Vega™ Series SS-OCT Systems

ThorImageOCT Documentation
ThorImageOCT Software Manual
Third-Party Software License Agreements

ThorImage^®OCT Software Index

• Introduction
  • Scan Control
  • Processing Options for Improving the Image Quality of OCT Images
  • Data Analysis for Measuring the Thickness of Layers
  • Third-Party Applications to Export/Reimport OCT Data
• Imaging Modes
• 1D Mode for Single Point Measurements
• 2D Mode for Cross-Sectional Imaging
• 3D Mode for Volume Imaging
• Doppler Mode for Doppler Flow Imaging
• Speckle Variance Mode for Angiographic Imaging
• Externally-Triggered Acquisition for Synchronized Measurements
• Analog Input for Synchronization with other Modalities
• Software Development Kits for Writing Custom Programs
• Probe Calibration for Different Configurations
• Video Showing Screencast of Rendering Capabilities

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Rendered Volume of a Zebrafish with Modifiable Clipping Plane

ThorImageOCT Software

• Interactive Scan Position Control through Video Display for Common Line Scans or Freeform Pattern Scans
• Advanced Dataset Management
• Access to Raw Spectra, Processsed Data, and All Calibration Files Necessary for User-Designed Processing Routines
• High-Speed Volume Rendering of 3D Data
• Doppler and Speckle Variance Imaging
• Versatile Scan and Acquisition Control, such as Averaging or Adjustable Scan Speeds

ThorImageOCT is a high-performance data acquisition software that is included with all Thorlabs OCT systems. This 64-bit Windows-based software acquires and displays OCT data, as well as includes scan control and processing options. Additionally, NI LabVIEW and C-based Software Development Kits (SDKs) are available, which contain a complete set of libraries for measurement control, data acquisition, and processing, as well as for storage and display of OCT images. The SDKs provide the means for developing highly specialized OCT imaging software for every individual application.

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Various acquisition parameters can be adjusted in ThorImageOCT.

Scan Control

ThorImageOCT provides numerous scan and acquisition controls. The camera integrated in the scanner of our OCT systems provides live video images in the application software. Defining the scan line for 2D imaging or the scan area for 3D imaging is accomplished through the easy-to-use "Draw and Scan" feature by clicking on the video image.

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The Sample Monitor can be used to define the scan pattern using the "Draw and Scan" feature.

Arbitrary forms defined by the Draw & Scan feature or loaded .txt files can be scanned. The scan pattern can also be adjusted by specifying suitable parameters in the controls of the software, as shown to the right.

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A predefined circle scan pattern can be loaded and scanned in the software. The size can be changed with the Zoom feature.

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A predefined triangle scan pattern can be loaded and scanned in the software. The size can be changed with the Zoom feature.

Additionally, one can further set processing parameters, averaging parameters, and the speed and sensitivity of the device using device presets. By using a high-speed preset, video-like frame rates in 2D and fast volume rendering in 3D are possible, whereas high-sensitivity acquisition is enabled by choosing a preset with a lower acquisition speed.

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Despeckle Filter Applied to an OCT Image of a Human Tooth

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OCT Image of a Human Tooth

Processing Options

ThorImageOCT provides features specifically designed to improve the quality of OCT images. The data can be modified during acquisition using processing parameters, such as image field correction and undersampling filters, or afterwards with filters. As shown to the right, the despeckle filter can be applied to an image to reduce speckle noise without blurring details of the imaged structure.

If additional processing functions are desired, ThorImageOCT can also integrate user-defined post-processing algorithms; see the Third Party Applications section for more details.

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The marker tool can be used to measure layer thickness.

Data Analysis

ThorImageOCT includes several tools for convenient data analysis. The integrated marker tool serves to measures distances, as well as the structure size. Additionally, this tool can be used to display intensity profile of the OCT data across a line. For precise distance and thickness measurements, the refractive index of the material under investigation can be set.

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The Dataset Management Window of ThorImageOCT

Dataset Management

ThorImageOCT provides advanced dataset management capabilities, which allow several datasets to be opened simultaneously. Datasets are uniquely defined using an identifier consisting of a study (or test series) name and an experiment number. Grouping of datasets can be achieved by using the same study name. The "Captured Datasets" list shows an overview of all open datasets, including the dataset identifier, the acquisition mode, and preview pictures of the still video image and the OCT data.

