The choroid provides oxygen and nourishment to the outer retina thus is related to the pathology of various ocular diseases. Optical coherence tomography (OCT) is advantageous in visualizing and quantifying the choroid in vivo. However, its application in the study of the choroid is still limited for two reasons. (1) The lower boundary of the choroid (choroid-sclera interface) in OCT is fuzzy, which makes the automatic segmentation difficult and inaccurate. (2) The visualization of the choroid is hindered by the vessel shadows from the superficial layers of the inner retina. In this paper, we propose to incorporate medical and imaging prior knowledge with deep learning to address these two problems. We propose a biomarker-infused global-to-local network (Bio-Net) for the choroid segmentation, which not only regularizes the segmentation via predicted choroid thickness, but also leverages a global-to-local segmentation strategy to provide global structure information and suppress overfitting. For eliminating the retinal vessel shadows, we propose a deep-learning pipeline, which firstly locate the shadows using their projection on the retinal pigment epithelium layer, then the contents of the choroidal vasculature at the shadow locations are predicted with an edge-to-texture generative adversarial inpainting network. The results show our method outperforms the existing methods on both tasks. We further apply the proposed method in a clinical prospective study for understanding the pathology of glaucoma, which demonstrates its capacity in detecting the structure and vascular changes of the choroid related to the elevation of intra-ocular pressure.
Automated segmentation of retinal optical coherence tomography (OCT) images has become an important recent direction in machine learning for medical applications. We hypothesize that the anatomic structure of layers and their high-frequency variation in OCT images make retinal OCT a fitting choice for extracting spectral-domain features and combining them with spatial domain features. In this work, we present $\Upsilon$-Net, an architecture that combines the frequency domain features with the image domain to improve the segmentation performance of OCT images. The results of this work demonstrate that the introduction of two branches, one for spectral and one for spatial domain features, brings a very significant improvement in fluid segmentation performance and allows outperformance as compared to the well-known U-Net model. Our improvement was 13% on the fluid segmentation dice score and 1.9% on the average dice score. Finally, removing selected frequency ranges in the spectral domain demonstrates the impact of these features on the fluid segmentation outperformance.
An accurate and automated tissue segmentation algorithm for retinal optical coherence tomography (OCT) images is crucial for the diagnosis of glaucoma. However, due to the presence of the optic disc, the anatomical structure of the peripapillary region of the retina is complicated and is challenging for segmentation. To address this issue, we developed a novel graph convolutional network (GCN)-assisted two-stage framework to simultaneously label the nine retinal layers and the optic disc. Specifically, a multi-scale global reasoning module is inserted between the encoder and decoder of a U-shape neural network to exploit anatomical prior knowledge and perform spatial reasoning. We conducted experiments on human peripapillary retinal OCT images. The Dice score of the proposed segmentation network is 0.820$\pm$0.001 and the pixel accuracy is 0.830$\pm$0.002, both of which outperform those from other state-of-the-art techniques.