Conventional Fourier-domain Optical Coherence Tomography (FD-OCT) systems depend on resampling into wavenumber (k) domain to extract the depth profile. This either necessitates additional hardware resources or amplifies the existing computational complexity. Moreover, the OCT images also suffer from speckle noise, due to systemic reliance on low coherence interferometry. We propose a streamlined and computationally efficient approach based on Deep-Learning (DL) which enables reconstructing speckle-reduced OCT images directly from the wavelength domain. For reconstruction, two encoder-decoder styled networks namely Spatial Domain Convolution Neural Network (SD-CNN) and Fourier Domain CNN (FD-CNN) are used sequentially. The SD-CNN exploits the highly degraded images obtained by Fourier transforming the domain fringes to reconstruct the deteriorated morphological structures along with suppression of unwanted noise. The FD-CNN leverages this output to enhance the image quality further by optimization in Fourier domain (FD). We quantitatively and visually demonstrate the efficacy of the method in obtaining high-quality OCT images. Furthermore, we illustrate the computational complexity reduction by harnessing the power of DL models. We believe that this work lays the framework for further innovations in the realm of OCT image reconstruction.

Skin, the primary regulator of heat exchange, relies on sweat glands for thermoregulation. Alterations in sweat gland morphology play a crucial role in various pathological conditions and clinical diagnoses. Current methods for observing sweat gland morphology are limited by their two-dimensional, in vitro, and destructive nature, underscoring the urgent need for real-time, non-invasive, quantifiable technologies. We proposed a novel three-dimensional (3D) transformer-based multi-object segmentation framework, integrating a sliding window approach, joint spatial-channel attention mechanism, and architectural heterogeneity between shallow and deep layers. Our proposed network enables precise 3D sweat gland segmentation from skin volume data captured by optical coherence tomography (OCT). For the first time, subtle variations of sweat gland 3D morphology in response to temperature changes, have been visualized and quantified. Our approach establishes a benchmark for normal sweat gland morphology and provides a real-time, non-invasive tool for quantifying 3D structural parameters. This enables the study of individual variability and pathological changes in sweat gland structure, advancing dermatological research and clinical applications, including thermoregulation and bromhidrosis treatment.

Serial sectioning Optical Coherence Tomography (sOCT) is a high-throughput, label free microscopic imaging technique that is becoming increasingly popular to study post-mortem neurovasculature. Quantitative analysis of the vasculature requires highly accurate segmentation; however, sOCT has low signal-to-noise-ratio and displays a wide range of contrasts and artifacts that depend on acquisition parameters. Furthermore, labeled data is scarce and extremely time consuming to generate. Here, we leverage synthetic datasets of vessels to train a deep learning segmentation model. We construct the vessels with semi-realistic splines that simulate the vascular geometry and compare our model with realistic vascular labels generated by constrained constructive optimization. Both approaches yield similar Dice scores, although with very different false positive and false negative rates. This method addresses the complexity inherent in OCT images and paves the way for more accurate and efficient analysis of neurovascular structures.

Automated medical diagnosis through image-based neural networks has increased in popularity and matured over years. Nevertheless, it is confined by the scarcity of medical images and the expensive labor annotation costs. Self-Supervised Learning (SSL) is an good alternative to Transfer Learning (TL) and is suitable for imbalanced image datasets. In this study, we assess four pretrained SSL models and two TL models in treatable retinal diseases classification using small-scale Optical Coherence Tomography (OCT) images ranging from 125 to 4000 with balanced or imbalanced distribution for training. The proposed SSL model achieves the state-of-art accuracy of 98.84% using only 4,000 training images. Our results suggest the SSL models provide superior performance under both the balanced and imbalanced training scenarios. The SSL model with MoCo-v2 scheme has consistent good performance under the imbalanced scenario and, especially, surpasses the other models when the training set is less than 500 images.

Retinal optical coherence tomography (OCT) images provide crucial insights into the health of the posterior ocular segment. Therefore, the advancement of automated image analysis methods is imperative to equip clinicians and researchers with quantitative data, thereby facilitating informed decision-making. The application of deep learning (DL)-based approaches has gained extensive traction for executing these analysis tasks, demonstrating remarkable performance compared to labor-intensive manual analyses. However, the acquisition of Retinal OCT images often presents challenges stemming from privacy concerns and the resource-intensive labeling procedures, which contradicts the prevailing notion that DL models necessitate substantial data volumes for achieving superior performance. Moreover, limitations in available computational resources constrain the progress of high-performance medical artificial intelligence, particularly in less developed regions and countries. This paper introduces a novel ensemble learning mechanism designed for recognizing retinal diseases under limited resources (e.g., data, computation). The mechanism leverages insights from multiple pre-trained models, facilitating the transfer and adaptation of their knowledge to Retinal OCT images. This approach establishes a robust model even when confronted with limited labeled data, eliminating the need for an extensive array of parameters, as required in learning from scratch. Comprehensive experimentation on real-world datasets demonstrates that the proposed approach can achieve superior performance in recognizing Retinal OCT images, even when dealing with exceedingly restricted labeled datasets. Furthermore, this method obviates the necessity of learning extensive-scale parameters, making it well-suited for deployment in low-resource scenarios.

Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 1600 high-resolution OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.

Purpose: To develop Choroidalyzer, an open-source, end-to-end pipeline for segmenting the choroid region, vessels, and fovea, and deriving choroidal thickness, area, and vascular index. Methods: We used 5,600 OCT B-scans (233 subjects, 6 systemic disease cohorts, 3 device types, 2 manufacturers). To generate region and vessel ground-truths, we used state-of-the-art automatic methods following manual correction of inaccurate segmentations, with foveal positions manually annotated. We trained a U-Net deep-learning model to detect the region, vessels, and fovea to calculate choroid thickness, area, and vascular index in a fovea-centred region of interest. We analysed segmentation agreement (AUC, Dice) and choroid metrics agreement (Pearson, Spearman, mean absolute error (MAE)) in internal and external test sets. We compared Choroidalyzer to two manual graders on a small subset of external test images and examined cases of high error. Results: Choroidalyzer took 0.299 seconds per image on a standard laptop and achieved excellent region (Dice: internal 0.9789, external 0.9749), very good vessel segmentation performance (Dice: internal 0.8817, external 0.8703) and excellent fovea location prediction (MAE: internal 3.9 pixels, external 3.4 pixels). For thickness, area, and vascular index, Pearson correlations were 0.9754, 0.9815, and 0.8285 (internal) / 0.9831, 0.9779, 0.7948 (external), respectively (all p<0.0001). Choroidalyzer's agreement with graders was comparable to the inter-grader agreement across all metrics. Conclusions: Choroidalyzer is an open-source, end-to-end pipeline that accurately segments the choroid and reliably extracts thickness, area, and vascular index. Especially choroidal vessel segmentation is a difficult and subjective task, and fully-automatic methods like Choroidalyzer could provide objectivity and standardisation.

Parkinson's disease is the world's fastest growing neurological disorder. Research to elucidate the mechanisms of Parkinson's disease and automate diagnostics would greatly improve the treatment of patients with Parkinson's disease. Current diagnostic methods are expensive with limited availability. Considering the long progression time of Parkinson's disease, a desirable screening should be diagnostically accurate even before the onset of symptoms to allow medical intervention. We promote attention for retinal fundus imaging, often termed a window to the brain, as a diagnostic screening modality for Parkinson's disease. We conducted a systematic evaluation of conventional machine learning and deep learning techniques to classify Parkinson's disease from UK Biobank fundus imaging. Our results suggest Parkinson's disease individuals can be differentiated from age and gender matched healthy subjects with 71% accuracy. This accuracy is maintained when predicting either prevalent or incident Parkinson's disease. Explainability and trustworthiness is enhanced by visual attribution maps of localized biomarkers and quantified metrics of model robustness to data perturbations.

Thin-cap fibroatheroma (TCFA) and plaque rupture have been recognized as the most frequent risk factor for thrombosis and acute coronary syndrome. Intravascular optical coherence tomography (IVOCT) can identify TCFA and assess cap thickness, which provides an opportunity to assess plaque vulnerability. We developed an automated method that can detect lipidous plaque and assess fibrous cap thickness in IVOCT images. This study analyzed a total of 4,360 IVOCT image frames of 77 lesions among 41 patients. To improve segmentation performance, preprocessing included lumen segmentation, pixel-shifting, and noise filtering on the raw polar (r, theta) IVOCT images. We used the DeepLab-v3 plus deep learning model to classify lipidous plaque pixels. After lipid detection, we automatically detected the outer border of the fibrous cap using a special dynamic programming algorithm and assessed the cap thickness. Our method provided excellent discriminability of lipid plaque with a sensitivity of 85.8% and A-line Dice coefficient of 0.837. By comparing lipid angle measurements between two analysts following editing of our automated software, we found good agreement by Bland-Altman analysis (difference 6.7+/-17 degree; mean 196 degree). Our method accurately detected the fibrous cap from the detected lipid plaque. Automated analysis required a significant modification for only 5.5% frames. Furthermore, our method showed a good agreement of fibrous cap thickness between two analysts with Bland-Altman analysis (4.2+/-14.6 micron; mean 175 micron), indicating little bias between users and good reproducibility of the measurement. We developed a fully automated method for fibrous cap quantification in IVOCT images, resulting in good agreement with determinations by analysts. The method has great potential to enable highly automated, repeatable, and comprehensive evaluations of TCFAs.

Optical coherence tomography (OCT) imaging from different camera devices causes challenging domain shifts and can cause a severe drop in accuracy for machine learning models. In this work, we introduce a minimal noise adaptation method based on a singular value decomposition (SVDNA) to overcome the domain gap between target domains from three different device manufacturers in retinal OCT imaging. Our method utilizes the difference in noise structure to successfully bridge the domain gap between different OCT devices and transfer the style from unlabeled target domain images to source images for which manual annotations are available. We demonstrate how this method, despite its simplicity, compares or even outperforms state-of-the-art unsupervised domain adaptation methods for semantic segmentation on a public OCT dataset. SVDNA can be integrated with just a few lines of code into the augmentation pipeline of any network which is in contrast to many state-of-the-art domain adaptation methods which often need to change the underlying model architecture or train a separate style transfer model.