Retinal layer segmentation in Optical Coherence Tomography (OCT) is a fundamental step for extracting quantitative biomarkers of retinal structure. Indeed, there is a growing interest in the analysis of OCTs in the context of neurodegenerative diseases. However, segmentation remains challenging due to speckle noise, shadowing artifacts, low contrast between adjacent layers, anatomical variability across subjects, and domain shifts arising from different acquisition protocols and clinical populations. While deep learning methods have achieved remarkable performance, their robustness and generalization across heterogeneous datasets remain limited. In this work, we investigate the role of spatial normalization as a preprocessing strategy to mitigate geometric domain shifts and improve the consistency of retinal layer segmentation. Inspired by standard practices in neuroimaging, we introduce a fovea-centered normalization framework that aligns OCT volumes into a common anatomical reference. We perform a comprehensive evaluation of state-of-the-art deep learning architectures. To provide a comprehensive assessment of segmentation quality, we combine conventional overlap-based metrics at B-scan level with topology-aware metrics at A-scan level and thickness-based measures at the en-face level. In cases where a ground truth is not available, we propose topology violation quantitative metrics that do not require ground truth annotations and a thickness-based qualitative assessment that captures structural consistency and clinically relevant patterns at the en-face level. The results demonstrate the importance of spatial normalization in OCT segmentation pipelines toward the development of robust and clinically meaningful retinal analysis tools, enabling reliable biomarker extraction and downstream computational analysis in neurodegenerative research.
Reliable automated analysis of Optical Coherence Tomography (OCT) imaging is crucial for diagnosing retinal disorders but faces a critical barrier: the need for expensive, labor-intensive expert annotations. Supervised deep learning models struggle to generalize across diverse pathologies, imaging devices, and patient populations due to their restricted vocabulary of annotated abnormalities. We propose an unsupervised anomaly detection framework that learns the normative distribution of healthy retinal anatomy without lesion annotations, directly addressing annotation efficiency challenges in clinical deployment. Our approach leverages a discrete latent model trained on normal B-scans to capture OCT-specific structural patterns. To enhance clinical robustness, we incorporate retinal layer-aware supervision and structured triplet learning to separate healthy from pathological representations, improving model reliability across varied imaging conditions. During inference, anomalies are detected and localized via reconstruction discrepancies, enabling both image and pixel-level identification without requiring disease-specific labels. On the Kermany dataset (AUROC: 0.799), our method substantially outperforms VAE, VQVAE, VQGAN, and f-AnoGAN baselines. Critically, cross-dataset evaluation on Srinivasan achieves AUROC 0.884 with superior generalization, demonstrating robust domain adaptation. On the external RETOUCH benchmark, unsupervised anomaly segmentation achieves competitive Dice (0.200) and mIoU (0.117) scores, validating reproducibility across institutions.
Accurate segmentation of corneal layers in optical coherence tomography (OCT) is essential for quantitative assessment of corneal morphology, including layer thickness and structural changes associated with disease or surgery. However, automatic segmentation remains challenging because corneal interfaces are thin, affected by speckle noise, and variable across acquisition devices. In this work, we propose ARCOS, a patch-based zero-shot boundary localization framework for corneal layer segmentation in clinical anterior-segment OCT images. Rather than performing conventional region classification, the method predicts boundary heatmaps for the main corneal interfaces from overlapping native-resolution patches. Patch-level predictions are stitched across the full B-scan and converted into boundary locations to obtain continuous, anatomically ordered layer segmentations. The network combines multi-scale feature fusion with a self-conditioned refinement module that uses intermediate boundary information to improve local heatmap predictions while preserving spatial detail. The method was evaluated on clinical OCT images acquired from multiple devices and compared with representative segmentation baselines using boundary localization and derived thickness metrics. The proposed method achieved an off-by-one boundary localization accuracy of 95.1% and a mean absolute boundary error of 0.514 pixels on the matched-device test set. In zero-shot cross-device evaluation, it maintained an average off-by-one accuracy of 84.3% and a mean absolute boundary error of 0.855 pixels across unseen acquisition devices, outperforming the baseline models. Thickness estimates derived from the predicted boundaries showed low error across corneal regions, supporting the method's use for quantitative corneal OCT analysis.
Nuno Vivas Brás, Benjamin Memmi, Maëlle Bouhassane +4
Measuring retinal fluid from optical coherence tomography (OCT) drives treatment decisions in macular disease, but manual annotation is slow and segmentation models trained on one scanner degrade on another. We present an attention-guided TransUNet that segments three fluid types across four independent OCT sources, combining a domain-adaptive normalisation scheme with an uncertainty estimate that flags unreliable pixels. The model reaches a mean fluid Dice of 0.78, and -- most usefully for clinicians -- its uncertainty is 1.34x higher exactly where expert graders disagree (p<10^-4), turning a raw segmentation map into an actionable clinical triage signal.