientific Camera (TSI-IOBOB)
1
Computer with Monitor, Keyboard, and Mouse
1
3-Axis Controller with Knob Box (MCM3001)
2
High-Power Light Source with Liquid Light Guide (HPLS343)
1
KURIOS Filter Controller with Optical Head Cable (KURIOS)
1
10X Nikon Plan Fluor Objective (N10X-PF)
1
Nikon D-CUD Universal Condenser 0.90 NA (CSC1002)
1
Rigid Stand on PLS-XY Translation Stage
1
BNC to SMA Cable
2
Auxiliary Cable (8050-CAB1)
2
M6 Socket Head Cap Screw
16
1/4-20 x 1/2" Socket Head Cap Screw
14
M6 Flat Washer
10
ThorCam Camera Software CD
1
Thorlabs Digital Camera Quick Start Guide
1
Inspect the device and its accessories for any missing or damaged parts. If there is any problem, please contact
our nearest office (see the Thorlabs Worldwide Contacts Chapter on page 24 for details).

CM401 Hyperspectral Imaging System Chapter 4: Getting Started
Page 6 TTN131444-D02
4.2. Setting up the CM401
4.2.1. General Setup
For optimal image acquisition, we strongly advise that the following standard practices are met:
•Acquire images using actively isolated or anti-vibrational table platforms. Failure to utilize appropriate
platforms results in poor quality images. Thorlabs offers a wide array of optical tables and platforms that
provide the necessary stability for your imaging needs.
•Whenever appropriate, avoid the placement of other instruments or machines that vibrate in close proximity
to your imaging setup. Such items include refrigeration units, cell culture incubators, hoods, etc.
•Minimize air drafts as it can result in movement of your imaging system. This can result in problems related
to focusing on your sample. Furthermore, drafts can also lead to particulate contamination that can damage
your hardware and/or introduce artifacts into your imaging field.
•Operate in light-controlled environments to ensure that images are at their best quality.
•Make sure that your hardware setup is operated within the appropriate environmental settings according to
the manufacturer’s specifications. Such considerations include enough space from surrounding walls and
ceilings from your hardware, sufficient sources of electrical power, and proper regulation of temperature
and humidity, etc.
4.2.2. System Installation
CAUTION
Initial component assembly required. Should you need assistance, arrangements can be made for a
service appointment to install the system. Please contact us ([e-mail] or
[e-mail], whichever you deem more appropriate) to obtain a quotation for
installation services.
A. Mounting the System
1. Mount the microscope body onto the optical table.
Figure 4-1 CM401 Initial Installation
2. Remove the shipping plates on the microscope body and rigid stand.

CM401 Hyperspectral Imaging System Chapter 4: Getting Started
Rev C, July 15, 2022 Page 7
3. Mount the objective, camera, and condenser onto the microscope body.
Figure 4-2 Mounting the Accessories
4. Mount the rigid stand onto the optical table.
5. Mount the MCM3001 Controller Boxes (2X) onto the optical table.
Figure 4-3 CM401 Final Arrangement
B. Computer
Please refer to the computer’s user manual for installation and operating instructions.
ThorImageLS 3.1 software comes preinstalled on the computer. Install the ThorCam camera software on the
computer (see the relevant user guide for details).

CM401 Hyperspectral Imaging System Chapter 4: Getting Started
Page 8 TTN131444-D02
C. Cable Connections
1. Connect the MCM3001 controllers to the Controller Boxes, as shown in the figure.
2. Connect the cables form the rigid stand (X and Y axes) and the motorized objective arm to one of the
MCM3001 Controller Boxes.
3. Use a USB cable to connect the MCM3001 Controller Box to the computer.
4. Connect the cable from the condenser arm to the other MCM3001 Controller Box.
5. Use the Liquid Light Guide to connect the LLG Port of Light Source (HPLS343) to the Illumination Module.
6. Use the Optical Head cable to connect the OPTICAL HEAD port of Filter Controller to the KURIOS filter.
7. Use a USB cable to connect the USB port of Filter Controller to the computer.
8. Use a BNC to SMA cable to connect the TRIGGER OUT port of Filter Controller to TRIGGER IN port of
TSI-IOBOB.
9. Use a BNC to SMA cable to connect the TRIGGER IN port of Filter Controller to FVAL OUT port of TSI-
IOBOB.
10. Use the auxiliary cable to connect the AUX port of the camera to TSI-IOBOB.
11. Connect the power suppy of all the devices to a standard power outlet.

