THORLABS GANYMEDE II HR User manual

GANYMEDE II HR
Spectral Domain OCT System
Operating Manual

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Table of Contents
Part 1. Introduction................................................................................................................................. 6
1.1. Safety.........................................................................................................................................................7
1.2. Care and Maintenance.............................................................................................................................8
1.2.1. Optical Cleaning.........................................................................................................................................8
1.2.2. Fiber Cleaning Techniques Using the FBC1..............................................................................................9
1.2.3. Service......................................................................................................................................................10
1.2.4. Accessories and Customization................................................................................................................10
Part 2. Description ................................................................................................................................ 11
2.1. Theory.....................................................................................................................................................11
2.1.1. Spectral Domain OCT Technology ..........................................................................................................11
2.1.2. Nomenclature in OCT imaging ................................................................................................................12
2.2. System Components...............................................................................................................................14
2.2.1. Packing List..............................................................................................................................................14
2.2.2. Base Unit..................................................................................................................................................16
2.2.3. Imaging Probe ..........................................................................................................................................17
2.2.4. Probe Stand...............................................................................................................................................20
2.2.5. Graphical User Interface...........................................................................................................................23
2.2.6. SDK..........................................................................................................................................................23
2.3. Warning Text..........................................................................................................................................24
Part 3. Installation ................................................................................................................................ 25
3.1. Unpacking...............................................................................................................................................25
3.2. System Connections ...............................................................................................................................25
3.3. System Installation.................................................................................................................................27
Part 4. System Operation ...................................................................................................................... 35
4.1. Starting the System................................................................................................................................35
4.2. Basic Adjustments..................................................................................................................................35
4.2.1. Adjusting the Focus..................................................................................................................................35
4.2.2. Adjusting the Reference Intensity ............................................................................................................36
4.2.3. Adjusting the Reference Length...............................................................................................................36
4.3. Shutting Down the System.....................................................................................................................37
4.4. Example Images .....................................................................................................................................38
Part 5. Imaging Artifacts ...................................................................................................................... 40
5.1. Saturation and Non-Linearity...............................................................................................................40
5.2. Wrong Reference Intensity Setting.......................................................................................................41
5.3. Auto-Interference...................................................................................................................................42
5.4. Multiple Scattering.................................................................................................................................43
5.5. Flipped Image.........................................................................................................................................44
5.6. Shadowing...............................................................................................................................................45
5.7. Image Distortion by Refractive Media.................................................................................................46

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5.7.1. Group Refractive Index............................................................................................................................47
5.7.2. Measurement Depth in OCT Systems ......................................................................................................48
5.7.3. Distortions in the Image ...........................................................................................................................49
Part 6. Troubleshooting........................................................................................................................ 51
6.1. Changing the Input Fuses......................................................................................................................52
Part 7. Certifications and Compliance................................................................................................. 53
Part 8. Warranty.................................................................................................................................... 54
8.1. Lasers and Imaging Systems.................................................................................................................54
8.2. Non-Warranty Repairs..........................................................................................................................54
8.3. Warranty Exclusions .............................................................................................................................54
Part 9. Specifications ............................................................................................................................ 55
Part 10. Mechanical Drawings............................................................................................................... 56
Part 11. Regulatory ................................................................................................................................. 58
11.1. Waste Treatment is Your Own Responsibility....................................................................................58
11.2. Ecological Background..........................................................................................................................58
Part 12. Thorlabs Worldwide Contacts .................................................................................................. 59