Datasets can be exported in various image formats, such as PNG, BMP, JPEG, PDF, or TIFF. The set can also be exported in complete data formats suited for post-processing purposes, such as RAW/SRM, FITS, VTK, VFF, and 32-bit floating-point TIFF.

The OCT file format native to ThorImageOCT allows OCT data, sample monitor data, and all relevant metadata to be stored in a single file. ThorImageOCT can also be installed and run on computers without OCT devices in order to view and export OCT data. The user has full access to the raw and processed data from the device, including additional data used for processing, e.g. offset errors.

Export buttons are accessible in the Action Toolbar of ThorImageOCT.

Third-Party Applications

If both ImageJ and ThorImageOCT are installed on the computer, opening acquired OCT data in ImageJ is one mouse click away. This enables a smooth workflow when requiring the advanced image processing functionality provided by ImageJ. Clicking the Explorer button will open the folder and select the file in Windows Explorer where the currently active dataset is stored.

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After smoothing the data in ImageJ, the marker tool in ThorImageOCT can be used to measure layer thickness.

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A filter for smoothing lateral directions is applied to the image in ImageJ.

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OCT data of a plastic multilayered film with speckle.

Acquired OCT datasets can also be exported and modified in a third-party program, and then reimported back into the ThorImageOCT software. This functionality allows for fast and customized modifications of OCT images, while still using the dataset management of the ThorImageOCT software. As shown in the example to the right, OCT data (left) can be exported to ImageJ and a smoothing filter applied in the lateral direction (center). Using the "External Program" button allows the modified data to be reimported into ThorImageOCT for further analysis. For example, the peak detection tool can be used to measure the layer thicknesses (right).

Imaging Modes

Different OCT imaging modes can be selected using the mode selector. If the ThorImageOCT software finds a compatible system connected and switched on, all operational modes will be selectable. If no OCT device is present, only the data viewing mode for viewing and OCT data export will be available.

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Several A-Scans at a Single Point Over Time (M-Scan)

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Spectral and Depth Information for a Single Point (A-Scan)

1D Mode

In this mode, single-point measurements can be made that provide spectral and depth information, as well as the ability to observe time-related sample behavior with an M-scan.

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ThorImageOCT Window in the 2D Mode

2D Mode

In the 2D imaging mode, the probe beam scans in one direction, acquiring cross-sectional OCT images which are then displayed in real time. Line averaging before or after the Fast Fourier Transform (FFT) is available, as well as B-Scan averaging. For long term measurements, a time series function, which has an adjustable time interval between two acquisitions, is included. Image display parameters, such as color mapping, can be controlled in this mode. We have also implemented an option for automatic calculation of the optimum contrast and brightness of the displayed OCT images.

3D Mode

In the 3D imaging mode, the OCT probe beam scans sequentially across the sample to collect a series of 2D cross-sectional images which are then processed to build a 3D image.

To accommodate long term measurements, a time series function that takes a series of 3D measurements is available. The number of volumes to be acquired and the time interval between scans are adjustable.

In the ThorImageOCT software, 3D volume datasets can be viewed as orthogonal cross-sectional planes (see below) and volume renderings.

The Sectional View features cross-sectional images in all three orthogonal planes, independent of the orientation in which the data was acquired. The view can be rotated as well as zoomed in and out.

The Rendering View provides a volumetric rendering of the acquired volume dataset. This view enables quick 3D visualization of the sample being imaged. Planes of any orientation can be clipped to expose structures within the volume. The 3D image can be zoomed in and out as well as rotated. Furthermore, the coloring and dynamic range settings can be adjusted.

Utilizing the full potential of our high-performance software in combination with our high-speed OCT systems, we have included a Fast Volume Rendering Mode in the ThorImageOCT software, which serves as a preview for high-resolution 3D acquisitions. In this mode, high-speed volume renderings can be displayed in real-time, providing rapid visualization of samples in three dimensions.

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Rendering View in ThorImageOCT

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Sectional View in ThorImageOCT

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Doppler dataset showing the velocity of a rotated plastic stick with opposite flow directions.

