Averaging techniques for OCT imaging

OCTA: Essential or Gimmick?

This commentary article delves into the transformative role of optical coherence tomography angiography (OCTA) in diagnosing and managing a wide array of eye conditions, including diabetic retinopathy, age-related macular degeneration, retinal vein occlusions, and white dot syndromes. Developed in 2005, OCTA has emerged as a non-invasive, high-resolution imaging technique that offers advantages over traditional fluorescein angiography (FA), providing quicker and safer monitoring of ocular conditions with similar diagnostic accuracy. In diabetic retinopathy, OCTA has been instrumental in early identification of retinal changes, offering quantifiable metrics including perfused capillary density (PCD) for assessing vascular alterations. For age-related macular degeneration (AMD), OCTA has deepened our understanding of non-exudative neovascular AMD, allowing for more effective monitoring and potential earlier initiation of treatment. In cases of retinal vein occlusions, OCTA can reveal specific microvascular features and allow for depth-resolved measurements of the foveal avascular zone, providing significant prognostic implications. OCTA has also been invaluable in studying rare white dot syndromes, enabling nuanced differentiation between conditions that often present similarly. Emerging research also suggests that OCTA can have potential utility in neurodegenerative diseases like Alzheimer's, where retinal vascular patterns could offer diagnostic insights. While OCTA is revolutionizing ophthalmic care, further clinical trials and standardization are needed for its broader adoption into clinical practice.

Probabilistic volumetric speckle suppression in OCT using deep learning

We present a deep learning framework for volumetric speckle reduction in optical coherence tomography (OCT) based on a conditional generative adversarial network (cGAN) that leverages the volumetric nature of OCT data. In order to utilize the volumetric nature of OCT data, our network takes partial OCT volumes as input, resulting in artifact-free despeckled volumes that exhibit excellent speckle reduction and resolution preservation in all three dimensions. Furthermore, we address the ongoing challenge of generating ground truth data for supervised speckle suppression deep learning frameworks by using volumetric non-local means despeckling-TNode- to generate training data. We show that, while TNode processing is computationally demanding, it serves as a convenient, accessible gold-standard source for training data; our cGAN replicates efficient suppression of speckle while preserving tissue structures with dimensions approaching the system resolution of non-local means despeckling while being two orders of magnitude faster than TNode. We demonstrate fast, effective, and high-quality despeckling of the proposed network in different tissue types that are not part of the training. This was achieved with training data composed of just three OCT volumes and demonstrated in three different OCT systems. The open-source nature of our work facilitates re-training and deployment in any OCT system with an all-software implementation, working around the challenge of generating high-quality, speckle-free training data.

Time-domain diffuse correlation spectroscopy at large source detector separation for cerebral blood flow recovery

Time-domain diffuse correlation spectroscopy (td-DCS) enables the depth discrimination in tissue's blood flow recovery, considering the fraction of photons detected with higher time of flight (TOF) and longer pathlength through the tissue. However, the recovery result depends on factors such as the instrument response function (IRF), analyzed TOF gate start time, gate width and the source-detector separation (SDS). In this research we evaluate the performance of the td-DCS technique at three SDSs of 1.5, 2 and 2.5 cm to recover cerebral blood flow (CBF). To do that we presented comprehensive characterization of the td-DCS system through a series of phantom experiments. First by quality metrices such as coefficient of variation and contrast-to-noise ratios, we identified optimal time gate(s) of the TOF to extract dynamics of particles. Then using sensitivity metrices, each SDS ability to detect dynamics of particles in superficial and deeper layer was evaluated. Finally, td-DCS at each SDS was tested on healthy volunteers during cuff occlusion test and breathing tasks. According to phantom measurements, the sensitivity to estimate perfusion within the deep layer located at depth of 1.5 cm from the surface can be increased more than two times when the SDS increases from 1.5 cm to 2.5 cm.

Time-Resolved Dynamic Optical Coherence Tomography for Retinal Blood Flow Analysis

Purpose

Optical coherence tomography (OCT) representations in clinical practice are static and do not allow for a dynamic visualization and quantification of blood flow. This study aims to present a method to analyze retinal blood flow dynamics using time-resolved structural OCT.

Methods

We developed novel imaging protocols to acquire video-rate time-resolved OCT B-scans (1024 × 496 pixels, 10 degrees field of view) at four different sensor integration times (integration time of 44.8 µs at a nominal A-scan rate of 20 kHz, 22.4 µs at 40 kHz, 11.2 µs at 85 kHz, and 7.24 µs at 125 kHz). The vessel centers were manually annotated for each B-scan and surrounding subvolumes were extracted. We used a velocity model based on signal-to-noise ratio (SNR) drops due to fringe washout to calculate blood flow velocity profiles in vessels within five optic disc diameters of the optic disc rim.

Results

Time-resolved dynamic structural OCT revealed pulsatile SNR changes in the analyzed vessels and allowed the calculation of potential blood flow velocities at all integration times. Fringe washout was stronger in acquisitions with longer integration times; however, the ratio of the average SNR to the peak SNR inside the vessel was similar across all integration times.

Conclusions

We demonstrated the feasibility of estimating blood flow profiles based on fringe washout analysis, showing pulsatile dynamics in vessels close to the optic nerve head using structural OCT. Time-resolved dynamic OCT has the potential to uncover valuable blood flow information in clinical settings.