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Table of Figures
Figure 1 FBC1 Extended Mode............................................................................................................ 9
Figure 2 Cleaning Fiber Bulkheads...................................................................................................... 9
Figure 3 Cleaning Fiber Connectors .................................................................................................. 10
Figure 4 Schematic Diagram of the SD-OCT System ....................................................................... 11
Figure 5 A-scan Data Set.................................................................................................................... 12
Figure 6 B-scan Data Set.................................................................................................................... 12
Figure 7 Rendered Volumetric Data Set ............................................................................................ 13
Figure 8 En-Face View or C-scan...................................................................................................... 13
Figure 9 Base Unit.............................................................................................................................. 16
Figure 10 Imaging Probe (Front View)................................................................................................ 17
Figure 11 Imaging Probe (Rear View)................................................................................................. 17
Figure 12 Optical Layout of Imaging Probe ........................................................................................ 18
Figure 13 Reference Intensity Adjustment........................................................................................... 18
Figure 14 Reference Length Adjustment ............................................................................................. 19
Figure 15 Probe Stand with Imaging Probe ......................................................................................... 20
Figure 16 OCT Stand Coarse Adjustment and Cable Clip(rear view)................................................. 21
Figure 17 OCT Stand Adjusters and Dove Tail Slide.......................................................................... 21
Figure 18 OCT Stand Sample Station.................................................................................................. 22
Figure 19 Laser Emission Warning Labels.......................................................................................... 24
Figure 20 Base Unit Warning Labels................................................................................................... 24
Figure 21 Imaging Probe Warning Label............................................................................................. 24
Figure 22 Rear View of Base Unit....................................................................................................... 25
Figure 23 Interconnections of the Imaging Probe................................................................................ 26
Figure 24 Connections of the CameraLink Frame Grabber Card ........................................................ 26
Figure 25 Mounting the Imaging Probe into the Dove Tail Slide of the OCT Stand .......................... 27
Figure 26 CameraLink Frame Grabber Card inside the PC................................................................. 28
Figure 27 Trigger and CameraLink Cable attached to the PC ............................................................. 28
Figure 28 Attaching Trigger Cable to Base Unit ................................................................................. 28
Figure 29 CameraLink Cable Base Unit Attached to Base Unit.......................................................... 29
Figure 30 Power Supply Plug Connected to the Base Unit.................................................................. 29
Figure 31 Plugging the Probe Connector into the Imaging Probe ....................................................... 30
Figure 32 Installation of the Fiber at the Probe Fiber Connector......................................................... 31
Figure 33 Installing the Probe Connection at the Base Unit................................................................ 32
Figure 34 Installation of the fiber at the base unit Connector.............................................................. 33
Figure 35 Fiber Loop at the Base Unit................................................................................................. 34
Figure 36 Protection Cap Removal...................................................................................................... 34
Figure 37 Basic Focus Adjustment ...................................................................................................... 35
Figure 38 Different states of reference intensity adjustments.............................................................. 36
Figure 39 B-scan of an IR Viewing Card............................................................................................. 37
Figure 40 B-scan of a Nailfold, imaged at 28kHz A-scan Rate........................................................... 38
Figure 41 B-scan of a Finger Tip, imaged at 28kHz A-scan rate......................................................... 38
Figure 42 B-scan of a semi-transparent molded Plastic Cap................................................................ 39
Figure 43 B-scan of a laminated IR Card (not included) ..................................................................... 39
Figure 44 B-scan of a Section of a Grape ............................................................................................ 39
Figure 45 High Surface Reflection Causing Saturation and Nonlinear Response............................... 40

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Figure 46 Avoiding Strong Surface Reflection Using an Immersed Wedge ....................................... 41
Figure 47 OCT Images Acquired with Low, High and Good Reference Intensity Setting ................. 41
Figure 48 Auto-Interference from a Highly reflective Sample in a B-scan......................................... 42
Figure 49 Auto-Interference with the Reference Arm of the Imaging Probe Deactivated .................. 42
Figure 50 Schematic of a Setup to show the Influence of multiple Scattering .................................... 43
Figure 51 OCT Image showing multiple Scattering ............................................................................ 43
Figure 52 Correct Reference Length Setting for Imaging of an IR Card............................................. 44
Figure 53 Incorrect Reference Length Setting showing a Flipped Image............................................ 44
Figure 54 Rendered Volume of a Screw on top of an IR Viewing Card displaying Shadowing......... 45
Figure 55 Schematic of a Setup to show Distortions from Refractive Media...................................... 46
Figure 56 Height Shift of OCT Imaging through Refractive Media.................................................... 46
Figure 57 Measurement Depth with Refractive Media........................................................................ 48
Figure 58 Different Materials in one Measurement............................................................................. 49
Figure 59 Complex Structure in Image................................................................................................ 50
Figure 60 Fuse Cover on Base Unit Rear Panel................................................................................... 52
Figure 61 base unit dimensions............................................................................................................ 56
Figure 62 Imaging probe dimensions................................................................................................... 56
Figure 63 Dimension of the rotation stage underneath the sample plate ............................................. 57

