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.

Fully automated OCT-based tissue screening system.

This study introduces an innovative optical coherence tomography (OCT) imaging system dedicated to high-throughput screening applications using ex vivo tissue culture. Leveraging OCT's non-invasive, high-resolution capabilities, the system is equipped with a custom-designed motorized platform and tissue detection ability for automated, successive imaging across samples. Transformer-based deep-learning segmentation algorithms further ensure robust, consistent, and efficient readouts meeting the standards for screening assays. Validated using retinal explant cultures from a mouse model of retinal degeneration, the system provides robust, rapid, reliable, unbiased, and comprehensive readouts of tissue response to treatments. This fully automated OCT-based system marks a significant advancement in tissue screening, promising to transform drug discovery, as well as other relevant research fields.

Compensation of inner retina to early-stage photoreceptor degeneration in a RhoP23H/+ mouse model of retinitis pigmentosa.

Retinitis pigmentosa (RP) is an inherited retinal disorder characterized by the degeneration of photoreceptors. RhoP23H/+ mice, which carry a Pro23His mutation in the RHODOPSIN (Rho) gene, are one of the most studied animal models for RP. However, except for the photoreceptors, other retinal neural cells have not been fully investigated in this model. Here, we record the temporal changes of the retina by optical coherence tomography (OCT) imaging of the RhoP23H/+ mice, from early to mid-phase of retinal degeneration. Based on thickness analysis, we identified a natural retinal thickness adaption in wild-type mice during early adulthood and observed morphological compensation of the inner retina layer to photoreceptor degeneration in the RhoP23H/+ mice, primarily on the inner nuclear layer (INL). RhoP23H/+ mice findings were further validated via: histology showing the negative correlation of INL and ONL thicknesses; as well as electroretinogram (ERG) showing an increased b-wave to a-wave ratio. These results unravel the sequential morphologic events in this model and suggest a better understanding of retinal degeneration of RP for future studies.

Retinal capillary oximetry with visible light optical coherence tomography.

Assessing oxygen saturation (sO2) remains challenging but is nonetheless necessary for understanding retinal metabolism. We and others previously achieved oximetry on major retinal vessels and measured the total retinal oxygen metabolic rate in rats using visible-light optical coherence tomography. Here we extend oximetry measurements to capillaries and investigate all three retinal vascular plexuses by amplifying and extracting the spectroscopic signal from each capillary segment under the guidance of optical coherence tomography (OCT) angiography. Using this approach, we measured capillary sO2 in the retinal circulation in rats, demonstrated reproducibility of the results, validated the measurements in superficial capillaries with known perfusion pathways, and determined sO2 responses to hypoxia and hyperoxia in the different retinal capillary beds. OCT capillary oximetry has the potential to provide new insights into the retinal circulation in the normal eye as well as in retinal vascular diseases.

Wide-field sensorless adaptive optics swept-source optical coherence tomographic angiography in rodents.

In this study, we present a sensorless adaptive optics swept-source optical coherence tomographic angiography (sAO-SS-OCTA) imaging system for mice. Real-time graphics processing unit (GPU)-based OCTA image acquisition and processing software were applied to guide wavefront correction using a deformable mirror based on signal strength index (SSI) from both OCT and OCTA images. High-resolution OCTA images with aberrations corrected and contrast enhanced were successfully acquired. Fifty-degree field of view high-resolution montaged OCTA images were also acquired.

Imaging retinal structures at cellular-level resolution by visible-light optical coherence tomography.

In vivo high-resolution images are the most direct way to understand retinal function and diseases. Here we report the use of visible-light optical coherence tomography with volumetric registration and averaging to achieve cellular-level retinal structural imaging in a rat eye, covering the entire depth of the retina. Vitreous fibers, nerve fiber bundles, and vasculature were clearly revealed, as well as at least three laminar sublayers in the inner plexiform layer. We also successfully visualized ganglion cell somas in the ganglion cell layer, cells in the inner nuclear layer, and photoreceptors in the outer nuclear layer and ellipsoid zone. This technique provides, to the best of our knowledge, a new means to visualize the retina in vivo at a cellular resolution and may enable detection or discovery of cellular neuronal biomarkers to help better diagnose ocular disease.

Real-time cross-sectional and en face OCT angiography guiding high-quality scan acquisition.

Defocusing, vignetting, and bulk motion degrade the image quality of optical coherence tomography angiography (OCTA) more significantly than structural OCT. The assessment of focus, alignment conditions, and stability of imaging subjects in commercially available OCTA systems are currently based on OCT signal quality alone, without knowledge of OCTA signal quality. This results in low yield rates for further quantification. In this Letter, we developed a novel OCTA platform based on a graphics processing unit (GPU) for a real-time, high refresh rate, B-san-by-B-scan split-spectrum amplitude-decorrelation angiography. The GPU provides a real-time display of both cross-sectional and en face images to assist operators during scan acquisition and ensure OCTA scan quality.

