THORLABS CM401 User manual

Hyperspectral Imaging System
CM401
User Guide

Copyright June 27, 2017 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. Specifications Overview 4
Chapter 4 Getting Started 6
4.1. Unpacking and Inspection 6
4.2. Setting up the CM401 7
4.2.1. General Setup 7
4.2.2. System Installation 8
Chapter 5 Capturing an Image 11
Chapter 6 Maintaining the CM401 16
6.1. Cleaning 16
Chapter 7 Specifications 17
7.1. Microscope Body Specifications 17
7.2. Sample Holder Specifications 17
7.3. XY Translation Stage Specifications 17
7.4. Objective Specifications 18
7.5. Condenser Specifications 18
7.6. Tunable Bandpass Filter Specifications 19
7.7. Camera Port Specifications 20
7.8. Camera Specifications 20
7.9. Motorized Controller Specifications 21
7.10. Plasma Light Source Specifications 22
Chapter 8 Mechanical Drawing 24
Chapter 9 Regulatory 26
9.1. Waste Treatment is Your Own Responsibility 26
9.2. Ecological Background 26
Chapter 10 Thorlabs Worldwide Contacts 27
Table of Contents
CM401

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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CM401 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 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
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.
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CM401 Chapter 2: Safety

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, Kurios filter
includes a benchtop controller with external triggers.
3.1. Features at a Glance
● General Microscope Features
♦Microscope body with 7.74" Throat Depth
♦10X Magnification Plan Fluor Objective
♦Nosepiece with 1" of Fine Z Travel
♦0.9 NA Condenser Suitable for Brightfield, Phase Contrast, Darkfield, and DIC (Differential
Interference Contrast)
♦Condenser Holder with 1" of Fine Z Travel
♦Two 3-Axis Controllers and Knob Boxes
● Sample Holder
♦Adjustable-Height Slide Holder
♦XY Translation Stage with 1" Motorized Travel
● Image Collection
♦Low-Noise 4 MP Scientific Camera
♦Monochrome CCD with High Quantum Efficiency
● Computer
♦High Performance Computer for Rapid Image Acquisition and Data Transfer
♦Automated Wavelength Switching and Image Capture using DAQ and ThorImage®LS
Software
● Illumination
♦High Power Plasma Light Source
♦Liquid Crystal Tunable Bandpass Filter for Vibrationless Wavelength Switching from 420 to
730 nm
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CM401 Chapter 3: Description

3.2. Specifications Overview
The following table provides an overview of the CM401 specifications. For detailed specifications
on individual devices, see Specifications Chapter on Page 17.
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: 21 nm FWHM
Wide: 55 nm FWHM
Minimum Incremental Step Size 1 nm
Tuning Accuracy ±FWHM/10
Switching Speedb
Narrow: <200 ms
Medium: <80 ms
Wide: <50 ms
Scientific Camera Specifications
Item# 4070M-GE
Sensor Type ONSemiconductor KAI-04070M Monochrome CCD
Number of Active Pixels 2048 x 2048 (Horizontal x Vertical)
Pixel Size 7.4 µm x 7.4 µm
Imaging Area 15.2 mm x 15.2 mm (Horizontal x Vertical)
Host PC Interface Gigabit Ethernet
Vertical Hardware BinningcContinuous Integer Values from 1 to 10
Horizontal Software BinningcContinuous Integer Values from 1 to 10
Exposure Time 0 to 1000 s in 1 ms Increments
CCD Size and BinningcOne Tap Two Taps
20 MHz 40 MHz 20 MHz 40 MHz
Full Sensor (2048 x 2048) 4.1 fps 7.7 fps 7.4 fps 13 fps
Full Sensor, Bin by 2 (1024 x 1024) 7.5 fps 13.1 fps 12.8 fps 20.5 fps
Full Sensor, Bin by 10 (204 x 204) 21.6 fps 30.5 fps 30.0 fps 38.1 fps
Rev A, June 27, 2017 Page 4
CM401 Chapter 3: Description

Specification Value
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 Powerd4.0 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 1µm
Backlash 1µm
Minimum Achievable Incremental
Movement 100 nm
Minimum Repeatable Incremental
Movement 200 nm
Included Software
ThorImageLS 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.
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CM401 Chapter 3: Description