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Part 1. Introduction
ATTENTION
Please read the instruction manual carefully before operating the SD-OCT system.
All statements regarding safety and technical specifications will only apply when the unit is
operated correctly.
This equipment is intended for laboratory use only and is not certified for medical
applications, including but not limited to life support situations.
Refer to this manual whenever the following symbols are encountered on the SD-OCT system:
Attention symbol indicates that additional information is given in this manual.
Laser Safety symbol indicates that laser radiation is present.
ATTENTION
Check the supply voltage of the system before plugging in the computer. Make sure the
included power cords for the base unit, computer and monitor are connected to a properly
grounded outlet (100 –240 VAC; 50 –60 Hz).
Transportation and delivery may cause the SD-OCT system to be warm or cool upon receipt.
Please wait for the system to reach room temperature before attempting to operate.
Operate this system on a flat, dry, and stable surface only.
WARRANTY WARNING
Do not open the Base Unit, Imaging Probe or PC. There are no user serviceable parts in this
product. Opening the device will void your warranty. Any modification or servicing of this
system by unqualified personnel renders Thorlabs free of any liability. This device can only
be returned when packed into the complete original packaging, including all foam packing
inserts. If necessary, ask for replacement packaging.

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1.1. Safety
SHOCK WARNING –HIGH VOLTAGE
Before applying power to the system, make sure that the protective conductor of the three-
conductor mains power cord is correctly connected to the protective earth contact of the
socket outlet. Improper grounding can cause electrical shock resulting in severe injury or
even death. Make sure that the line voltage rating agrees with your local supply and that the
appropriate fuses are installed. Fuses should only be changed by qualified service personnel.
Contact Thorlabs for assistance. Do not operate without cover installed. Refer servicing to
qualified personnel.
ATTENTION
Do not obstruct the air-ventilation slots in the computer housing. Do not obstruct air-
ventilation into the bottom of the base unit or out of the exhaust fan on the rear of the unit.
Mobile telephones, cellular phones, or other radio transmitters are not to be used within the
range of three meters of this unit, since the electromagnetic field intensity may exceed the
maximum allowed disturbance values according to IEC 61000-6-1:2005.
LASER RADIATION WARNING
Laser emission may be emitted
a) from the scan lens of the Imaging Probe (intended use)
b) from the back of the base unit when the fiber cap is removed and the fiber disconnected
c) from the output of the fiber when the fiber is not connected to the Imaging Probe
Do not look into the optical output when the device is operating. The laser radiation is not
visible to the human eye and can cause serious damage to your eyesight.
UNSICHTBARE LASERSTRAHLUNG
NICHT DIREKT MIT OPTISCHEN
INSTRUMENTEN BETRACHTEN
LASER KLASSE 1M
KLASSIFIZIERT NACH DIN EN 60825-1:2008
INVISIBLE LASER RADIATION
DO NOT STARE INTO BEAM OR VIEW
DIRECTLY WITH OPTICAL INSTRUMENTS
CLASS 1M LASER PRODUCT
CLASSIFIED ACCORDING TO DIN EN 60825-1:2008

