27 Nov 23. Featured Paper

An Open-Source Deep Learning Algorithm for Efficient and Fully Automatic Analysis of the Choroid in Optical Coherence Tomography

Link to paper at Translational Vision Science & Technology 

Authors

Jamie Burke, Justin Engelmann, Charlene Hamid, Megan Reid-Schachter, Tom Pearson, Dan Pugh, Neeraj Dhaun, Amos Storkey, Stuart King, Tom J. MacGillivray, Miguel O. Bernabeu, and Ian J. C. MacCormick

Abstract

Purpose

To develop an open-source, fully automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT).

Methods

We used a dataset of 715 OCT B-scans (82 subjects, 115 eyes) from three clinical studies related to systemic disease. Ground-truth segmentations were generated using a clinically validated, semiautomatic choroid segmentation method, Gaussian Process Edge Tracing (GPET). We finetuned a U-Net with the MobileNetV3 backbone pretrained on ImageNet. Standard segmentation agreement metrics, as well as derived measures of choroidal thickness and area, were used to evaluate DeepGPET, alongside qualitative evaluation from a clinical ophthalmologist.

Results

DeepGPET, a fully automatic, open-source algorithm for choroidal segmentation, will enable researchers to efficiently extract choroidal measurements, even for large datasets. As no manual interventions are required, DeepGPET is less subjective than semiautomatic methods and could be deployed in clinical practice without requiring a trained operator.

Conclusions

DeepGPET, a fully automatic, open-source algorithm for choroidal segmentation, will enable researchers to efficiently extract choroidal measurements, even for large datasets. As no manual interventions are required, DeepGPET is less subjective than semiautomatic methods and could be deployed in clinical practice without requiring a trained operator.

Translational Relevance

DeepGPET addresses the lack of open-source, fully automatic, and clinically relevant choroid segmentation algorithms, and its subsequent public release will facilitate future choroidal research in both ophthalmology and wider systemic health. 

Keywords

• DeepGPET
• Optical coherence tomography (OCT).