Doppler Mode

Doppler OCT imaging comes standard with all OCT systems. In the Doppler mode, phase shifts between adjacent A-scans are averaged to calculate the Doppler frequency shift induced by particle motion or flow. The number of lateral and axial pixels can be modified to change velocity sensitivity and resolution during phase shift calculation. The Doppler images are displayed in the main window with a color map indicating forward- or backward-directed flow, relative to the OCT beam.

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Speckle variance measurement showing blood vessels of a mouse brain.

Speckle Variance Mode

The speckle variance imaging mode is an acquisition mode which uses the variance of speckle noise to calculate angiographic images. It can be used to visualize three dimensional vessel trees without requiring significant blood flow and without requiring a specific acquisition speed window. The speckle variance data can be overlaid on top of intensity pictures providing morphological information. Different color maps can be used to display the multimodal pictures.

Externally-Triggered Acquisition

ThorImageOCT and the SDK APIs provide the ability to externally trigger the acquisition of A-Scans. This enables the user to synchronize measurements from different modalities (e.g. vibrometry and synchronized positioning) with an OCT measurement. Synchronization is greatly simplified with all current CameraLink-based Thorlabs OCT systems (a TTL level trigger signal source required). External triggering is available for all imaging modes and can be toggled in the settings dialog in ThorImageOCT.

Thorlabs' current generation of Ganymede (Item # GANxxx) and Telesto (Item #s TELxx1 & TELxx1PS) SD-OCT Systems include an external B-Scan trigger for synchronization with other experiments.

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Analog Data Visualization in the 2D Display

Analog Input for Synchronization with Other Modalities

Thorlabs' current generation of Ganymede (Item # GANxxx) and Telesto (Item #s TELxx1 & TELxx1PS) SD-OCT Systems include two analog input channels, which can be used to combine imaging modalities. The analog signal from another data source (i.e., fluorescence signal) is sampled and displayed simultaneously with the OCT signal.

Software Development Kits

For maximum flexibility, customized solutions can be implemented in ThorImageOCT using software development kits (SDKs). Experienced software developers can use these in a multitude of programming environments to tailor the use of Thorlabs OCT systems to their specific application. SDKs are available in:

• ANSI C with C++ Demo Programs
• LabVIEW^® Including Demo Programs and Advanced Sample Code

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Probe Calibration Window in ThorImageOCT

Probe Calibration

Changing to a different scan lens kit will generally require a different probe configuration in order to adapt to changes in the optical parameters of the system. When an additional scan lens is purchased for your Thorlabs OCT scanner system, ThorImageOCT enables you to easily create a fitting configuration for your new scan lens by using the calibration sample shipped with the lens and an intuitive step-by-step calibration process (shown to the right).

Video Showing Screencast of ThorImageOCT Rendering Capabilities

In this video, OCT images of a finger are acquired and manipulated in the 3D volume and cross section modes.

VCSEL Overview
Vertical Cavity Surface Emitting Lasers (VCSELs) are semiconductor-based devices that emit light perpendicular to the chip surface, as shown in Figure 1. VCSELs were originally developed as low-cost, low-power alternatives to edge-emitting diodes, mainly for high-volume datacom applications. Quickly thereafter, the advantages of VCSELs became evident, leading them to being preferred light sources over edge-emitters in many applications. Compared to edge-emitting sources, VCSELs offer superior output beam quality and single mode operation.

MEMS-tunable VCSELs utilize microelectromechanical mirror systems (MEMS) to vary the cavity length of the laser, thereby tuning the output wavelength. MEMS-tunable VCSELs have existed for several years; however, the limited tuning range and output power of these devices have precluded them from being used in OCT applications. Praevium Research, in cooperation with Thorlabs and MIT, has since developed a MEMS-tunable VSCEL design that overcomes these previous limitations.

In order for a MEMS-tunable VCSEL to be successful for applications in OCT, it needs to meet certain standards:

• Rapid Sweep Speed
• Broad Tuning Range
• Long Coherence Length
• High Laser Output Power

Rapid Sweep Speed
Applications using OCT demand high-speed imaging without sacrificing imaging quality. Fast imaging rates allow better time resolution, dense collection of 3D datasets, and decreased laser exposure times to the sample.