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 lists the
standard accessories shipped with the device.
Name Quantity
Microscope Body 1
Monochrome Scientific Camera (4070M-GE) 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
1/4-20x1/2" 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 parts or damage. If there is any problem,
please contact our nearest office (see Thorlabs Worldwide Contacts Chapter on Page 27 for details).
Rev A, June 27, 2017 Page 6
CM401 Chapter 4: Getting Started

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 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 make sure of best quality images.
● 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.
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CM401 Chapter 4: Getting Started

4.2.2. System Installation
CAUTION
DONOTinstall the Hyperspectral Imaging System by yourself. Only an authorized personnel
should install this system.
A. Mounting the System
1. Mount the microscope body onto the optical table.
2. Remove the shipping plates on the microscope body and rigid stand.
3. Mount the objective, camera, condenser onto the microscope body.
Rev A, June 27, 2017 Page 8
CM401 Chapter 4: Getting Started

4. Mount the rigid stand onto the optical table.
5. Mount the MCM3000 Controller Boxes(2X) onto the optical table.
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).
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CM401 Chapter 4: Getting Started

C. Cable Connections
CM401
MCM3000 MCM3000
TSI-IOBOB
Computer
HPLS343
Liquid Light Guide
Gigabit Ethernet Cable
Auxiliary Cable
Motorized Objective Arm Cable
X Axis Cable
Y Axis Cable
USB Cable
Filter Controller (Back View)
BNC Cable
BNC Cable
USB Cable
Optical Head Cable
1. Connect the 3 Axis Controllers to the MCM3000 Controller Boxes.
2. Connect the cables from the rigid stand and motorized objective arm to one of the
MCM3000 Controller Box.
3. Use an USBcable to connect the MCM3000 Controller Box to the computer.
4. Connect the cable from the condenser arm to the other MCM3000 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 an 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 supply of all the devices to a standard power outlet.
Rev A, June 27, 2017 Page 10
CM401 Chapter 4: Getting Started

Chapter 5 Capturing an Image
Make sure to install the required software before you start the experiment.
1. Open ThorImageLS application on the computer.
2. Select the desired devices from the Hardware Configuration window.
The following image shows the standard devices required for Hyperspectral system. Wait till
a green dot appears next to all the selected devices, and then click OK.
3. Use the Z Control panel to focus on the sample.
4. In the 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 Hardware Connections window. When imaging with a scientific camera only one channel
(A) appears on the Image Control panel.
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CM401 Chapter 5: Capturing an Image

5. In the Kurios Filter panel, set the value for Start, Stop, and Step Size.
You can set the Start and Stop value between 420–730 nm.
In the below image, the Start value 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 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 paper.
Rev A, June 27, 2017 Page 12
CM401 Chapter 5: Capturing an Image

8. Enter the Stop value as the Wavelength value (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 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.
11. Choose an arbitrary value between the Start and Stop wavelengths. In 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 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
+ 1
Stop Wavelength Start Wavelength
Step Size
( − )
.
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CM401 Chapter 5: Capturing an Image

In the above example, 11 different wavelengths have been recorded. The hyperspectral
acquisition uses the graph as reference to get the exposure corresponding to each
wavelength.
15. In the 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 a .raw and .hdr files.
Deselect the option to save every image as a .tiff file.
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CM401 Chapter 5: Capturing an Image

16. Click to start the acquisition.
17. Click 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.
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CM401 Chapter 5: Capturing an Image

Chapter 6 Maintaining the CM401
The 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 Thorlabs Worldwide
Contacts Chapter on Page 27 for details).
6.1. Cleaning
Refer to the user guide of the individual product for cleaning instructions.
WARNING
Disconnect the power supply before cleaning the unit to prevent any 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.
Rev A, June 27, 2017 Page 16
CM401 Chapter 6: Maintaining the CM401

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 1µm
Backlash 1µm
Minimum Achievable Incremental Movement 100 nm
Minimum Achievable Repeatable Movement 200 nm
Velocity (Max) 7 mm/s
Acceleration 11 mm/s2
Cable Length 6' (1.8m)
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
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CM401 Chapter 7: Specifications