Bayesian maximum likelihood estimator of phase retardation for quantitative polarization-sensitive optical coherence tomography

Reducing noise in polarization-sensitive optical coherence tomography for high-quality local phase retardation imaging

Local phase retardation (LPR) is increasingly recognized as a crucial biomarker for assessing disease progression. However, the presence of speckle noise significantly challenges its accuracy and polarization contrast. To address this challenge, we propose a signal-processing strategy aimed at reducing the impact of noise on LPR measurements. In this approach, the LPR is reconstructed by polar decomposition after averaging multiple Mueller matrices from different overlapping sub-spectra. To optimize measurement accuracy, we systematically combined and traversed different sub-spectral numbers and bandwidths. By examining the quarter-wave plate and glass slide, high-accuracy phase retardation measurements were successfully verified, and the maximum polarization contrast was improved by 23%. Moreover, experimental results from multi-tissue imaging vividly illustrate that the equivalent number of looks (ENL) and polarization contrast were improved by 18% and 19%, respectively. This outcome indicates that our proposed strategy can effectively reduce the noise spikes, enhancing tissue discrimination capabilities.

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.

Recent advances in optical coherence tomography for anterior segment imaging in small animals and their clinical implications

Anterior segment optical coherence tomography (AS-OCT) is a rapidly evolving area of OCT imaging, providing high-resolution and non-invasive volumetric imaging of the anterior segment. This review focuses on recent advances in AS-OCT imaging in small animals, which we categorize into ultrahigh-resolution, spectroscopic, magnetomotive, polarization-sensitive, and angiographic AS-OCTs. We summarize their technical foundations, review their applications to small animal imaging, and briefly discuss their current and future clinical applications.

Longitudinal investigation of a xenograft tumor zebrafish model using polarization-sensitive optical coherence tomography

Breast cancer is a leading cause of death in female patients worldwide. Further research is needed to get a deeper insight into the mechanisms involved in the development of this devastating disease and to find new therapy strategies. The zebrafish is an established animal model, especially in the field of oncology, which has shown to be a promising candidate for pre-clinical research and precision-based medicine. To investigate cancer growth in vivo in zebrafish, one approach is to explore xenograft tumor models. In this article, we present the investigation of a juvenile xenograft zebrafish model using a Jones matrix optical coherence tomography (JM-OCT) prototype. Immunosuppressed wild-type fish at 1-month post-fertilization were injected with human breast cancer cells and control animals with phosphate buffered saline in the tail musculature. In a longitudinal study, the scatter, polarization, and vasculature changes over time were investigated and quantified in control versus tumor injected animals. A significant decrease in birefringence and an increase in scattering signal was detected in tumor injected zebrafish in comparison to the control once. This work shows the potential of JM-OCT as a non-invasive, label-free, three-dimensional, high-resolution, and tissue-specific imaging tool in pre-clinical cancer research based on juvenile zebrafish models.

Comparative study of OCTA algorithms with a high-sensitivity multi-contrast Jones matrix OCT system for human skin imaging

The multi-contrast Jones matrix OCT (JMT) system can not only improve the tissue-specific contrast but also enhance the sensitivity of detecting flow, which is gaining increasing attention. However, for the JMT system, there is currently a lack of studies evaluating and guiding the selection of suitable angiography algorithms to map the most appealing quality of angiograms for clinical use. In this paper, by a homemade high-sensitivity multi-contrast JMT system based 200 kHz swept source, the performance of two complex-signal-based OCTA methods that are insensitive to phase instability and one amplitude-signal-based OCTA method are compared for in-vivo imaging of human skin qualitatively and quantitatively. Six metrics, including vascular connectivity, image contrast-to-noise ratio, image signal-to-noise ratio, vessel diameter index, blood vessel density, and processing time, are assessed. The results show that the vascular networks processed by all OCTA methods and the texture of skin could be visualized simultaneously and markedly. Additionally, the complex-signal-based OCTA methods successfully suppress phase instabilities and even outperform the amplitude-signal-based OCTA algorithm in some indicators. This paper has a certain guiding significance for selecting an appropriate angiography algorithm and expanding the application field with this system.