Currently, there exist a few swept-source lasers that offer high-speed scanning. Fourier domain mode-locked lasers, for example, achieve extremely high imaging speeds but require the use of very long fiber optic delays in the laser cavity and can only operate in wavelength ranges where the fiber loss is low. Of the commercially available high-speed swept lasers, many operate with multiple longitudinal modes or have long cavity lengths, which limit coherence length or tuning speed, respectively.

The low mass of the MEMS-tuning mirror in a MEMS-based tunable VCSEL and the short cavity length both contribute to its high-speed operation. The short cavity length also places only one mode in the gain spectrum, enabling single-mode continuous operation. We have recently measured greater than 500 kHz sweep rates using a MEMS-tunable VCSEL prototype, without using optical multiplexing to increase the sweep speed.

Broad Tuning Range
High-resolution imaging depends on the overall tuning bandwidth of the swept-source laser. Praevium boasts the broadest bandwidth MEMS-tunable VCSEL that has ever been developed. A unique design incorporating broadband, fully oxidized mirrors, as well as wideband gain regions and thin active regions, has currently resulted in greater than 100 nm of continuous mode-hop-free tuning, centered around 1300 nm. For details, please see Figure 3.

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Figure 4: Spectrum of MEMS-tunable VCSEL operating at 200 kHz, with a center wavelength around 1310 nm, and post amplification using a BOA.

Long Coherence Length
A significant limitation to most OCT systems is the depth of view (maximum imaging depth range). Especially in clinical applications, where sample thickness, patient motion, and sample location cannot be controlled, a long depth of view is advantageous. A long coherence length alone, however, is not enough. Image sensitivity needs to be virtually unaffected throughout the entire depth. Due to the micron-scale cavity length of the VCSEL and single mode, mode-hop-free operation, we have measured coherence lengths of greater than 100 mm from our MEMS-tunable VCSEL with nearly no signal degradation. Currently limited by detector bandwidth, we are confident that the MEMS-tunable VCSEL is able to achieve even longer imaging depths than have been measured to date. This remarkable depth of view will not only benefit the medical imaging community but also open doors to other applications such as large objective surface profiling, fast frequency domain reflectometry, and fast spectroscopic measurements with high spectral resolution.

High Output Power
Increased imaging speed often comes at the cost of decreased output power and/or optical power on the sample. One advantage of edge-emitting light sources over VCSELs is that they can emit greater output powers. As a general rule, most OCT imaging applications need a minimum of 20 mW of laser output power to maintain image quality when operating at faster scan rates. To reach this goal, the MEMS-tunable VCSEL is coupled with a booster optical amplifier (BOA) to achieve greater than 25 mW of power. An additional advantage of this post-amplification scheme is that the BOA reshapes the MEMS-VCSEL output spectrum such that it is much more uniform.

Additional Considerations and Manufacturing Capabilities
A special feature of the MEMS-tunable VCSEL is that it is scalable for different wavelengths. Through innovative combinations of gain materials and dielectric mirrors, a wide wavelength range in the visible or near infrared can be reached, enabling expansion of this new family of light sources.

As we further develop this light source, we look forward to finding new and exciting applications for its use. Please contact us to discuss how a MEMS-tunable VCSEL may advance your research.

Fabrication of a MEMS-Tunable VCSEL

Optical Coherence Tomography Tutorial

Optical Coherence Tomography (OCT) is a noninvasive optical imaging modality that provides real-time, 1D depth, 2D cross-sectional, and 3D volumetric images with micron-level resolution and millimeters of imaging depth. OCT images consist of structural information from a sample based on light backscattered from different layers of material within the sample. It can provide real-time imaging and is capable of being enhanced using birefringence contrast or functional blood flow imaging with optional extensions to the technology.

Thorlabs has designed a broad range of OCT imaging systems that cover several wavelengths, imaging resolutions, and speeds, while having a compact footprint for easy portability. Also, to increase our ability to provide OCT imaging systems that meet each customer’s unique requirements, we have designed a highly modular technology that can be optimized for varying applications.