Sub2Full: split spectrum to boost optical coherence tomography despeckling without clean data

Optical coherence tomography (OCT) suffers from speckle noise, causing the deterioration of image quality, especially in high-resolution modalities such as visible light OCT (vis-OCT). Here, we proposed an innovative self-supervised strategy called Sub2Full (S2F) for OCT despeckling without clean data. This approach works by acquiring two repeated B-scans, splitting the spectrum of the first repeat as a low-resolution input, and utilizing the full spectrum of the second repeat as the high-resolution target. The proposed method was validated on vis-OCT retinal images visualizing sublaminar structures in the outer retina and demonstrated superior performance over state-of-the-art Noise2Noise (N2N) and Noise2Void (N2V) schemes.

Polarization-artifact reduction and accuracy improvement of Jones-matrix polarization-sensitive optical coherence tomography by multi-focus-averaging based multiple scattering reduction

Polarization-sensitive optical coherence tomography (PS-OCT) is a promising biomedical imaging tool for the differentiation of various tissue properties. However, the presence of multiple-scattering (MS) signals can degrade the quantitative polarization measurement accuracy. We demonstrate a method to reduce MS signals and increase the measurement accuracy of Jones matrix PS-OCT. This method suppresses MS signals by averaging multiple Jones matrix volumes measured using different focal positions. The MS signals are decorrelated among the volumes by focus position modulation and are thus reduced by averaging. However, the single scattering signals are kept consistent among the focus-modulated volumes by computational refocusing. We validated the proposed method using a scattering phantom and a postmortem medaka fish. The results showed reduced artifacts in birefringence and degree-of-polarization uniformity measurements, particularly in deeper regions in the samples. This method offers a practical solution to mitigate MS-induced artifacts in PS-OCT imaging and improves quantitative polarization measurement accuracy.

Speckle contrast reduction through the use of a modally-specific photonic lantern for optical coherence tomography

A few-mode optical coherence tomography (FM-OCT) system was developed around a 2 × 1 modally-specific photonic lantern (MSPL) centered at 1310 nm. The MSPL allowed FM-OCT to acquire two coregistered images with uncorrelated speckle patterns generated by their specific coherent spread function. Here, we showed that averaging such images in vitro and in vivo reduced the speckle contrast by up to 28% and increased signal-to-noise ratio (SNR) by up to 48% with negligible impact on image spatial resolution. This method is compatible with other speckle reduction techniques to further improve OCT image quality.

SNR-Net OCT: brighten and denoise low-light optical coherence tomography images via deep learning

Low-light optical coherence tomography (OCT) images generated when using low input power, low-quantum-efficiency detection units, low exposure time, or facing high-reflective surfaces, have low bright and signal-to-noise rates (SNR), and restrict OCT technique and clinical applications. While low input power, low quantum efficiency, and low exposure time can help reduce the hardware requirements and accelerate imaging speed; high-reflective surfaces are unavoidable sometimes. Here we propose a deep-learning-based technique to brighten and denoise low-light OCT images, termed SNR-Net OCT. The proposed SNR-Net OCT deeply integrated a conventional OCT setup and a residual-dense-block U-Net generative adversarial network with channel-wise attention connections trained using a customized large speckle-free SNR-enhanced brighter OCT dataset. Results demonstrated that the proposed SNR-Net OCT can brighten low-light OCT images and remove the speckle noise effectively, with enhancing SNR and maintaining the tissue microstructures well. Moreover, compared to the hardware-based techniques, the proposed SNR-Net OCT can be of lower cost and better performance.

Live 4D-OCT denoising with self-supervised deep learning

By providing three-dimensional visualization of tissues and instruments at high resolution, live volumetric optical coherence tomography (4D-OCT) has the potential to revolutionize ophthalmic surgery. However, the necessary imaging speed is accompanied by increased noise levels. A high data rate and the requirement for minimal latency impose major limitations for real-time noise reduction. In this work, we propose a low complexity neural network for denoising, directly incorporated into the image reconstruction pipeline of a microscope-integrated 4D-OCT prototype with an A-scan rate of 1.2 MHz. For this purpose, we trained a blind-spot network on unpaired OCT images using a self-supervised learning approach. With an optimized U-Net, only a few milliseconds of additional latency were introduced. Simultaneously, these architectural adaptations improved the numerical denoising performance compared to the basic setup, outperforming non-local filtering algorithms. Layers and edges of anatomical structures in B-scans were better preserved than with Gaussian filtering despite comparable processing time. By comparing scenes with and without denoising employed, we show that neural networks can be used to improve visual appearance of volumetric renderings in real time. Enhancing the rendering quality is an important step for the clinical acceptance and translation of 4D-OCT as an intra-surgical guidance tool.

In Vivo Imaging of Retinal and Choroidal Morphology and Vascular Plexuses of Vertebrates Using Swept-Source Optical Coherence Tomography

Purpose

To perform in vivo evaluation of the structural morphology and vascular plexuses of the neurosensory retina and choroid across vertebrate species using swept-source optical coherence tomography (SS-OCT) and SS-OCT angiography (SS-OCTA) imaging.

Methods

A custom-built SS-OCT system with an incorporated flexible imaging arm was used to acquire the three-dimensional (3D) retinal OCT and vascular OCTA data of five different vertebrates: a mouse (C57BL/6J), a rat (Long Evans), a gray short-tailed opossum (Monodelphis domestica), a white sturgeon (Acipenser transmontanus), and a great horned owl (Bubo virginianus).

Results

In vivo structural morphology of the retina and choroid, as well as en face OCTA images of retinal and choroidal vasculature of all species were generated. The retinal morphology and vascular plexuses were similar between rat and mouse, whereas distinct choroidal and paired superficial vessels were observed in the opossum retina. The retinal and vascular structure of the sturgeon, as well as the pecten oculi and overlying the avascular and choroidal vasculature in the owl retina are reported in vivo.