Computational refocusing of Jones matrix polarization-sensitive optical coherence tomography and investigation of defocus-induced polarization artifacts

Here we demonstrate a long-depth-of-focus imaging method using polarization sensitive optical coherence tomography (PS-OCT). This method involves a combination of Fresnel-diffraction-model-based phase sensitive computational refocusing and Jones-matrix based PS-OCT (JM-OCT). JM-OCT measures four complex OCT images corresponding to four polarization channels. These OCT images are computationally refocused as preserving the mutual phase consistency. This method is validated using a static phantom, postmortem zebrafish, and ex vivo porcine muscle samples. All the samples demonstrated successful computationally-refocused birefringence and degree-of-polarization-uniformity (DOPU) images. We found that defocusing induces polarization artifacts, i.e., incorrectly high birefringence values and low DOPU values, which are substantially mitigated by computational refocusing.

Non-destructive characterization of adult zebrafish models using Jones matrix optical coherence tomography

The zebrafish is a valuable vertebrate animal model in pre-clinical cancer research. A Jones matrix optical coherence tomography (JM-OCT) prototype operating at 1310 nm and an intensity-based spectral-domain OCT setup at 840 nm were utilized to investigate adult wildtype and a tumor-developing zebrafish model. Various anatomical features were characterized based on their inherent scattering and polarization signature. A motorized translation stage in combination with the JM-OCT prototype enabled large field-of-view imaging to investigate adult zebrafish in a non-destructive way. The diseased animals exhibited tumor-related abnormalities in the brain and near the eye region. The scatter intensity, the attenuation coefficients and local polarization parameters such as the birefringence and the degree of polarization uniformity were analyzed to quantify differences in tumor versus control regions. The proof-of-concept study in a limited number of animals revealed a significant decrease in birefringence in tumors found in the brain and near the eye compared to control regions. The presented work showed the potential of OCT and JM-OCT as non-destructive, high-resolution, and real-time imaging modalities for pre-clinical research based on zebrafish.

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.

Deep convolutional neural network-based scatterer density and resolution estimators in optical coherence tomography

We present deep convolutional neural network (DCNN)-based estimators of the tissue scatterer density (SD), lateral and axial resolutions, signal-to-noise ratio (SNR), and effective number of scatterers (ENS, the number of scatterers within a resolution volume). The estimators analyze the speckle pattern of an optical coherence tomography (OCT) image in estimating these parameters. The DCNN is trained by a large number (1,280,000) of image patches that are fully numerically generated in OCT imaging simulation. Numerical and experimental validations were performed. The numerical validation shows good estimation accuracy as the root mean square errors were 0.23%, 3.65%, 3.58%, 3.79%, and 6.15% for SD, lateral and axial resolutions, SNR, and ENS, respectively. The experimental validation using scattering phantoms (Intralipid emulsion) shows reasonable estimations. Namely, the estimated SDs were proportional to the Intralipid concentrations, and the average estimation errors of lateral and axial resolutions were 1.36% and 0.68%, respectively. The scatterer density estimator was also applied to an in vitro tumor cell spheroid, and a reduction in the scatterer density during cell necrosis was found.

Multicontrast investigation of in vivo wildtype zebrafish in three development stages using polarization-sensitive optical coherence tomography

SIGNIFICANCE

The scattering and polarization characteristics of various organs of in vivo wildtype zebrafish in three development stages were investigated using a non-destructive and label-free approach. The presented results showed a promising first step for the usability of Jones-matrix optical coherence tomography (JM-OCT) in zebrafish-based research.

AIM

We aim to visualize and quantify the scatter and polarization signatures of various zebrafish organs for larvae, juvenile, and young adult animals in vivo in a non-invasive and label-free way.

APPROACH

A custom-built polarization-sensitive JM-OCT setup in combination with a motorized translation stage was utilized to investigate live zebrafish. Depth-resolved scattering (intensity and attenuation coefficient) and polarization (birefringence and degree of polarization uniformity) properties were analyzed. OCT angiography (OCT-A) was utilized to investigate the vasculature label-free and non-destructively.

RESULTS

The scatter and polarization signatures of the zebrafish organs such as the eye, gills, and muscles were investigated. The attenuation coefficient and birefringence changes between 1- and 2-month-old animals were evaluated in selected organs. OCT-A revealed the vasculature of in vivo larvae and juvenile zebrafish in a label-free manner.