Application Examples

Art Conservation

Drug Coatings

3D Profiling

In Vivo

Small Animal

Biology

Tissue Birefringence

Mouse Lung

Retina Cone Cells

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Figure 2

OCT is the optical analog of ultrasound, with the tradeoff being lower imaging depth for significantly higher resolution (see Figure 1). With up to 15 mm imaging range and better than 5 micrometers in axial resolution, OCT fills a niche between ultrasound and confocal microscopy.

In addition to high resolution and greater imaging depth, the non-contact, noninvasive advantage of OCT makes it well suited for imaging samples such as biological tissue, small animals, and materials. Recent advances in OCT have led to a new class of technologies called Fourier Domain OCT, which has enabled high-speed imaging at rates greater than 700,000 lines per second.¹ 

Fourier Domain Optical Coherence Tomography (FD-OCT; Figure 2) is based on low-coherence interferometry, which utilizes the coherent properties of a light source to measure optical path length delays in a sample. In OCT, to obtain cross-sectional images with micron-level resolution, and interferometer is set up to measure optical path length differences between light reflected from the sample and reference arms.

There are two types of FD-OCT systems, each characterized by its light source and detection schemes: Spectral Domain OCT (SD-OCT) and Swept Source OCT (SS-OCT). In both types of systems, light is divided into sample and reference arms of an interferometer setup, as illustrated in Figure 3. SS-OCT uses coherent and narrowband light, whereas SD-OCT systems utilize broadband, low-coherence light sources. Back scattered light, attributed to variations in the index of refraction within a sample, is recoupled into the sample arm fiber and then combined with the light that has traveled a fixed optical path length along the reference arm. A resulting interferogram is measured through the detection arm of the interferometer.

The frequency of the interferogram measured by the sensor is related to depth locations of the reflectors in the sample. As a result, a depth reflectivity profile (A-scan) is produced by taking a Fourier transform of the detected interferogram. 2D cross-sectional images (B-scans) are produced by scanning the OCT sample beam across the sample. As the sample arm beam is scanned across the sample, a series of A-scans are collected to create the 2D image.

Similarly, when the OCT beam is scanned in a second direction, a series of 2D images are collected to produce a 3D volume data set. With FD-OCT, 2D images are collected on a time scale of milliseconds, and 3D images can be collected at rates now below 1 second. 

Spectral Domain OCT vs. Swept Source OCT

Spectral Domain and Swept Source OCT systems are based on the same fundamental principle but incorporate different technical approaches for producing the OCT interferogram. SD-OCT systems have no moving parts and therefore have high mechanical stability and low phase noise. Availability of a broad range of line cameras has also enabled development of SD-OCT systems with varying imaging speeds and sensitivities.

SS-OCT systems utilize a frequency swept light source and photodetector to rapidly generate the same type of interferogram. Due to the rapid sweeping of the swept laser source, high peak powers at each discrete wavelength can be used to illuminate the sample to provide greater sensitivity with little risk of optical damage.

FD-OCT Signal Processing

In Fourier Domain OCT, the interferogram is detected as a function of optical frequency. With a fixed optical delay in the reference arm, light reflected from different sample depths produces interference patterns with the different frequency components. A Fourier transform is used to resolve different depth reflections, thereby generating a depth profile of the sample (A-scan).

¹V.Jayaraman, J. Jiang, H.Li, P. Heim, G. Cole, B. Potsaid, J. Fujimoto, and A. Cable, "OCT Imaging up to 760 kHz Axial Scan Rate Using Single-Mode 1310 nm MEMs-Tunable VCSELs with 100 nm Tuning Range," CLEO 2011 - Laser Applications to Photonic Applications, paper PDPB2 (2011).

To schedule an in-person or virtual demo appointment, please email OCT@thorlabs.com.

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Lübeck Demo Room

Try Our OCT Imaging Systems In Person or Virtually

From our OCT facility in Lüebeck, Germany and offices in Virginia, USA; Tokyo, Japan; and Shanghai, China; Thorlabs' application specialists and sales engineers look forward to helping you determine the best OCT system to meet your specific experimental needs. We can provide tailored recommendations and partner with you to obtain images of your samples, demonstrating the impact of the OCT base unit and probe optics on image quality.

