An open-source deep learning algorithm for efficient and fully-automatic analysis of the choroid in optical coherence tomography

TL;DR

This paper introduces DeepGPET, an open-source deep learning algorithm that automatically segments the choroid in OCT images with high accuracy and speed, facilitating large-scale research and clinical applications.

Contribution

The paper presents a novel fully-automatic deep learning method, DeepGPET, for choroid segmentation in OCT images, outperforming semi-automatic methods in speed and maintaining high accuracy.

Findings

DeepGPET achieves near-perfect agreement with the semi-automatic GPET method.

Processing time per image is reduced from over 34 seconds to 1.25 seconds.

Qualitative evaluation confirms comparable segmentation quality to GPET.

Abstract

Purpose: To develop an open-source, fully-automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT) data. Methods: We used a dataset of 715 OCT B-scans (82 subjects, 115 eyes) from 3 clinical studies related to systemic disease. Ground truth segmentations were generated using a clinically validated, semi-automatic choroid segmentation method, Gaussian Process Edge Tracing (GPET). We finetuned a UNet with MobileNetV3 backbone pre-trained 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 achieves excellent agreement with GPET on data from 3 clinical studies (AUC=0.9994, Dice=0.9664; Pearson correlation of 0.8908 for choroidal thickness and 0.9082 for choroidal area), while reducing the mean processing time per image on a standard laptop CPU from 34.49s ($\pm$15.09) using GPET to 1.25s ($\pm$0.10) using DeepGPET. Both methods performed similarly according to a clinical ophthalmologist, who qualitatively judged a subset of segmentations by GPET and DeepGPET, based on smoothness and accuracy of segmentations. 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 semi-automatic methods and could be deployed in clinical practice without necessitating a trained operator.