CONCLUSIONS

JM-OCT offers a rapid, label-free, non-invasive, tissue specific, and three-dimensional imaging tool to investigate in vivo processes in zebrafish in various development stages.

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.

Depth-resolved investigation of multiple optical properties and wrinkle morphology in eye-corner areas with multi-contrast Jones matrix optical coherence tomography

BACKGROUND

Multi-contrast Jones matrix optical coherence tomography (JM-OCT) can provide quantitative depth-resolved local optical properties by improving the measurement algorithm.

MATERIALS AND METHODS

We examined the relationship between depth-resolved local optical properties of eye-corner skin measured by JM-OCT and corresponding wrinkle morphology of aged women (n = 21; age range, 71.7 ± 1.7 years). Wrinkle morphology was analyzed by measuring the surface topography of three-dimensional replicas. The same regions were measured three-dimensionally by JM-OCT, and the local optical properties at each depth were computed.

RESULTS

Birefringence (BR) and mean wrinkle depth correlated significantly at a depth of 88.2-138.6 µm from the skin surface, and attenuation coefficient (AC) and mean wrinkle depth correlated significantly at a depth of 12.6-18.9 µm and 189-459.9 μm from the skin surface, although a degree of polarization uniformity (DOPU) did not. Stepwise multiple regression analysis demonstrated that a significant regression equation (R²  = 0.649, P < .001) for predicting mean wrinkle depth was determined by BR at 107.1 µm depth (BR _{107.1 µm} ), DOPU at 170.1 µm (DOPU _170.1µm ), and AC at 252 µm (AC _{252 µm} ) as independent variables and that these standardized beta regression coefficients were -0.860, -0.593, and -0.440, respectively, suggesting that BR, DOPU, and AC sufficiently explained mean wrinkle depth.

CONCLUSION

These results suggest that BR _{107.1 µm} , DOPU _{170.1 µm,} and AC _{252 µm} may indicate collagen-related structure in the papillary, upper-reticular dermis, and microstructure or tissue density in reticular dermis, respectively, and may be involved in wrinkle formation.

Full-field quantitative phase and polarisation-resolved imaging through an optical fibre bundle

Flexible optical fibres, used in conventional medical endoscopy and industrial inspection, scramble phase and polarisation information, restricting users to amplitude-only imaging. Here, we exploit the near-diagonality of the multi-core fibre (MCF) transmission matrix in a parallelised fibre characterisation architecture, enabling accurate imaging of quantitative phase (error <0.3 rad) and polarisation-resolved (errors <10%) properties. We first demonstrate accurate recovery of optical amplitude and phase in two polarisations through the MCF by measuring and inverting the transmission matrix, and then present a robust Bayesian inference approach to resolving 5 polarimetric properties of samples. Our method produces high-resolution (9.0±2.6μm amplitude, phase; 36.0±10.4μm polarimetric) full-field images at working distances up to 1mm over a field-of-view up to 750×750μm 2 using an MCF with potential for flexible operation. We demonstrate the potential of using quantitative phase for computational image focusing and polarisation-resolved properties in imaging birefringence.

Pixel-wise segmentation of severely pathologic retinal pigment epithelium and choroidal stroma using multi-contrast Jones matrix optical coherence tomography

Tissue segmentation of retinal optical coherence tomography (OCT) is widely used in ophthalmic diagnosis. However, its performance in severe pathologic cases is still insufficient. We propose a pixel-wise segmentation method that uses the multi-contrast measurement capability of Jones matrix OCT (JM-OCT). This method is applicable to both normal and pathologic retinal pigment epithelium (RPE) and choroidal stroma. In this method, "features," which are sensitive to specific tissues of interest, are synthesized by combining the multi-contrast images of JM-OCT, including attenuation coefficient, degree-of-polarization-uniformity, and OCT angiography. The tissue segmentation is done by simple thresholding of the feature. Compared with conventional segmentation methods for pathologic maculae, the proposed method is less computationally intensive. The segmentation method was validated by applying it to images from normal and severely pathologic cases. The segmentation results enabled the development of several types of en face visualizations, including melano-layer thickness maps, RPE elevation maps, choroidal thickness maps, and choroidal stromal attenuation coefficient maps. These facilitate close examination of macular pathology. The melano-layer thickness map is very similar to a near infrared fundus autofluorescence image, so the map can be used to identify the source of a hyper-autofluorescent signal.