Thorlabs' worldwide network allows us to operate demo rooms in a number of locations where you can see our OCT systems in action. We welcome the opportunity to work with you in person or virtually. A demo can be scheduled at any of our showrooms or virtually by contacting OCT@thorlabs.com.

Demo Rooms and Customer Support Sites
(Click Each Location for More Details)

Lübeck, Germany

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Thorlabs GmbH

Maria-Goeppert-Straße 9
23562 Lübeck

Customer Support

• Phone: +49 (0) 8131-5956-40840
• Email: oct@thorlabs.com

Demo Rooms

• Ganymede™ Series SD-OCT Systems
• Telesto^® Series SD-OCT Systems
• Telesto^® Series PS-OCT Systems
• Atria® Series SS-OCT Systems
• Vega™ Series SS-OCT Systems

Sterling, Virginia, USA

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Thorlabs Imaging Systems HQ

108 Powers Court
Sterling, VA 20166

Customer Support

• Phone: (703) 651-1700
• E-mail: ImagingTechSupport@thorlabs.com

Demo Rooms

• Ganymede™ Series SD-OCT Systems
• Telesto^® Series SD-OCT Systems

Nerima-ku, Tokyo, Japan

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Thorlabs Japan, Inc.

3-6-3 Kitamachi
Nerima-ku, Tokyo 179-0081

Customer Support

• Phone: +81-3-6915-7701
• Email: sales@thorlabs.jp

Demo Rooms

• Ganymede™ Series SD-OCT Systems

Shanghai, China

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Thorlabs China

Room A101, No. 100, Lane 2891, South Qilianshan Road
Shanghai 200331

Customer Support

• Phone: +86 (0)21-60561122
• Email: techsupport-cn@thorlabs.com

Demo Rooms

• Ganymede™ Series SD-OCT Systems
• Telesto^® Series SD-OCT Systems

Customer Support Sites
(Click Each Location for More Details)

Newton, New Jersey, USA

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Thorlabs HQ

43 Sparta Avenue
Newton, NJ 07860

Customer Support

• Phone: (973) 300-3000
• E-mail: techsupport@thorlabs.com

Ely, United Kingdom

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Thorlabs Ltd.

1 Saint Thomas Place, Ely
Ely CB7 4EX

Customer Support

• Phone: +44 (0)1353-654440
• E-mail: techsupport.uk@thorlabs.com

Bergkirchen, Germany

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Thorlabs GmbH

Münchner Weg 1
85232 Bergkirchen

Customer Support

• Phone: +49 (0) 8131-5956-0
• E-mail: europe@thorlabs.com

Maisons-Laffitte, France

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Thorlabs SAS

109, rue des Cotes
Maisons-Laffitte 78600

Customer Support

• Phone: +33 (0)970 440 844
• E-mail: techsupport.fr@thorlabs.com

São Carlos, SP, Brazil

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Thorlabs Vendas de Fotônicos Ltda.

Rua Rosalino Bellini, 175
Jardim Santa Paula
São Carlos, SP, 13564-050

Customer Support

• Phone: +55-16-3413 7062
• E-mail: brasil@thorlabs.com

Thorlabs offers a variety of OCT Imaging Systems to meet a range of application requirements. The OCT base unit and scan lens kit are key to OCT system performance. Significant performance characteristics, including axial resolution, A-Scan rate, and imaging depth, are entirely or strongly dependent on the design of the OCT base unit. The choice of scan lens kit determines other parameters, such as lateral resolution and field of view. Thorlabs offers a variety of OCT base units and scan lens kits that provide foundations for systems with a wide range of capabilities. The tables below present key performance parameters of our base units and include links to our other OCT imaging system pages. We encourage you to contact us directly at oct@thorlabs.com or via our online request form to discuss specific imaging requirements.

• These Item #s are OCT base units that can be customized using a wide selection of OCT scanners, lens kits, and optional accessories.
• Axial resolution and actual imaging depth are dependent on the optical properties of the sample being imaged.
• Values for the TEL2xx(PS) and TEL3xx(PS) Telesto systems are typical and were measured using a scanner with a common sample/reference path and 50% path split.
• Values for the TEL411 and TEL511 Telesto systems are typical and were measured using a scanner with a common sample/reference path and 70%/30% path split.