CM401 Hyperspectral Imaging System Chapter 5: Capturing an Image
Rev C, July 15, 2022 Page 9
Chapter 5 Capturing an Image
Make sure to install the required software before you start the experiment.
1. Open the ThorImageLS application on the computer.
2. Select the desired devices from the Hardware Configuration window.
Figure 5-1 shows the standard devices required for the Hyperspectral Imaging System. Wait until a green
dot appears next to all of the selected devices, and then click OK.
3. Use the Z Control panel to focus on the sample.
4. In the Capture Setup tab, make sure that the Camera Control panel, Kurios Filter panel, and Z Control
panel are visible.
If you cannot see a panel, click Edit > Settings > Display Options, and select the desired panel. Click OK.
Note: The Kurios Filter panel appears only if you select ThorKurios as the Spectrum Filter in the
Hardware Connections window. When imaging with a scientific camera, only one channel (A) appears on
the Image Control panel.
Figure 5-1 Standard Device Requirement for CM401

CM401 Hyperspectral Imaging System Chapter 5: Capturing an Image
Page 10 TTN131444-D02
5. In the Kurios Filter panel, set the value for Start, Stop, and Step Size. You can set the Start and Stop
values between 420-730 nm.
Figure 5-2 displays a Start value that is set to the minimum wavelength (420 nm) of the KURIOS filter.
The Stop value is set to the maximum wavelength (730 nm) of the KURIOS filter. The ThorImageLS
application supports three different bandwidth modes: WIDE, MEDIUM, and NARROW.
6. Enter the Start value for the Wavelength value (for example, 420 nm), and then click the Live Icon (blue
circle with white triangle in the middle) in the Capture Setup panel.
7. In the Camera Control panel, change the Exposure value until you see the desired brightness on the
image.
Record the desired exposure value (Start Exposure) on a piece of paper.
Figure 5-2 KURIOS Filter Panel

CM401 Hyperspectral Imaging System Chapter 5: Capturing an Image
Rev C, July 15, 2022 Page 11
8. Enter the Stop value as the Wavelength (for example, 730 nm).
9. In the Camera Control panel, change the Exposure value until you see the desired brightness on the
image.
Record the desired Exposure value (Stop exposure) on a piece of paper.
10. In the Kurios Filter panel, click Add to create a new Hyperspectral sequence.
Enter a Name, Start Exposure, and Stop Exposure value. Click OK. A Hyperspectral Sequence window
appears.
Figure 5-3 Camera Control Panel
Figure 5-4 Setting Up New Hyperspectral Sequence

CM401 Hyperspectral Imaging System Chapter 5: Capturing an Image
Page 12 TTN131444-D02
11. Choose an arbitrary value between the Start and Stop wavelengths. In the Kurios Filter panel, enter the
arbitrary value for the Wavelength.
12. In the Camera Control panel, change the Exposure value until you see the desired brightness on the
image.
13. In the Hyperspectral Sequence window, click Record to save the point.
14. Repeat steps 11-13 for different wavelengths between the Start and Stop wavelengths.
Note: For best calibration, the number of wavelengths must be equal to
(𝑆𝑡𝑜𝑝 𝑊𝑎𝑣𝑒𝑙𝑒𝑛𝑔𝑡ℎ − 𝑆𝑡𝑎𝑟𝑡 𝑊𝑎𝑣𝑒𝑙𝑒𝑛𝑔𝑡ℎ)
𝑆𝑡𝑒𝑝 𝑆𝑖𝑧𝑒 + 1
Figure 5-5 Hyperspectral Sequence
Figure 5-6 Hyperspectral Experiment

CM401 Hyperspectral Imaging System Chapter 5: Capturing an Image
Rev C, July 15, 2022 Page 13
15. In the Capture tab, select Hyperspectral for Capture Mode.
This option is only visible if you select Scientific Camera as the Image Detector and ThorKurios as the
Spectrum Filter in the Hardware Connection window.
Select Raw Data Capture if you want to save the experiment as .raw and .hdr files. Deselect the option to
save every image as a .tiff file.
16. Click Start to start the acquisition.
17. Click the Review tab to load the captured experiment.
A new slider appears that shows the spectral wavelength of the current image and its index. For
information about the hyperspectral acquisition and camera settings, expand the Info panel.
Figure 5-6 Hyperspectral Experiment

CM401 Hyperspectral Imaging System Chapter 6: Maintaining the CM401
Page 14 TTN131444-D02
Chapter 6 Maintaining the CM401
This unit does not need regular maintenance. If you suspect a problem with your CM401, please contact our nearest
office for assistance from an application engineer (see the Thorlabs Worldwide Contacts Chapter on page 24
for details).
6.1. Cleaning
Refer to the user guide of the individual product for cleaning instructions.
CAUTION
Disconnect the power supply before cleaning the unit to prevent injuries.
CAUTION
DO NOT expose the unit to spray, liquids, or solvents. This may damage the unit. Use a damp, lint-free
cloth to clean the unit.