Comparison of intensity, phase retardation, and local birefringence images for filtering blebs using polarization-sensitive optical coherence tomography

Polarization-sensitive optical coherence tomography (PS-OCT) allows the recording of depth-resolved polarimetric measurements. It has been reported that phase retardation and local birefringence images can noninvasively detect fibrotic area in blebs after glaucoma surgery. Evaluation of scar fibrosis in blebs is important not only for predicting bleb function, but also for planning revision trabeculectomy. Herein, we characterize the intensity, phase retardation, and local birefringence images of blebs using PS-OCT. A total of 85 blebs from 85 patients who had undergone trabeculectomy were examined. Both phase retardation and local birefringence images detected fibrotic changes in blebs after glaucoma surgery. Phase retardation images detected slight fibrotic change during the early stage after surgery, whereas local birefringence images showed localized fibrotic tissue. There are two main patterns of local birefringence image changes in blebs: plate-like birefringence changes and diffuse changes. The area of plate-like birefringence change was significantly larger in poorly functioning blebs and is thus correlated with bleb function. These data suggest that the plate-like fibrotic change evaluation by PS-OCT may be useful not only for noninvasive evaluation of fibrotic scar tissue in blebs, but also for developing strategies for revision trabeculectomy.

Generation and optimization of superpixels as image processing kernels for Jones matrix optical coherence tomography

Jones matrix-based polarization sensitive optical coherence tomography (JM-OCT) simultaneously measures optical intensity, birefringence, degree of polarization uniformity, and OCT angiography. The statistics of the optical features in a local region, such as the local mean of the OCT intensity, are frequently used for image processing and the quantitative analysis of JM-OCT. Conventionally, local statistics have been computed with fixed-size rectangular kernels. However, this results in a trade-off between image sharpness and statistical accuracy. We introduce a superpixel method to JM-OCT for generating the flexible kernels of local statistics. A superpixel is a cluster of image pixels that is formed by the pixels' spatial and signal value proximities. An algorithm for superpixel generation specialized for JM-OCT and its optimization methods are presented in this paper. The spatial proximity is in two-dimensional cross-sectional space and the signal values are the four optical features. Hence, the superpixel method is a six-dimensional clustering technique for JM-OCT pixels. The performance of the JM-OCT superpixels and its optimization methods are evaluated in detail using JM-OCT datasets of posterior eyes. The superpixels were found to well preserve tissue structures, such as layer structures, sclera, vessels, and retinal pigment epithelium. And hence, they are more suitable for local statistics kernels than conventional uniform rectangular kernels.

Noise-bias and polarization-artifact corrected optical coherence tomography by maximum a-posteriori intensity estimation

We propose using maximum a-posteriori (MAP) estimation to improve the image signal-to-noise ratio (SNR) in polarization diversity (PD) optical coherence tomography. PD-detection removes polarization artifacts, which are common when imaging highly birefringent tissue or when using a flexible fiber catheter. However, dividing the probe power to two polarization detection channels inevitably reduces the SNR. Applying MAP estimation to PD-OCT allows for the removal of polarization artifacts while maintaining and improving image SNR. The effectiveness of the MAP-PD method is evaluated by comparing it with MAP-non-PD, intensity averaged PD, and intensity averaged non-PD methods. Evaluation was conducted in vivo with human eyes. The MAP-PD method is found to be optimal, demonstrating high SNR and artifact suppression, especially for highly birefringent tissue, such as the peripapillary sclera. The MAP-PD based attenuation coefficient image also shows better differentiation of attenuation levels than non-MAP attenuation images.

Three-dimensional multi-contrast imaging of in vivo human skin by Jones matrix optical coherence tomography

A custom made dermatological Jones matrix optical coherence tomography (JM-OCT) is presented. It uses a passive-polarization-delay component based swept-source JM-OCT configuration, but is specially designed for in vivo human skin measurement. The center wavelength of its probe beam is 1310 nm and the A-line rate is 49.6 kHz. The JM-OCT is capable of simultaneously providing birefringence (local retardation) tomography, degree-of-polarization-uniformity tomography, complex-correlation-based optical coherence angiography, and conventional scattering OCT. To evaluate the performance of this JM-OCT, we measured in vivo human skin at several locations. Using the four kinds of OCT contrasts, the morphological characteristics and optical properties of different skin types were visualized.