Conclusions

A high-quality two-dimensional and 3D in vivo visualization of the retinal structures and en face visualization of the retina and choroidal vascular plexus of vertebrates was possible. Our studies affirm that SS-OCT and SS-OCTA are viable methods for evaluating the in vivo retinal and choroidal structure across terrestrial, aquatic, and aerial vertebrates.

Translational Relevance

In vivo characterization of retinal morphology and vasculature plexus of multiple species using SS-OCT and SS-OCTA imaging can increase the pool of species available as models of human retinal diseases.

Analysis and reduction of noise-induced depolarization in catheter based polarization sensitive optical coherence tomography

In catheter based polarization sensitive optical coherence tomography (PS-OCT), a optical fiber with a rapid rotation in the catheter can cause low signal-to-noise ratio (SNR), polarization state instability, phase change of PS-OCT signals and then heavy noise-induced depolarization, which has a strong impact on the phase retardation measurement of the sample. In this paper, we analyze the noise-induced depolarization and find that the effect of depolarization can be reduced by polar decomposition after incoherent averaging in the Mueller matrix averaging (MMA) method. Namely, MMA can reduce impact of noise on phase retardation mapping. We present a Monte Carlo method based on PS-OCT to numerically describe noise-induced depolarization effect and contrast phase retardation imaging results by MMA and Jones matrix averaging (JMA) methods. The peak signal to noise ratio (PSNR) of simulated images processed by MMA is higher than about 8.9 dB than that processed by JMA. We also implement experiments of multiple biological tissues using the catheter based PS-OCT system. From the simulation and experimental results, we find the polarization contrasts processed by the MMA are better than those by JMA, especially at areas with high depolarization, because the MMA can reduce effect of noise-induced depolarization on the phase retardation measurement.

Refractive-index matching enhanced polarization sensitive optical coherence tomography quantification in human brain tissue

The importance of polarization-sensitive optical coherence tomography (PS-OCT) has been increasingly recognized in human brain imaging. Despite the recent progress of PS-OCT in revealing white matter architecture and orientation, quantification of fine-scale fiber tracts in the human brain cortex has been a challenging problem, due to a low birefringence in the gray matter. In this study, we investigated the effect of refractive index matching by 2,2'-thiodiethanol (TDE) immersion on the improvement of PS-OCT measurements in ex vivo human brain tissue. We show that we can obtain fiber orientation maps of U-fibers that underlie sulci, as well as cortical fibers in the gray matter, including radial fibers in gyri and distinct layers of fibers exhibiting laminar organization. Further analysis shows that index matching reduces the noise in axis orientation measurements by 56% and 39%, in white and gray matter, respectively. Index matching also enables precise measurements of apparent birefringence, which was underestimated in the white matter by 82% but overestimated in the gray matter by 16% prior to TDE immersion. Mathematical simulations show that the improvements are primarily attributed to the reduction in the tissue scattering coefficient, leading to an enhanced signal-to-noise ratio in deeper tissue regions, which could not be achieved by conventional noise reduction methods.

Digital ocular swept source optical coherence aberrometry

Ocular aberrometry is an essential technique in vision science and ophthalmology. We demonstrate how a phase-sensitive single mode fiber-based swept source optical coherence tomography (SS-OCT) setup can be employed for quantitative ocular aberrometry with digital adaptive optics (DAO). The system records the volumetric point spread function at the retina in a de-scanning geometry using a guide star pencil beam. Succeeding test-retest repeatability assessment with defocus and astigmatism analysis on a model eye within ± 3 D dynamic range, the feasibility of technique is demonstrated in-vivo at a B-scan rate of >1 kHz in comparison with a commercially available aberrometer.

Resolution-enhanced OCT and expanded framework of information capacity and resolution in coherent imaging

Spatial resolution in conventional optical microscopy has traditionally been treated as a fixed parameter of the optical system. Here, we present an approach to enhance transverse resolution in beam-scanned optical coherence tomography (OCT) beyond its aberration-free resolution limit, without any modification to the optical system. Based on the theorem of invariance of information capacity, resolution-enhanced (RE)-OCT navigates the exchange of information between resolution and signal-to-noise ratio (SNR) by exploiting efficient noise suppression via coherent averaging and a simple computational bandwidth expansion procedure. We demonstrate a resolution enhancement of 1.5 × relative to the aberration-free limit while maintaining comparable SNR in silicone phantom. We show that RE-OCT can significantly enhance the visualization of fine microstructural features in collagen gel and ex vivo mouse brain. Beyond RE-OCT, our analysis in the spatial-frequency domain leads to an expanded framework of information capacity and resolution in coherent imaging that contributes new implications to the theory of coherent imaging. RE-OCT can be readily implemented on most OCT systems worldwide, immediately unlocking information that is beyond their current imaging capabilities, and so has the potential for widespread impact in the numerous areas in which OCT is utilized, including the basic sciences and translational medicine.

Performance assessment of laser sources for time-domain diffuse correlation spectroscopy

Time-domain diffuse correlation spectroscopy (TD-DCS) is an emerging optical technique that enables noninvasive measurement of microvascular blood flow with photon path-length resolution. In TD-DCS, a picosecond pulsed laser with a long coherence length, adequate illumination power, and narrow instrument response function (IRF) is required, and satisfying all these features is challenging. To this purpose, in this study we characterized the performance of three different laser sources for TD-DCS. First, the sources were evaluated based on their emission spectrum and IRF. Then, we compared the signal-to-noise ratio and the sensitivity to velocity changes of scattering particles in a series of phantom measurements. We also compared the results for in vivo measurements, performing an arterial occlusion protocol on the forearm of three adult subjects. Overall, each laser has the potential to be successfully used both for laboratory and clinical applications. However, we found that the effects caused by the IRF are more significant than the effect of a limited temporal coherence.