Fast and robust standard-deviation-based method for bulk motion compensation in phase-based functional OCT.

Phase-based optical coherence tomography (OCT), such as OCT angiography (OCTA) and Doppler OCT, is sensitive to the confounding phase shift introduced by subject bulk motion. Traditional bulk motion compensation methods are limited by their accuracy and computing cost-effectiveness. In this Letter, to the best of our knowledge, we present a novel bulk motion compensation method for phase-based functional OCT. Bulk motion associated phase shift can be directly derived by solving its equation using a standard deviation of phase-based OCTA and Doppler OCT flow signals. This method was evaluated on rodent retinal images acquired by a prototype visible light OCT and human retinal images acquired by a commercial system. The image quality and computational speed were significantly improved, compared to two conventional phase compensation methods.

High-spatial-resolution localization algorithm based on cascade deconvolution in a distributed Sagnac interferometer invasion monitoring system.

In the Sagnac fiber optic interferometer system, the phase difference signal can be illustrated as a convolution of the waveform of the invasion with its occurring-position-associated transfer function h(t); deconvolution is introduced to improve the spatial resolution of the localization. In general, to get a 26 m spatial resolution at a sampling rate of 4×106 s-1, the algorithm should mainly go through three steps after the preprocessing operations. First, the decimated phase difference signal is transformed from the time domain into the real cepstrum domain, where a probable region of invasion distance can be ascertained. Second, a narrower region of invasion distance is acquired by coarsely assuming and sweeping a transfer function h(t) within the probable region and examining where the restored invasion waveform x(t) gets its minimum standard deviation. Third, fine sweeping the narrow region point by point with the same criteria is used to get the final localization. Also, the original waveform of invasion can be restored for the first time as a by-product, which provides more accurate and pure characteristics for further processing, such as subsequent pattern recognition.

Harmonic peak locations based on the twice fast Fourier transform algorithm in a Sagnac intrusion sensing system.

Null frequencies in the spectrum of a phase difference signal are used for intrusion localization since their values are associated with the position of intrusion in a Sagnac interferometer. However, searching the null frequencies individually is troublesome and unreliable for localization. In this paper, an algorithm which directly captures the interval of null frequencies is proposed to achieve a simpler and more robust intrusion localization. By applying the modified spectrum to a second fast Fourier transform, the interval responds as multiple peaks in the resulting location curve. After determining the values of the base peak and its harmonic peaks, the intrusion's distance can be localized. Intrusions are applied at a position of 130 km in a sensing fiber. Due to the resolution increase as peak order, localization performance of 2nd harmonic peak is 25 m, which is 34% better than the base peaks. By calculating the average of the localization results by all remarkable peaks, localization performance improves by 47% in laboratory experiments and by 24% in practical applications over the previous single-peak localization algorithm.

Deep learning based characterization of human organoids using optical coherence tomography.

Organoids, derived from human induced pluripotent stem cells (hiPSCs), are intricate three-dimensional in vitro structures that mimic many key aspects of the complex morphology and functions of in vivo organs such as the retina and heart. Traditional histological methods, while crucial, often fall short in analyzing these dynamic structures due to their inherently static and destructive nature. In this study, we leveraged the capabilities of optical coherence tomography (OCT) for rapid, non-invasive imaging of both retinal, cerebral, and cardiac organoids. Complementing this, we developed a sophisticated deep learning approach to automatically segment the organoid tissues and their internal structures, such as hollows and chambers. Utilizing this advanced imaging and analysis platform, we quantitatively assessed critical parameters, including size, area, volume, and cardiac beating, offering a comprehensive live characterization and classification of the organoids. These findings provide profound insights into the differentiation and developmental processes of organoids, positioning quantitative OCT imaging as a potentially transformative tool for future organoid research.

Fully Automated OCT-based Tissue Screening System.

This study introduces a groundbreaking optical coherence tomography (OCT) imaging system dedicated for high-throughput screening applications using ex vivo tissue culture. Leveraging OCT's non-invasive, high-resolution capabilities, the system is equipped with a custom-designed motorized platform and tissue detection ability for automated, successive imaging across samples. Transformer-based deep learning segmentation algorithms further ensure robust, consistent, and efficient readouts meeting the standards for screening assays. Validated using retinal explant cultures from a mouse model of retinal degeneration, the system provides robust, rapid, reliable, unbiased, and comprehensive readouts of tissue response to treatments. This fully automated OCT-based system marks a significant advancement in tissue screening, promising to transform drug discovery, as well as other relevant research fields.