CM401 Hyperspectral Imaging System Chapter 7: Specifications
Rev C, July 15, 2022 Page 15
Chapter 7 Specifications
7.1. Microscope Body Specifications
Specification
Value
Rail Length
95 mm
Throat Depth
196.5 mm (7.74")
Objective Thread Adapter (Included)
External M32 x 0.75 Threads
Internal M25 x 0.75 Threads
7.2. Sample Holder Specifications
Specification
Value
Included Sample Holder
Adjustable-Height Slide Holder
Sample Holder Stage
XY Translation Stage, 1" Motorized Travel
7.3. XY Translation Stage Specifications
Specification
Value
Travel Range
25.4 mm (1")
Bidirectional Repeatability
1 µm
Backlash
1 µm
Minimum Achievable Incremental Movement
100 nm
Minimum Achievable Repeatable Movement
200 nm
Velocity (Max)
7 mm/s
Acceleration
11 mm/s2
Cable Length
6' (1.8 m)
Load Capacity
Stage Mounted to Vertical Rail
Recommended: ≤10 lbs (4.5 kg)
Maximum: 10 lbs (4.5 kg)
Stage Mounted to Horizontal Rail
Recommended: ≤33.5 lbs (15.2 kg)
Maximum: 42 lbs (19.1 kg)
Stepper Motor Specifications
Thread Screw Pitch
0.3 mm
Step Angle
1.8°
Limit Switches
Hall Effect Sensors
Phase Current
0.49 A
Phase Resistance
5.1 Ω
Phase Inductance
1.5 mH
Insulation Resistance
20 MΩ

CM401 Hyperspectral Imaging System Chapter 7: Specifications
Page 16 TTN131444-D02
7.4. Objective Specifications
Specification
Value
Item #
N10X-PF
Magnification
10X
Manufacturer Part #
MRH00101
Numerical Aperture (NA)
0.3
Working Distance (WD)
16 mm
Parfocal Length
60 mm
Compatible Tube Lens Focal Length
200 mm
Coverslip Correction
0.17 mm
Barrel Diameter
30.0 mm
Length
48.7 mm
Threading
M25 x 0.75
7.5. Condenser Specifications
Specification
Value
Item #
CSC1002
Manufacturer Part #
MBL99005
Air or Oil Immersion
Air
Condenser Type
Achromatic
Numeric Aperture (NA)
0.9
Aperture Adjustment
Yes
Working Distance
2.3 mm
Recommended Objective Magnification
2X –100X
Dovetail
Male D3N
Internal Turret Slots
Number of Slots
7
Through Hole
Ø32.5 mm (Ø1.28")
DIC Prisma
Slot for N1
Slot for N2
Oblique
No
Darkfield
1 Slot (Not Included)
Phase
3 Slots for Phase Annulus (Not Included)
a. N1 and N2 condenser prisms should be paired with a compatible dry objective.

CM401 Hyperspectral Imaging System Chapter 7: Specifications
Rev C, July 15, 2022 Page 17
7.6. Tunable Bandpass Filter Specifications
Specification
Value
Item #
KURIOS-VB1
Wavelength
420 –730 nm
Bandwidth, CWL = 550 nma
Narrow: 10 nm FWHM
Medium: 18 nm FWHM
Wide: 32 nm FWHM
Switching Speedb
Narrow: <230 ms
Medium: <150 ms
Wide: <100 ms
Clear Aperture
Ø20 mm
Polarized Transmission, CWL = 550 nmc
Narrow: 13%
Medium: 17%
Wide: 20%
Out-of-Band Blocking
OD>2
Minimum Incremental Step Size
1 nm
Tuning Accuracy
±FWHM/10
Angle of Incidence (Field of View)
±6°
Wavelength Uniformity
FWHM/4 over Clear Aperture
Damage Threshold
Pulsed (ns)
0.1 J/cm2
Pulsed (fs)
0.02 J/cm2 (532 nm, 76 Hz, 100 fs, Ø162 µm)
CWd
0.8 W/cm (532 nm, Ø0.471 mm)
Filter Head Dimensions
52.6 mm x 52.6 mm x 78.5 mm
(2.07" x 2.07" x 3.09")
Filter Head Front/Rear Threading
SM1 (1.035"-40) Internal Threads
Filter Head Mounting Options
8-32 (M4) Tap for Post Mounting (3 Places)
> 4-40 Taps for Cage System
Operating Temperature
0 to 40 °C
Storage Temperature
-15 to 65 °C
a. The bandpass width increases linearly with wavelength.
b. The switching speed depends upon the bandpass width setting and the initial and final wavelength.
c. Typical transmission for input light polarized parallel to the filter’s transmission axis.
d. The power density of your beam should be calculated in terms of W/cm.
7.7. Camera Port Specifications
Specification
Value
Magnification
1X
Dovetail
Male D1N
Tube Lens Focal Length
200 mm
Camera Threading
C-Mount (1.00"-32)