Phase stable swept-source optical coherence tomography with active mode-locking laser for contrast enhancements of retinal angiography

Swept-source optical coherence tomography (SS-OCT) is an attractive high-speed imaging technique for retinal angiography. However, conventional swept lasers vary the cavity length of the laser mechanically to tune the output wavelength. This causes sweep-timing jitter and hence low phase stability in OCT angiography. Here, we improve an earlier phase-stabilized, akinetic, SS-OCT angiography (OCTA) method by introducing coherent averaging. We develop an active mode-locking (AML) laser as a high phase-stable akinetic swept source for the OCTA system. The phase stability of the improved system was analyzed, and the effects of coherent averaging were validated using a retina phantom. The effectiveness of the coherent averaging method was further confirmed by comparing coherently and conventionally averaged en face images of human retinal vasculature for their contrast-to-noise ratio, signal-to-noise ratio, and vasculature connectivity. The contrast-to-noise ratio was approximately 1.3 times larger when applying the coherent averaging method in the human retinal experiment. Our coherent averaging method with the high phase-stability AML laser source for OCTA provides a valuable tool for studying healthy and diseased retinas.

Optical density based quantification of total haemoglobin concentrations with spectroscopic optical coherence tomography

Spectroscopic optical coherence tomography (sOCT) has emerged as a new possibility for non-invasive quantification of total haemoglobin concentrations [tHb]. Recently, we demonstrated that [tHb] measured in ex-vivo human whole-blood with a conventional sOCT system achieves a precision of 9.10 g/dL with a bias of 1.50 g/dL. This precision improved by acquiring data with a combination of focus tracking and zero-delay acquisition (FZA) that compensated for experimental limitations, increasing to 3.80 g/dL with a bias of 1.50 g/dL. Nevertheless, sOCT precision should improve at least to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim 2$$\end{document}∼2 g/dL to be clinically relevant. Therefore, sOCT-based [tHb] determinations require the development of new analysis methods that reduce the variability of [tHb] estimations. In this work, we aim to increase sOCT precision by retrieving the [tHb] content from a numerical optimisation of the optical density (OD), while considering the blood absorption flattening effect. The OD-based approach simplifies previous two-step Lambert–Beer fitting approaches to a single step, thereby reducing errors during the fitting procedure. We validated our model with ex-vivo [tHb] measurements on flowing whole-blood samples in the clinical range (7–23 g/dL). Our results show that, with the new model, conventional sOCT can determine [tHb] with a precision of 3.09 g/dL and a bias of 0.86 g/dL compared to a commercial blood analyser. We present further precision improvement by combining the OD methodology with FZA, leading to a precision of 2.08 g/dL with a bias of 0.46 g/dL.

Improved accuracy of quantitative birefringence imaging by polarization sensitive OCT with simple noise correction and its application to neuroimaging

Polarization-sensitive optical coherence tomography (PS-OCT) enables three-dimensional imaging of biological tissues based on the inherent contrast provided by scattering and polarization properties. In fibrous tissue such as the white matter of the brain, PS-OCT allows quantitative mapping of tissue birefringence. For the popular PS-OCT layout using a single circular input state, birefringence measurements are based on a straight-forward evaluation of phase retardation data. However, the accuracy of these measurements strongly depends on the signal-to-noise ratio (SNR) and is prone to mapping artifacts when the SNR is low. Here we present a simple yet effective approach for improving the accuracy of PS-OCT phase retardation and birefringence measurements. By performing a noise bias correction of the detected OCT signal amplitudes, the impact of the noise floor on retardation measurements can be markedly reduced. We present simulation data to illustrate the influence of the noise bias correction on phase retardation measurements and support our analysis with real-world PS-OCT image data.

Intrinsic spectrally-dependent background in spectroscopic visible-light optical coherence tomography

Visible-light optical coherence tomography (vis-OCT) has enabled new spectroscopic applications, such as retinal oximetry, as a result of increased optical absorption and scattering contacts in biological tissue and improved axial resolution. Besides extracting tissue properties from back-scattered light, spectroscopic analyses must consider spectral alterations induced by image reconstruction itself. We investigated an intrinsic spectral bias in the background noise floor, which is hereby referred to as the spectrally-dependent background (SDBG). We developed an analytical model to predict the SDBG-induced bias and validated this model using numerically simulated and experimentally acquired data. We found that SDBG systemically altered the measured spectra of blood in human retinal vessels in vis-OCT, as compared to literature data. We provided solutions to quantify and compensate for SDBG in retinal oximetry. This work is particularly significant for clinical applications of vis-OCT.

400 MHz ultrafast optical coherence tomography

An ultrafast time-stretched swept source with a sweep rate of 400 MHz is demonstrated based on the buffering of a 100 MHz femtosecond laser pulse train. To the best of our knowledge, this is the highest sweep rate of swept sources for optical coherence tomography (OCT) that has been reported. With a 10 dB sweep range of ∼100nm, an axial resolution of 19 µm is obtained in the OCT. OCT imaging of high-speed rotating disks is demonstrated. A composite complex apodization method is proposed and demonstrated to enhance the signal to noise ratio in the OCT imaging.