A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis.

Atoh7 is transiently expressed in retinal progenitor cells (RPCs) and is required for retinal ganglion cell (RGC) differentiation. In humans, a deletion in a distal non-coding regulatory region upstream of ATOH7 is associated with optic nerve atrophy and blindness. Here, we functionally interrogate the significance of the Atoh7 regulatory landscape to retinogenesis in mice. Deletion of the Atoh7 enhancer structure leads to RGC deficiency, optic nerve hypoplasia, and retinal blood vascular abnormalities, phenocopying inactivation of Atoh7. Further, loss of the Atoh7 remote enhancer impacts ipsilaterally projecting RGCs and disrupts proper axonal projections to the visual thalamus. Deletion of the Atoh7 remote enhancer is also associated with the dysregulation of axonogenesis genes, including the derepression of the axon repulsive cue Robo3. Our data provide insights into how Atoh7 enhancer elements function to promote RGC development and optic nerve formation and highlight a key role of Atoh7 in the transcriptional control of axon guidance molecules.

Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1.

Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as pivotal organelles responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, pyrvinium pamoate reduced tauopathy and alleviated retina degeneration by promoting autophagy and ubiquitin-proteasome system. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.

Volumetrically tracking retinal and choroidal structural changes in central serous chorioretinopathy.

Central serous chorioretinopathy (CSCR) leads to the accumulation of subretinal fluid and retinal thickness change, which can be readily detected in clinics using optical coherence tomography (OCT). However, current quantification methods usually require sophisticated processing such as retinal layer segmentations, and volumetric visualization of structural changes is generally challenging, which can hinder fast and accurate assessment of disease progression and/or treatment efficacy. In this study, we developed an algorithm that can register the OCT scans acquired from different visits without requiring prior layer segmentation and calculated the three-dimensional (3-D) structural change maps for patients with CSCR. Our results demonstrate that this tool can be useful in monitoring the progression of CSCR and revealing the resolution of pathologies following treatment automatically with minimal pre-processing.

Volumetrically tracking retinal and choroidal structural changes in central serous chorioretinopathy.

Central serous chorioretinopathy (CSCR) leads to accumulation of subretinal fluid and retinal thickness change, which can be readily detected in clinics using optical coherence tomography (OCT). However, current quantification methods usually require sophisticated processing such as retinal layer segmentations, and volumetric visualization of structural changes is generally challenging, which can hinder fast and accurate assessment of disease progression and/or treatment efficacy. In this study, we developed an algorithm that can register the OCT scans acquired from different visits without requiring prior layer segmentation and calculated the three-dimensional (3-D) structural change maps for patients with CSCR. Our results demonstrate that this tool can be useful in monitoring the progression of CSCR and revealing the resolution of pathologies following treatment automatically with minimal pre-processing.

Posterior corneoscleral limbus: Architecture, stem cells, and clinical implications.

The limbus is a transition from the cornea to conjunctiva and sclera. In human eyes, this thin strip has a rich variation of tissue structures and composition, typifying a change from scleral irregularity and opacity to corneal regularity and transparency; a variation from richly vascularized conjunctiva and sclera to avascular cornea; the neural passage and drainage of aqueous humor. The limbal stroma is enriched with circular fibres running parallel to the corneal circumference, giving its unique role in absorbing small pressure changes to maintain corneal curvature and refractivity. It contains specific niches housing different types of stem cells for the corneal epithelium, stromal keratocytes, corneal endothelium, and trabecular meshwork. This truly reflects the important roles of the limbus in ocular physiology, and the limbal functionality is crucial for corneal health and the entire visual system. Since the anterior limbus containing epithelial structures and limbal epithelial stem cells has been extensively reviewed, this article is focused on the posterior limbus. We have discussed the structural organization and cellular components of the region beneath the limbal epithelium, the characteristics of stem cell types: namely corneal stromal stem cells, endothelial progenitors and trabecular meshwork stem cells, and recent advances leading to the emergence of potential cell therapy options to replenish their respective mature cell types and to correct defects causing corneal abnormalities. We have reviewed different clinical disorders associated with defects of the posterior limbus and summarized the available preclinical and clinical evidence about the developing topic of cell-based therapy for corneal disorders.

Longitudinal Observation of Retinal Response to Optic Nerve Transection in Rats Using Visible Light Optical Coherence Tomography.