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1.2. Care and Maintenance
Handle the system with care during transportation and unpacking. Banging or dropping the system can
damage the unit or lower system performance. If the system is mishandled during shipment, the optical
components may become misaligned, which could lead to a decrease in image quality. If this occurs, the
system will need to be realigned by qualified personnel. If the system is dropped from a height greater
than 15", Thorlabs will need to perform an electrical security check. Please contact Thorlabs Technical
Support for more information.
Do not store or operate in a damp, closed environment.
Do not store or operate on surfaces that are susceptible to vibrations.
Do not expose to direct sunlight.
Do not use solvents on or near the equipment.
Keep away from dust, dirt, and air-borne pollutants (including cigarette smoke). The system is
not designed for outdoor use. Protect the equipment from rain, snow, and humidity.
Do not expose to mechanical and thermal extremes. Protect the equipment from rapid variation
in temperature.
Handle all connectors, both electrical and optical, with care. Do not use unnecessary force, as
this may damage the connectors.
Handle the optical fiber with care. Mechanical stress can decrease performance and potentially
destroy the fiber. Continual bending of the optical fiber can cause damage. It is important,
therefore, to keep the optical fiber patch cable as straight as possible to minimize bending.
Note: The most common cause of low signal intensity is contamination of the fiber due to airborne
pollutants. To minimize exposure, avoid unnecessarily disconnecting the optical fiber patch cable. In
addition, it is advisable to check the fiber before making other adjustments to the optical system, such as
changing the focus or optical path length. Be sure to check the patch cord for a loose connection, and
make sure that the fiber is kept as straight as possible.
All lasers, especially lasers with resonator cavities that are defined by mechanical tolerances, are
delicate precision instruments and must be handled accordingly. The SD-OCT system is designed to
withstand normal transportation and operating conditions. Do not move the system while it is connected
and in operation.
1.2.1. Optical Cleaning
Good performance and image quality of the OCT microscope relies on clean optical connections.
Whenever using the Thorlabs OCT system, the following guidelines for optical fiber connection should
be followed:
1) Always inspect and clean the fiber end before plugging it into a receptacle.
2) Always cover the fiber end that is not in use with a fiber cap or dust protection cover.

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1.2.2. Fiber Cleaning Techniques Using the FBC1
This section details how to clean fiber bulkheads and fiber connectors using the FBC1 one-step cleaner.
Using Extended Mode
Figure 1 FBC1 Extended Mode
To use extended mode, pull the tip outward while simultaneously pushing down on the lock button.
Extended mode is useful for panels with multiple bulkhead connectors or other tight spaces.
Cleaning Fiber Bulkheads
Figure 2 Cleaning Fiber Bulkheads
Remove the guide cap completely from the device, and insert the tip of the cleaner into the bulkhead
connector. Push the case to start the cleaning process; a click indicates that the cleaning is complete.

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Cleaning Fiber Connectors
Figure 3 Cleaning Fiber Connectors
Open the cover on the guide cap, and insert the fiber connector over the guide cap. Push the case to start
the cleaning process; a click indicates that the cleaning is complete.
1.2.3. Service
Only trained and approved Thorlabs personnel are allowed to service the system. Please contact
Thorlabs Technical Support for more information.
1.2.4. Accessories and Customization
The GANYMEDE-II-HR Spectral Domain OCT System can easily be adapted for custom interfaces. To
achieve the listed specifications however this system should only be used with the accessories that
Thorlabs provides. Any modification or maintenance by unqualified personnel will render the warranty
null and void, leaving Thorlabs free of liability. Please contact Thorlabs Technical Support for questions
on customization.