Flexible A-scan rate MHz-OCT: efficient computational downscaling by coherent averaging

In order to realize adjustable A-scan rates of fast optical coherence tomography (OCT) systems, we investigate averaging of OCT image data acquired with a MHz-OCT system based on a Fourier Domain Mode Locked (FDML) laser. Increased system sensitivity and image quality can be achieved with the same system at the cost of lower imaging speed. Effectively, the A-scan rate can be reduced in software by a freely selectable factor. We demonstrate a detailed technical layout of the strategies necessary to achieve efficient coherent averaging. Since there are many new challenges specific to coherent averaging in swept source MHz-OCT, we analyze them point by point and describe the appropriate solutions. We prove that coherent averaging is possible at MHz OCT-speed without special interferometer designs or digital phase stabilization. We find, that in our system up to ∼100x coherent averaging is possible while achieving a sensitivity increase close to the ideal values. This corresponds to a speed reduction from 3.3 MHz to 33 kHz and a sensitivity gain of 20 dB. We show an imaging comparison between coherent and magnitude averaging of a human finger knuckle joint in vivo with 121 dB sensitivity for the coherent case. Further, the benefits of computational downscaling in low sensitivity MHz-OCT systems are analyzed.

Processing-Aware Real-Time Rendering for Optimized Tissue Visualization in Intraoperative 4D OCT

Intraoperative Optical Coherence Tomography (iOCT) has advanced in recent years to provide real-time high resolution volumetric imaging for ophthalmic surgery. It enables real-time 3D feedback during precise surgical maneuvers. Intraoperative 4D OCT generally exhibits lower signal-to-noise ratio compared to diagnostic OCT and visualization is complicated by instrument shadows occluding retinal tissue. Additional constraints of processing data rates upwards of 6GB/s create unique challenges for advanced visualization of 4D OCT. Prior approaches for real-time 4D iOCT rendering have been limited to applying simple denoising filters and colorization to improve visualization. We present a novel real-time rendering pipeline that provides enhanced intraoperative visualization and is specifically designed for the high data rates of 4D iOCT. We decompose the volume into a static part consisting of the retinal tissue and a dynamic part including the instrument. Aligning the static parts over time allows temporal compounding of these structures for improved image quality. We employ a translational motion model and use axial projection images to reduce the dimensionality of the alignment. A model-based instrument segmentation on the projections discriminates static from dynamic parts and is used to exclude instruments from the compounding. Our real-time rendering method combines the compounded static information with the latest iOCT data to provide a visualization which compensates instrument shadows and improves instrument visibility. We evaluate the individual parts of our pipeline on pre-recorded OCT volumes and demonstrate the effectiveness of our method on a recorded volume sequence with a moving retinal forceps.

Speckle Reduction in Optical Coherence Tomography via Super-Resolution Reconstruction

Reducing speckle noise from the optical coherence tomograms (OCT) of human retina is a fundamental step to a better visualization and analysis in retinal imaging, as thus to support examination, diagnosis and treatment of many eye diseases. In this study, we propose a new method for speckle reduction in OCT images using the super-resolution technology. It merges multiple images for the same scene but with sub-pixel movements and restores the missing signals in one pixel, which significantly improves the image quality. The proposed method is evaluated on a dataset of 20 OCT volumes (5120 images), through the mean square error, peak signal to noise ratio and the mean structure similarity index using high quality line-scan images as reference. The experimental results show that the proposed method outperforms existing state-of-the-art approaches in applicability, effectiveness, and accuracy.

Signal averaging improves signal-to-noise in OCT images: But which approach works best, and when?

The high acquisition speed of state-of-the-art optical coherence tomography (OCT) enables massive signal-to-noise ratio (SNR) improvements by signal averaging. Here, we investigate the performance of two commonly used approaches for OCT signal averaging. We present the theoretical SNR performance of (a) computing the average of OCT magnitude data and (b) averaging the complex phasors, and substantiate our findings with simulations and experimentally acquired OCT data. We show that the achieved SNR performance strongly depends on both the SNR of the input signals and the number of averaged signals when the signal bias caused by the noise floor is not accounted for. Therefore we also explore the SNR for the two averaging approaches after correcting for the noise bias and, provided that the phases of the phasors are accurately aligned prior to averaging, then find that complex phasor averaging always leads to higher SNR than magnitude averaging.

Analysis and evaluation of BC-mode OCT image visualization for microsurgery guidance

Optical coherence tomography (OCT) has been gaining acceptance in image-guided microsurgery as a noninvasive imaging technique. However, when using B-mode OCT imaging, it is difficult to continuously keep the surgical tool in the imaging field, and the image of the tissue beneath the tool is corrupted by shadow effects. The alternative using C-mode OCT imaging is either too slow in imaging speed when operating in a high-resolution mode, or provides a poor image resolution in a high-speed mode, with the sweep rate less than one million hertz. Moreover, the 3-dimensional rendering of C-mode OCT image makes it difficult to visualize the tissue structure and track the surgical tool beneath the tissue surface. To solve these problems, we propose a BC-mode OCT image visualization method. This method uses a sparse C-scanning scheme, which provides a set of high-resolution B-mode OCT images at sparsely spaced cross sections. The final BC-mode OCT image is obtained by averaging the image set, with inter frame variance processing to enhance the signal of the surgical tool and tissue layers. The performance of BC-mode OCT images, such as image resolution, signal to noise ratio (SNR), imaging speed, and surgical tool tracking accuracy, is analyzed theoretically and verified experimentally. The feasibility of the proposed method is evaluated by guiding the insertion of a 30-gauge needle into the cornea of an ex-vivo human eye freehand. The results show that this provides better visualization of both the surgical tool and the tissue structure than the conventional B- or C- mode OCT image.

