The wavenumber linearisation without calibration device for spectral-domain optical coherence tomography.

The wavenumber nonlinearity leads to blurred reconstructed images in spectral-domain optical coherence tomography (SDOCT). In this work, a wavenumber-linearisation method without calibration devices is presented, based on the fact that the difference between the phases of adjacent peak and valley points is equal to . The theoretical model is derived, and the efficacy of the method was proven by acquiring SDOCT data from TiO phantom and zebrafish.

Light-scattering-induced retardation as a high-sensitivity image contrast revealing collagen fibers.

Retardation induced by media can be used as an image contrast to depict the cumulative birefringent features and local variations of the sample, respectively. It is commonly assumed that the retardation is induced by the light propagation; however, the light scattering would generate the retardation as well. In our work, the scattering-induced retardation as a high-sensitivity image contrast for revealing collagen fibers is presented.

High-contrast handheld FFOCT system for tissue imaging.

A low contrast is a limiting factor for imaging a microstructure beneath the biological sample surface. In this work, we describe a novel, to our knowledge, full-field optical coherence tomography (FFOCT) system with a probe connected by a fiber bundle and a multimode optical fiber. The device is based on the tandem structure of the Michelson interferometer and the Fizeau interferometer.

Self-denoising method for OCT images with single spectrogram-based deep learning.

The presence of noise in images reconstructed with optical coherence tomography (OCT) is a key issue which limits the further improvement of the image quality. In this Letter, for the first time, to the best of our knowledge, a self-denoising method for OCT images is presented with single spectrogram-based deep learning. Different noises in different images could be customized with an extremely low computation.

Mueller matrix polarization imaging and quantitative parameters analysis method.

Mueller matrix polarization imaging is a new biomedical optical imaging method that can generate both polarization and isotropic intensity images of structures of the biological tissue sample surface. In this paper, a Mueller polarization imaging system in the reflection mode is described for obtaining the Mueller matrix of the specimens. Diattenuation, phase retardation, and depolarization of the specimens are derived by using the conventional Mueller matrix polarization decomposition method and a newly proposed direct method.

Fourier spatial transform-based method of suppressing motion noises in OCTA.

A large amount of lateral noise will be generated in blood flow imaging with optical coherence tomography angiography (OCTA) due to the presence of muscle shaking, heartbeat, and respiration, resulting in the deterioration of images. In this paper, to the best of our knowledge, for the first time, the spatial frequency information of motion noise in the blood flow signal region is used to remove the motion noise and false connections in the blood flow signal region. The effectiveness of the proposed adaptive denoising algorithm is verified by the imaging of finger blood flow.

Improved zebra finch brain transcriptome identifies novel proteins with sex differences.

The zebra finch (Taeniopygia guttata), a representative oscine songbird species, has been widely studied to investigate behavioral neuroscience, most notably the neurobiological basis of vocal learning, a rare trait shared in only a few animal groups including humans. In 2019, an updated zebra finch genome annotation (bTaeGut1_v1.p) was released from the Ensembl database and is substantially more comprehensive than the first version published in 2010.

Effects of orientation deviation of a beam splitter and a reference mirror on the stability of a two-interferometer-based handheld FFOCT imaging probe.

In this work, we present a handheld full-field optical coherence tomography (FFOCT) system based on a series connection of two interferometers: the Michelson interferometer is used as a compensation part and the Fizeau interferometer is used as a detection part. Owing to the common-path arrangement of the Fizeau interferometer, this handheld FFOCT system has a compact detection arm and is insensitive to the external disturbance. A high-output halogen lamp and high NA microscope objective contribute to achieving the spatial resolution of 0.

Anisotropic dielectric susceptibility matrix of anisotropic medium.

In this work, we introduce the concept of anisotropic dielectric susceptibility matrix of anisotropic medium for both nondepolarizing and depolarizing medium. The concept provides a new way of analyzing light scattering properties of anisotropic media illuminated by polarized light. The explicit expressions for the elements of the scattering matrix are given in terms of the elements of the Fourier transform of the anisotropic dielectric susceptibility matrix of the medium.