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Part 2. Description
2.1. Theory
2.1.1. Spectral Domain OCT Technology
Spectral Domain Optical Coherence Tomography (SD-OCT) is a measurement method based on the
detection of optical path length differences. It incorporates a broadband light source with a high-speed
spectrometer to provide depth profiles that can be added to cross-sectional images. These cross-sectional
images can be used for 3-dimensional reconstructions.
SD-OCT uses Fourier Domain technology to determine the optical properties of an unknown sample by
analyzing the back-reflected and scattered light from an illuminated volume of the sample. The light of a
broadband source travels to the sample and illuminates it perpendicularly and with a small focus that
provides a good lateral resolution. The back-scattered light travels to the spectrometer where the unique
phase delay for each wavelength is detected. The depth information is acquired using a Fast Fourier
Transformation (FFT).
Figure 4 Schematic Diagram of the SD-OCT System
When added to a 2-dimensional image, the two main features of the scanned image are the axial and
lateral resolutions. The axial resolution does not depend on the optics; it is driven by the spectral
bandwidth of the light source. The lateral resolution, on the other hand, is affected by the chosen
application optics.
The SD-OCT system has four main parts: the base unit, a PC, an imaging probe and a probe stand (see
Figure 4 above for a schematic diagram of the SD-OCT system).
SLD
Trigger
CameraLink
USB
2.0
Probe Control
SM Fiber
0
0
High-Speed Signal Processing
Software
High-Level Application Software (GUI)
Driver Board
Spectrometer
Camera
Interferometer
Application
Scan System
Base Unit
Probe
PC
coupler

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2.1.2. Nomenclature in OCT imaging
As described before, the SD-OCT engine creates a depth profile from the interference of photons sent
into the sample and received back with photons reflected in the reference arm. This depth profile is
referred to as A-scan. Figure 5 shows a tomato’s A-scan data.
Figure 5 A-scan Data Set
The imaging probe is equipped with two galvanometer driven scanners. When scanning one mirror
while collecting multiple A-scans, a 2-dimensional image is created. This is referred to as a B-scan.
Here, the depth information is typically displayed from top to bottom, while the scan axis in Figure 2 is
from left to right. Figure 6 shows a B-scan data set.
Figure 6 B-scan Data Set

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When scanning both galvanometer mirrors, a volume can be acquired. This can be imaged by movable
sections through the volume or by 3D rendering (see Figure 7). Please refer to the SD-OCT Software
Manual for all features available.
Figure 7 Rendered Volumetric Data Set
When displaying a plane with both scan directions as axes, an en-face image is created. Here, the
viewing plane is parallel to the image plane of the color camera inside the imaging probe. This plane is
referred to as C-scan.
Figure 8 En-Face View or C-scan

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2.2. System Components
2.2.1. Packing List
Refer to the packing lists below to ensure that the system is complete. If any item is missing, contact
Thorlabs for assistance. Do not use your own spare parts. Please use the appropriate tools when
assembling a Spectral Domain SD-OCT system and handle all components of the system with care.
The system is shipped in three carton boxes containing the OCT engine, the computer system and the
OCT probe stand
GANYMEDE-II-HR System Box
This box should contain:
Qty
Part
Part
1
OCT Base Unit GANYMEDE-II-HR
1
OCT 3D Imaging Probe LSM03-BB
1
Distribution DVD -- OCT System Software
1
Manual SD-OCT Software
1
Manual SD-OCT GANYMEDE-II-HR
1
Power Cord
1
USB-Cable, 2m, A-B, USB 2.0
2
Fuse 2A (T), 5x20mm, Littlefuse 218P
1
Viewing Card for 400-640nm & 800-1700nm
1
connection cable set 2m, Base unit Imaging Probe
1
Fiber Patch Cord 2m, single mode 780nm, FC/APC
1
CameraLink Cable 2m
1
Trigger Cable SMB-SMB 2m

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Computer Box
This box should contain:
Qty
Part
1
Computer for Operating GANYMEDE II
1
CameraLink Data Acquisition Card
2
Power Cord
1
TFT Display for OCT-Computer
1
USB Keyboard
1
Dell Laser Mouse
1
Display Cable
Probe Stand Box
This box should contain:
Qty
Part
1
Baseplate with Translation & Rotation Stage
1
Post
1
Focus Block
1
Safety Ring
1
1/4"-20 Cap Screw
1
#8-32 Cap Screw
1
3/16" Hex Key
1
9/64" Hex Key
Note: Before operating the system, check to see if any parts have been damaged during transportation. If
so, please contact Thorlabs for further assistance.

