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Biomed Opt Express. 2019 Sep 12;10(10):5042-5058. doi: 10.1364/BOE.10.005042. eCollection 2019 Oct 1.

Deep learning based topology guaranteed surface and MME segmentation of multiple sclerosis subjects from retinal OCT.

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Deptartment of Electrical and Computer Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Computer Science, The Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Mathematics & Statistics, Portland State University, Portland, OR 97201, USA.
Wilmer Eye Institute, The Johns Hopkins University School of Medicine, MD 21287, USA.
Department of Neurology, The Johns Hopkins University School of Medicine, MD 21287, USA.


Optical coherence tomography (OCT) is a noninvasive imaging modality that can be used to obtain depth images of the retina. Patients with multiple sclerosis (MS) have thinning retinal nerve fiber and ganglion cell layers, and approximately 5% of MS patients will develop microcystic macular edema (MME) within the retina. Segmentation of both the retinal layers and MME can provide important information to help monitor MS progression. Graph-based segmentation with machine learning preprocessing is the leading method for retinal layer segmentation, providing accurate surface delineations with the correct topological ordering. However, graph methods are time-consuming and they do not optimally incorporate joint MME segmentation. This paper presents a deep network that extracts continuous, smooth, and topology-guaranteed surfaces and MMEs. The network learns shape priors automatically during training rather than being hard-coded as in graph methods. In this new approach, retinal surfaces and MMEs are segmented together with two cascaded deep networks in a single feed forward propagation. The proposed framework obtains retinal surfaces (separating the layers) with sub-pixel surface accuracy comparable to the best existing graph methods and MMEs with better accuracy than the state-of-the-art method. The full segmentation operation takes only ten seconds for a 3D volume.

Conflict of interest statement

The authors declare that there are no conflicts of interest related to this article.

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