Infrared imaging confirms the role of the transparent surface zone in arresting dental caries.

Several studies have demonstrated the potential of short wavelength infrared (SWIR) reflectance, thermal imaging and optical coherence tomography for the nondestructive assessment of the activity of caries lesions. The purpose of this study was to test the hypothesis that the activity of arrested caries lesions on the coronal surfaces of extracted teeth would be changed by reducing the thickness of the highly mineralized transparent surface layer, which was measured using polarization sensitive optical coherence tomography (PS-OCT). The lesion activity was assessed using SWIR reflectance and thermal imaging during forced air drying of the lesion before and after mechanical removal of a surface layer ~ 50-μm thick covering the lesion.

Coupling effects among elementary polarization properties.

In this work, we propose that there exist coupling effects among birefringence, dichroism and off-diagonal depolarization parameters of differential Mueller matrix of random anisotropic media. An anisotropic spatial correlation function of anisotropic random medium is proposed to explain this phenomenon. The consequences of these effects are then pointed out.

Liver tissue classification of en face images by fractal dimension-based support vector machine.

Full-field optical coherence tomography (FF-OCT) has been reported with its label-free subcellular imaging performance. To realize quantitive cancer detection, the support vector machine model of classifying normal and cancerous human liver tissue is proposed with en face tomographic images. Twenty samples (10 normal and 10 cancerous) were operated from humans and composed of 285 en face tomographic images.

Brain Lesion Segmentation Based on Joint Constraints of Low-Rank Representation and Sparse Representation.

The segmentation of brain lesions from a brain magnetic resonance (MR) image is of great significance for the clinical diagnosis and follow-up treatment. An automatic segmentation method for brain lesions is proposed based on the low-rank representation (LRR) and the sparse representation (SR) theory. The proposed method decomposes the brain image into the background part composed of brain tissue and the brain lesion part.

2D MEMS-based high-speed beam-shifting technique for speckle noise reduction and flow rate measurement in optical coherence tomography.

In this manuscript, a two-dimensional (2D) micro-electro-mechanical system (MEMS)-based, high-speed beam-shifting spectral domain optical coherence tomography (MHB-SDOCT) is proposed for speckle noise reduction and absolute flow rate measurement. By combining a zigzag scanning protocol, the frame rates of 45.2 Hz for speckle reduction and 25.

Differential phase standard-deviation-based optical coherence tomographic angiography for human retinal imaging in vivo.

We present a differential phase standard-deviation (DPSD)-based optical coherence tomographic (OCT) angiography (OCTA) technique to calculate the angiography images of the human retina. The standard deviation was calculated along the depth direction on the differential phase image of two B-scans (from the same position, at different times) to contrast dynamic vascular signals. The performance of a DPSD was verified by both phantom and in vivo experiments.

Single-shot wavelength-independent phase-shifting method for full-field optical coherence tomography.

One limitation of a piezoelectric translator-based phase-shifting method in full-field optical coherence tomography (FF-OCT) is that there exist interference residuals because a light source with broadband is used. In this work, an achromatic phase-shifting method was proposed in which a linear polarizer and a quarter-wave plate were employed to generate the circularly polarized light in the reference arm of a basic Linnik interferometer. The light field reflected from the reference arm is supposed with the unpolarized light backscattered from the sample when the path difference is within the coherence length of the light source.

Quantitative depth-resolved microcirculation imaging with optical coherence tomography angiography (Part ΙΙ): Microvascular network imaging.

In this work, we review the main phenomena that have been explored in OCT angiography to image the vessels of the microcirculation within living tissues with the emphasis on how the different processing algorithms were derived to circumvent specific limitations. Parameters are then discussed that can quantitatively describe the depth-resolved microvascular network for possible clinical diagnosis applications. Finally, future directions in continuing OCT development are discussed.

Quantitative depth-resolved microcirculation imaging with optical coherence tomography angiography (Part Ι): Blood flow velocity imaging.