First Clinical Application of Low-Cost OCT

Purpose

We present the design of a new low-cost optical coherence tomography (OCT) system and compare its retinal imaging capabilities to a standard commercial system through a clinical study.

Methods

A spectral-domain OCT system was designed using various cost-reduction techniques to be low-cost, highly portable, and completely stand-alone. Clinical imaging was performed on 120 eyes of 60 patients (60 eyes of normal volunteers and 60 eyes with retinal disease) using both the low-cost OCT and a Heidelberg Engineering Spectralis OCT. Contrast-to-noise ratio (CNR) was measured from resulting images to determine system performance.

Results

The low-cost OCT system was successfully applied to clinical imaging of the retina. The system offers an axial resolution of 8.0 μm, a lateral resolution of 19.6 μm, and an imaging depth of 2.7 mm for a 6.6-mm field of view in the X and Y directions. Total cost is $5037, a significant size reduction compared to current commercial higher performance systems. Mean CNR value of low-cost OCT images is only 5.6% lower compared to the Heidelberg Spectralis.

Conclusions

The images captured with the low-cost OCT were of adequate resolution and allowed for clinical diagnostics. It offers comparable performance as a retinal screening tool at a fraction of the cost of current commercial systems.

Translational Relevance

Low-cost OCT has the potential to increase access to retinal imaging.

Spatiotemporal optical coherence (STOC) manipulation suppresses coherent cross-talk in full-field swept-source optical coherence tomography

Full-field swept-source optical coherence tomography (FF-SS-OCT) provides high-resolution depth-resolved images of the sample by parallel Fourier-domain interferometric detection. Although FF-SS-OCT implements high-speed volumetric imaging, it suffers from the cross-talk-generated noise from spatially coherent lasers. This noise reduces the transversal image resolution, which in turn, limits the wide adaptation of FF-SS-OCT for practical and clinical applications. Here, we introduce the novel spatiotemporal optical coherence (STOC) manipulation. In STOC the time-varying inhomogeneous phase masks are used to modulate the light incident on the sample. By properly adjusting these phase masks, the spatial coherence can be reduced. Consequently, the cross-talk-generated noise is suppressed, the transversal image resolution is improved by the factor of2 , and sample features become visible. STOC approach is validated by imaging 1951 USAF resolution test chart covered by the diffuser, scattering phantom and the rat skin ex vivo. In all these cases STOC suppresses the cross-talk-generated noise, and importantly, do not compromise the transversal resolution. Thus, our method provides an enhancement of FF-SS-OCT that can be beneficial for imaging biological samples.

Three-dimensional optical coherence tomography image denoising through multi-input fully-convolutional networks

In recent years, there has been a growing interest in applying convolutional neural networks (CNNs) to low-level vision tasks such as denoising and super-resolution. Due to the coherent nature of the image formation process, the optical coherence tomography (OCT) images are inevitably affected by noise. This paper proposes a new method named the multi-input fully-convolutional networks (MIFCN) for denoising of OCT images. In contrast to recently proposed natural image denoising CNNs, the proposed architecture allows the exploitation of high degrees of correlation and complementary information among neighboring OCT images through pixel by pixel fusion of multiple FCNs. The parameters of the proposed multi-input architecture are learned by considering the consistency between the overall output and the contribution of each input image. The proposed MIFCN method is compared with the state-of-the-art denoising methods adopted on OCT images of normal and age-related macular degeneration eyes in a quantitative and qualitative manner.

Ultra low noise Fourier domain mode locked laser for high quality megahertz optical coherence tomography

We investigate the origin of high frequency noise in Fourier domain mode locked (FDML) lasers and present an extremely well dispersion compensated setup which virtually eliminates intensity noise and dramatically improves coherence properties. We show optical coherence tomography (OCT) imaging at 3.2 MHz A-scan rate and demonstrate the positive impact of the described improvements on the image quality. Especially in highly scattering samples, at specular reflections and for strong signals at large depth, the noise in optical coherence tomography images is significantly reduced. We also describe a simple model that suggests a passive physical stabilizing mechanism that leads to an automatic compensation of remaining cavity dispersion in FDML lasers.

Volumetric non-local-means based speckle reduction for optical coherence tomography

We present a novel tomographic non-local-means based despeckling technique, TNode, for optical coherence tomography. TNode is built upon a weighting similarity criterion derived for speckle in a three-dimensional similarity window. We present an implementation using a two-dimensional search window, enabling the despeckling of volumes in the presence of motion artifacts, and an implementation using a three-dimensional window with improved performance in motion-free volumes. We show that our technique provides effective speckle reduction, comparable with B-scan compounding or out-of-plane averaging, while preserving isotropic resolution, even to the level of speckle-sized structures. We demonstrate its superior despeckling performance in a phantom data set, and in an ophthalmic data set we show that small, speckle-sized retinal vessels are clearly preserved in intensity images en-face and in two orthogonal, cross-sectional views. TNode does not rely on dictionaries or segmentation and therefore can readily be applied to arbitrary optical coherence tomography volumes. We show that despeckled esophageal volumes exhibit improved image quality and detail, even in the presence of significant motion artifacts.