Polarization sensitive optical coherence tomography - a review [Invited]

Optical coherence tomography (OCT) is now a well-established modality for high-resolution cross-sectional and three-dimensional imaging of transparent and translucent samples and tissues. Conventional, intensity based OCT, however, does not provide a tissue-specific contrast, causing an ambiguity with image interpretation in several cases. Polarization sensitive (PS) OCT draws advantage from the fact that several materials and tissues can change the light's polarization state, adding an additional contrast channel and providing quantitative information. In this paper, we review basic and advanced methods of PS-OCT and demonstrate its use in selected biomedical applications.

Noise stochastic corrected maximum a posteriori estimator for birefringence imaging using polarization-sensitive optical coherence tomography

This paper presents a noise-stochastic corrected maximum a posteriori estimator for birefringence imaging using Jones matrix optical coherence tomography. The estimator described in this paper is based on the relationship between probability distribution functions of the measured birefringence and the effective signal to noise ratio (ESNR) as well as the true birefringence and the true ESNR. The Monte Carlo method is used to numerically describe this relationship and adaptive 2D kernel density estimation provides the likelihood for a posteriori estimation of the true birefringence. Improved estimation is shown for the new estimator with stochastic model of ESNR in comparison to the old estimator, both based on the Jones matrix noise model. A comparison with the mean estimator is also done. Numerical simulation validates the superiority of the new estimator. The superior performance of the new estimator was also shown by in vivo measurement of optic nerve head.

Estimation of Jones matrix, birefringence and entropy using Cloude-Pottier decomposition in polarization-sensitive optical coherence tomography

Estimation of polarimetric parameters has been a fundamental issue to assess biological tissues that have form birefringence or polarization scrambling in polarization-sensitive optical coherence tomography (PS-OCT). We present a mathematical framework to provide a maximum likelihood estimation of the target covariance matrix and its incoherent target decomposition to estimate a Jones matrix of a dominant scattering mechanism, called Cloude-Pottier decomposition, thereby deriving the phase retardation and the optic axis of the sample. In addition, we introduce entropy that shows the randomness of the polarization property. Underestimation of the entropy at a low sampling number is mitigated by asymptotic quasi maximum likelihood estimator. A bias of the entropy from random noises is corrected to show only the polarization property inherent in the sample. The theory is validated with experimental measurements of a glass plate and waveplates, and applied to the imaging of a healthy human eye anterior segment as an image filter.

Maximum a posteriori estimator for high-contrast image composition of optical coherence tomography

A quantitative signal amplitude estimator for optical coherence tomography (OCT) is presented. It is based on a statistical model of OCT signal and noise, using a Bayesian maximum a posteriori (MAP) estimation framework. Multiple OCT images are used for estimation, similar to the widely utilized intensity averaging method. The estimator is less biased especially at low-intensity regions, where intensity averaging approaches the noise power and hence is biased. The estimator is applied to posterior ocular OCT images and provides high-contrast visualization of pathologies. In addition, histogram analysis objectively shows the superior performance of the estimator compared with intensity averaging.

Birefringence imaging of posterior eye by multi-functional Jones matrix optical coherence tomography

A clinical grade prototype of posterior multifunctional Jones matrix optical coherence tomography (JM-OCT) is presented. This JM-OCT visualized depth-localized birefringence in addition to conventional cumulative phase retardation imaging through local Jones matrix analysis. In addition, it simultaneously provides a sensitivity enhanced scattering OCT, a quantitative polarization uniformity contrast, and OCT-based angiography. The probe beam is at 1-μm wavelength band. The measurement speed and the depth-resolution were 100,000 A-lines/s, and 6.6 μm in tissue, respectively. Normal and pathologic eyes are examined and several clinical features are revealed, which includes high birefringence in the choroid and lamina cribrosa, and birefringent layered structure of the sclera. The theoretical details of the depth-localized birefringence imaging and conventional phase retardation imaging are formulated. This formulation indicates that the birefringence imaging correctly measures a depth-localized single-trip phase retardation of a tissue, while the conventional phase retardation can provide correct single-trip phase retardation only for some specific types of samples.