The research goal of the microvascular network imaging with OCT angiography is to achieve depth-resolved blood flow and vessel imaging in vivo in the clinical management of patents. In this review, we review the main phenomena that have been explored in OCT to image the blood flow velocity vector and the vessels of the microcirculation within living tissues. Parameters that limit the accurate measurements of blood flow velocity are then considered.

High speed, wide velocity dynamic range Doppler optical coherence tomography (Part V): Optimal utilization of multi-beam scanning for Doppler and speckle variance microvascular imaging.

In this paper, a multi-beam scanning technique is proposed to optimize the microvascular images of human skin obtained with Doppler effect based methods and speckle variance processing. Flow phantom experiments were performed to investigate the suitability for combining multi-beam data to achieve enhanced microvascular imaging. To our surprise, the highly variable spot sizes (ranging from 13 to 77 μm) encountered in high numerical aperture multi-beam OCT system imaging the same target provided reasonably uniform Doppler variance and speckle variance responses as functions of flow velocity, which formed the basis for combining them to obtain better microvascular imaging without scanning penalty.

Differential standard deviation of log-scale intensity based optical coherence tomography angiography.

In this paper, a differential standard deviation of log-scale intensity (DSDLI) based optical coherence tomography angiography (OCTA) is presented for calculating microvascular images of human skin. The DSDLI algorithm calculates the variance in difference images of two consecutive log-scale intensity based structural images from the same position along depth direction to contrast blood flow. The en face microvascular images were then generated by calculating the standard deviation of the differential log-scale intensities within the specific depth range, resulting in an improvement in spatial resolution and SNR in microvascular images compared to speckle variance OCT and power intensity differential method.

Image contrast reduction mechanism in full-field optical coherence tomography.

Correct interpretation of image contrast obtained with full-field optical coherence tomography (FFOCT) technique is required for accurate medical diagnosis applications. In this work, first, the characteristics of microscopic structures of tissue that generate the contrast in en-face tomographic image obtained with FFOCT are discussed. Then an overview is given of the parameters that affect image contrast.

Estimation of parameters for evaluating subsurface microcracks in glass with in-line digital holographic microscopy.

In this work, a new method for imaging subsurface damage (SSD) is proposed, which is, to the best of our knowledge, the first application of the in-line digital holographic microscopy (IDHM) to the reconstruction of the subsurface damage in glass. By combination of the in-line arrangement and an objective lens to image the hologram on the CCD surface, the method is characterized by its high resolution in both the lateral and depth directions. Then the three-dimensional reconstruction of the microcracks within the glass was realized by numerically focusing en-face images at different depths, and the sizes of SSD along the transversal and depth directions were estimated.

Rapid and high-resolution imaging of human liver specimens by full-field optical coherence tomography.

We report rapid and high-resolution tomographic en face imaging of human liver specimens by full-field optical coherence tomography (FF-OCT). First, the arrangement of the FF-OCT system was described and the performance of the system was measured. The measured axial and lateral resolutions of the system are 0.

Imaginary part-based correlation mapping optical coherence tomography for imaging of blood vessels in vivo.

We present an imaginary part-based correlation mapping optical coherence tomography (IMcmOCT) technique for in vivo blood vessels imaging. In the conventional correlation mapping optical coherence tomography (cmOCT) method, two adjacent frames of intensity-based structural images are correlated to extract blood flow information and the size of correlation window has to be increased to improve the signal-to-noise ratio of microcirculation maps, which may cause image blur and miss the small blood vessels. In the IMcmOCT method, the imaginary part of a depth-resolved complex analytic signal in two adjacent B-scans is correlated to reconstruct microcirculation maps.

A general model for resolution of digital holographic microscopy.

For digital holographic microscopic imaging, the resolution in the reconstructed image is one of the most important parameters. To optimize the lateral resolution, a general model for the resolution of digital holographic microscopy (DHM) is proposed in this work, in which the effects of the sizes of each pixel, total area of the charge coupled device (CCD) and the microscopic objective lens are taken into account. Comparison between our model and others was carried out by calculating the point spread function (PSF) of DHM at different reconstruction distances and with different fill factors.