Complex regression Doppler optical coherence tomography

We introduce a new method to measure Doppler shifts more accurately and extend the dynamic range of Doppler optical coherence tomography (OCT). The two-point estimate of the conventional Doppler method is replaced with a regression that is applied to high-density B-scans in polar coordinates. We built a high-speed OCT system using a 1.68-MHz Fourier domain mode locked laser to acquire high-density B-scans (16,000 A-lines) at high enough frame rates (∼100  fps) to accurately capture the dynamics of the beating embryonic heart. Flow phantom experiments confirm that the complex regression lowers the minimum detectable velocity from 12.25  mm  /  s to 374  μm  /  s, whereas the maximum velocity of 400  mm  /  s is measured without phase wrapping. Complex regression Doppler OCT also demonstrates higher accuracy and precision compared with the conventional method, particularly when signal-to-noise ratio is low. The extended dynamic range allows monitoring of blood flow over several stages of development in embryos without adjusting the imaging parameters. In addition, applying complex averaging recovers hidden features in structural images.

Complex differential variance angiography with noise-bias correction for optical coherence tomography of the retina

Complex differential variance (CDV) provides phase-sensitive angiographic imaging for optical coherence tomography (OCT) with immunity to phase-instabilities of the imaging system and small-scale axial bulk motion. However, like all angiographic methods, measurement noise can result in erroneous indications of blood flow that confuse the interpretation of angiographic images. In this paper, a modified CDV algorithm that corrects for this noise-bias is presented. This is achieved by normalizing the CDV signal by analytically derived upper and lower limits. The noise-bias corrected CDV algorithm was implemented into an experimental 1 μm wavelength OCT system for retinal imaging that used an eye tracking scanner laser ophthalmoscope at 815 nm for compensation of lateral eye motions. The noise-bias correction improved the CDV imaging of the blood flow in tissue layers with a low signal-to-noise ratio and suppressed false indications of blood flow outside the tissue. In addition, the CDV signal normalization suppressed noise induced by galvanometer scanning errors and small-scale lateral motion. High quality cross-section and motion-corrected en face angiograms of the retina and choroid are presented.

Classification of biological micro-objects using optical coherence tomography: in silico study

We report on the development of a technique for differentiating between biological micro-objects using a rigorous, full-wave model of OCT image formation. We model an existing experimental prototype which uses OCT to interrogate a microfluidic chip containing the blood cells. A full-wave model is required since the technique uses light back-scattered by a scattering substrate, rather than by the cells directly. The light back-scattered by the substrate is perturbed upon propagation through the cells, which flow between the substrate and imaging system's objective lens. We present the key elements of the 3D, Maxwell equation-based computational model, the key findings of the computational study and a comparison with experimental results.

Complex decorrelation averaging in optical coherence tomography: a way to reduce the effect of multiple scattering and improve image contrast in a dynamic scattering medium

We demonstrate that complex decorrelation averaging can reduce the effect of multiple scattering and improve optical coherence tomography (OCT) imaging contrast. Complex decorrelation averaging calculates the product of an A-scan and the complex conjugate of a subsequent A-scan. The resultant signal is the product of the amplitudes and the phase difference. All these resulting complex signals at a particular location are then averaged. We take advantage of the fact that complex averaging, in contrast to conventional magnitude averaging, is sensitive to phase decorrelation. Sample motion that increases signal phase variance results in lower signal magnitude after complex averaging. Such motion preferentially results in a faster decorrelation of the multiple scattering signal when compared to the single scattering signal with each scattering event spreading the phase. This indicates that we may reduce multiple scattering by implementing complex decorrelation averaging to preferentially reduce the magnitude of the multiply scattered light signal in OCT images. By adjusting the time between phase-differenced A-scans, one can regulate the amount of measured decorrelation. We have performed experiments on liquid phantoms that give experimental evidence for this hypothesis. A substantial improvement in OCT image contrast using complex decorrelation averaging is demonstrated.

Efficient OCT Volume Reconstruction From Slitlamp Microscopes

Since its introduction 25 years ago, Optical Coherence Tomography (OCT) has contributed tremendously to diagnostic and monitoring capabilities of pathologies in the field of ophthalmology. Despite rapid progress in hardware and software technology however, the price of OCT devices has remained high, limiting their use in private practice, and in screening examinations. In this paper, we present a slitlamp-integrated OCT device, built with off-the-shelf components, which can generate high-quality volumetric images of the posterior eye segment. To do so, we present a novel strategy for 3D image reconstruction in this challenging domain that allows us for state-of-the-art OCT volumes to be generated at fast speeds. The result is an OCT device that can match current systems in clinical practice, at a significantly lower cost.

Spectrometer calibration for spectroscopic Fourier domain optical coherence tomography

We propose a simple and robust procedure for Fourier domain optical coherence tomography (FdOCT) that allows to linearize the detected FdOCT spectra to wavenumber domain and, at the same time, to determine the wavelength of light for each point of detected spectrum. We show that in this approach it is possible to use any measurable physical quantity that has linear dependency on wavenumber and can be extracted from spectral fringes. The actual values of the measured quantity have no importance for the algorithm and do not need to be known at any stage of the procedure. As example we calibrate a spectral OCT spectrometer using Doppler frequency. The technique of spectral calibration can be in principle adapted to of all kind of Fourier domain OCT devices.