Purpose: To characterize rat retinal responses after optic nerve transection (ONT) by visible-light optical coherence tomography (vis-OCT). Methods: Unilateral ONT was performed in Brown Norway rats (n = 8). In vivo, vis-OCT retinal imaging was performed on the experimental eyes before ONT (baseline), and two days, one week, two weeks, and four weeks (endpoint) after ONT, as well as on fellow eyes at the endpoint. The system was operated at a 70 kHz A-line sampling rate with both raster scans (512 × 2 × 512 A-lines), and circular scans (2048 × 100 A-lines) acquired around the optic disc. Retinal layers were segmented to calculate layer thicknesses and project en face images for visualization and quantifications. Vessel densities and oxygen saturation were used to evaluate the morphologic and functional impact on the retinal vasculature. Results: After ONT, retinal nerve fiber bundles demonstrated significant degeneration, starting at two weeks, with a reduction of thicknesses quantified on the nerve fiber layer, ganglion cell complex, and total retina. Along with that, the activation of macrophage-like cells in the vitreoretinal interface was also observed. Vessel densities for all three retinal plexuses were unaffected over the period of observation. However, oxygen saturation in retinal arteries and veins was significantly reduced at four weeks after ONT. Conclusions: Vis-OCT can provide high-definition, in vivo characterization of retinal responses to ONT in rats. Despite a significant reduction in retinal layer thickness, this was not accompanied by alterations in vascular density. Despite this, oximetry indicates reduced retinal oxygen saturation, suggesting that altered vascular physiology is not reflected in the anatomic appearance of retinal blood vessel density alone.

Volume-based, layer-independent, disease-agnostic detection of abnormal retinal reflectivity, nonperfusion, and neovascularization using structural and angiographic OCT.

Optical coherence tomography (OCT) is widely used in ophthalmic practice because it can visualize retinal structure and vasculature in vivo and 3-dimensionally (3D). Even though OCT procedures yield data volumes, clinicians typically interpret the 3D images using two-dimensional (2D) data subsets, such as cross-sectional scans or en face projections. Since a single OCT volume can contain hundreds of cross-sections (each of which must be processed with retinal layer segmentation to produce en face images), a thorough manual analysis of the complete OCT volume can be prohibitively time-consuming. Furthermore, 2D reductions of the full OCT volume may obscure relationships between disease progression and the (volumetric) location of pathology within the retina and can be prone to mis-segmentation artifacts. In this work, we propose a novel framework that can detect several retinal pathologies in three dimensions using structural and angiographic OCT. Our framework operates by detecting deviations in reflectance, angiography, and simulated perfusion from a percent depth normalized standard retina created by merging and averaging scans from healthy subjects. We show that these deviations from the standard retina can highlight multiple key features, while the depth normalization obviates the need to segment several retinal layers. We also construct a composite pathology index that measures average deviation from the standard retina in several categories (hypo- and hyper-reflectance, nonperfusion, presence of choroidal neovascularization, and thickness change) and show that this index correlates with DR severity. Requiring minimal retinal layer segmentation and being fully automated, this 3D framework has a strong potential to be integrated into commercial OCT systems and to benefit ophthalmology research and clinical care.

Effect of algorithms and covariates in glaucoma diagnosis with optical coherence tomography angiography.

PURPOSE: To assess the effects of algorithms and covariates in glaucoma diagnosis with optical coherence tomography angiography (OCTA). METHODS: In this prospective cross-sectional study, one eye each of 36 normal controls and 64 patients with glaucoma underwent 4.5 mm disc-centred and 6 mm macula-centred OCTA scans. The peripapillary nerve fibre layer plexus capillary density (NFLP-CD) and macular superficial vascular complex vessel density (SVC-VD) were measured using both a commercial algorithm (AngioAnalytics) and a custom algorithm (Center for Ophthalmic Optics & Lasers Angiography Reading Toolkit (COOL-ART)). The nerve fibre layer and ganglion cell complex thicknesses were measured on structural OCT. RESULTS: The overall peripapillary NFLP-CD and macular SVC-VD measured with the two algorithms were highly correlated but poorly agreed. Among the normal controls, the perfusion measurements made by both algorithms were significantly correlated with age. AngioAnalytics measurements were also correlated with signal strength index, while COOL-ART measurements were not. These covariates were adjusted. The diagnostic accuracy, measured as the area under the receiver operating characteristic curve for glaucoma detection, was not significantly different between algorithms, between structural and perfusion parameters and between the peripapillary and macular regions (All p>0.05). The macular SVC-VD in the 6 mm square had a significantly higher diagnostic accuracy than that of the central 3 mm square area (p=0.005). CONCLUSIONS: AngioAnalytics and COOL-ART vessel density measurements are not interchangeable but potentially interconvertible. Age and signal strength are significant covariates that need to be considered. Both algorithms and both peripapillary and macular perfusion parameters have similarly good diagnostic accuracy comparable to structural OCT. A larger macular analytic area provides higher diagnostic accuracy.