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2.2.2. Base Unit
The base unit is the main component of the SD-OCT system. This unit sends light to the imaging probe,
communicates with the PC through a USB connection, triggers the camera of the spectrometer, and
delivers the measurement data to the frame grabber card of the PC via CameraLink interface. The base
unit contains a broadband super luminescent diode (SLD) which is connected to a fiber optic coupler
and directed to the probe and auxiliary ports at the backside of the device. The back-scattered and
reflected light from the imaging probe is returned through the fiber optic coupler, which directs the light
to a spectrometer (as described in Figure 4). Other components in the base unit include a high-speed
linear imaging sensor, analog and digital timing circuitry, analog control signals for the application, and
data acquisition hardware.
Figure 9 Base Unit
The central wavelength of the SLD based light source in this system is 900nm. Using near-IR broadband
sources balances the desire for low scattering losses with the need to operate within the wavelength
range that will provide higher penetration depth into the sample. As such, near-IR broadband sources are
a perfect compromise between sufficient transparency and a significantly reduced scattering coefficient.

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2.2.3. Imaging Probe
ThorlabsʼSD-OCT systems use a common path OCT setup in which the interferometer is located within
the imaging probe (see Figure 10). Integration of the interferometer eliminates the problems associated
with chromatic and polarization mode dispersion that are introduced by differences between individual
fibers in the sample and reference arms. The imaging probe is equipped with a white light illumination
ring.
Figure 10 Imaging Probe (Front View)
Figure 11 Imaging Probe (Rear View)
Reference Length
Adjustment Knob
Reference Intensity
Adjustment Knob
Ring Light Illumination
Probe
Control
Interface
Fiber
Connection
Dove Tail

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Figure 12 Optical Layout of Imaging Probe
Figure 12 illustrates the optical layout of the imaging probe. The output of an FC/APC fiber is
collimated and routed to a beam splitter cube. Here the beam is divided into a sample beam and a
reference beam, similar to a Michelson Interferometer. The sample beam is routed over two
galvanometer-actuated mirrors to allow for scanning in two axes. Then, the scan objective focuses the
beam in the sample. Back-scattered and back-reflected light from the sample is collected by the scan
objective again and travels back to the fiber. Light reflected into the reference arm is retro-reflected back
into the fiber. The intensity of the back-reflected light can be adjusted using the reference intensity
adjustment knob which will open or close a variable aperture inside the imaging probe.
Figure 13 Reference Intensity Adjustment
locked
unlocked

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In order to adjust the reference intensity adjustment knob, pull the knob approximately 5 mm outwards
(see Figure 10) until you feel the knob coming to a rest. A clockwise rotation will increase the amount of
reference light. For a qualitative indicator of the reference light intensity, observe the reference intensity
bar in the OCT software. Please refer to the Software Manual and chapter 5.1 for additional guidance.
The length of the reference arm can be adjusted with the reference length adjustment knob (see Figure
14). This adjustment will lead to a height shift of the OCT data set displayed. This adjustment is
necessary when imaging in a refractive sample medium. It can also be used to alter the height at which
the focal plane in the displayed OCT image.
Figure 14 Reference Length Adjustment
In order to adjust the reference length adjustment knob, pull the knob approximately 5 mm outwards
(see Figure 11) until you feel the knob coming to a rest. A clockwise rotation will increase the reference
length.
locked
unlocked

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2.2.4. Probe Stand
The Thorlabs SD-OCT system is shipped with a probe stand. To set up the probe stand, please consult
the instructions that you find in the probe stand box. The probe stand is equipped with a dove tail slide
for holding the imaging probe.
Figure 15 Probe Stand with Imaging Probe