Speckle Reduction in 3D Optical Coherence Tomography of Retina by A-Scan Reconstruction

Optical coherence tomography (OCT) is a micrometer-scale, cross-sectional imaging modality for biological tissue. It has been widely used for retinal imaging in ophthalmology. Speckle noise is problematic in OCT. A raw OCT image/volume usually has very poor image quality due to speckle noise, which often obscures the retinal structures. Overlapping scan is often used for speckle reduction in a 2D line-scan. However, it leads to an increase of the data acquisition time. Therefore, it is unpractical in 3D scan as it requires a much longer data acquisition time. In this paper, we propose a new method for speckle reduction in 3D OCT. The proposed method models each A -scan as the sum of underlying clean A -scan and noise. Based on the assumption that neighboring A -scans are highly similar in the retina, the method reconstructs each A -scan from its neighboring scans. In the method, the neighboring A -scans are aligned/registered to the A -scan to be reconstructed and form a matrix together. Then low rank matrix completion using bilateral random projection is utilized to iteratively estimate the noise and recover the underlying clean A -scan. The proposed method is evaluated through the mean square error, peak signal to noise ratio and the mean structure similarity index using high quality line-scan images as reference. Experimental results show that the proposed method performs better than other methods. In addition, the subsequent retinal layer segmentation also shows that the proposed method makes the automatic retinal layer segmentation more accurate. The technology can be embedded into current OCT machines to enhance the image quality for visualization and subsequent analysis such as retinal layer segmentation.

Noise characterization of supercontinuum sources for low-coherence interferometry applications

We examine the noise properties of supercontinuum light sources when used in low-coherence interferometry applications. The first application is a multiple-scattering low-coherence interferometry (ms2/LCI) system, where high power and long image acquisition times are required to image deep into tissue. For this system, we compare the noise characteristics of two supercontinuum sources from different suppliers. Both sources have long-term drift that limits the amount of time over which signal averaging is advantageous for reducing noise. The second application is a high-resolution optical coherence tomography system, where broadband light is needed for high axial resolution. For this system, we compare the noise performance of the two supercontinuum sources and a light source based on four superluminescent diodes (SLD) using imaging contrast as a comparative metric. We find that the NKT SuperK has superior noise performance compared with the Fianium SC-450-4, but neither meets the performance of the SLD.

Speckle reduction in optical coherence tomography by image registration and matrix completion

Speckle noise is problematic in optical coherence tomography (OCT). With the fast scan rate, swept source OCT scans the same position in the retina for multiple times rapidly and computes an average image from the multiple scans for speckle reduction. However, the eye movement poses some challenges. In this paper, we propose a new method for speckle reduction from multiply-scanned OCT slices. The proposed method applies a preliminary speckle reduction on the OCT slices and then registers them using a global alignment followed by a local alignment based on fast iterative diamond search. After that, low rank matrix completion using bilateral random projection is utilized to iteratively estimate the noise and recover the underlying clean image. Experimental results show that the proposed method achieves average contrast to noise ratio 15.65, better than 13.78 by the baseline method used currently in swept source OCT devices. The technology can be embedded into current OCT machines to enhance the image quality for subsequent analysis.

Speckle reduction in optical coherence tomography by matrix completion using bilateral random projection

Speckle noise is problematic in optical coherence tomography (OCT) and often obscures the structure details. In this paper, we propose a new method to reduce speckle noise from multiply scanned OCT slices. The proposed method registers the OCT scans using a global alignment followed by a local alignment based on global and local motion estimation. Then low rank matrix completion using bilateral random projection is utilized to estimate the noise and recover the clean image. Experimental results show that the proposed method archives average contrast to noise ratio 14.90, better than 13.78 by the state-of-the-art method used in current OCT machines. The technology can be embedded into current OCT machines to enhance the image quality.

Multi-penalty conditional random field approach to super-resolved reconstruction of optical coherence tomography images

Improving the spatial resolution of Optical Coherence Tomography (OCT) images is important for the visualization and analysis of small morphological features in biological tissue such as blood vessels, membranes, cellular layers, etc. In this paper, we propose a novel reconstruction approach to obtaining super-resolved OCT tomograms from multiple lower resolution images. The proposed Multi-Penalty Conditional Random Field (MPCRF) method combines four different penalty factors (spatial proximity, first and second order intensity variations, as well as a spline-based smoothness of fit) into the prior model within a Maximum A Posteriori (MAP) estimation framework. Test carried out in retinal OCT images illustrate the effectiveness of the proposed MPCRF reconstruction approach in terms of spatial resolution enhancement, as compared to previously published super resolved image reconstruction methods. Visual assessment of the MPCRF results demonstrate the potential of this method in better preservation of fine details and structures of the imaged sample, as well as retaining the sharpness of biological tissue boundaries while reducing the effects of speckle noise inherent to OCT. Quantitative evaluation using imaging metrics such as Signal-to-Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Equivalent Number of Looks (ENL), and Edge Preservation Parameter show significant visual quality improvement with the MPCRF approach. Therefore, the proposed MPCRF reconstruction approach is an effective tool for enhancing the spatial resolution of OCT images without the necessity for significant imaging hardware modifications.

Multi-MHz retinal OCT

We analyze the benefits and problems of in vivo optical coherence tomography (OCT) imaging of the human retina at A-scan rates in excess of 1 MHz, using a 1050 nm Fourier-domain mode-locked (FDML) laser. Different scanning strategies enabled by MHz OCT line rates are investigated, and a simple multi-volume data processing approach is presented. In-vivo OCT of the human ocular fundus is performed at different axial scan rates of up to 6.7 MHz. High quality non-mydriatic retinal imaging over an ultra-wide field is achieved by a combination of several key improvements compared to previous setups. For the FDML laser, long coherence lengths and 72 nm wavelength tuning range are achieved using a chirped fiber Bragg grating in a laser cavity at 419.1 kHz fundamental tuning rate. Very large data sets can be acquired with sustained data transfer from the data acquisition card to host computer memory, enabling high-quality averaging of many frames and of multiple aligned data sets. Three imaging modes are investigated: Alignment and averaging of 24 data sets at 1.68 MHz axial line rate, ultra-dense transverse sampling at 3.35 MHz line rate, and dual-beam imaging with two laser spots on the retina at an effective line rate of 6.7 MHz.