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 AuthorsJamie 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. MacCormickAbstractPurposeTo develop an open-source, fully automatic deep learning algorithm, DeepGPET, for choroid region segmentation in optical coherence tomography (OCT).MethodsWe 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.ResultsDeepGPET, 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.ConclusionsDeepGPET, 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 RelevanceDeepGPET 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. KeywordsDeepGPETOptical coherence tomography (OCT). Related linksLink to paper at Translational Vision Science & Technology The Row Fogo CentreEdinburgh ImagingDeepGPETOptical coherence tomography (OCT). Social media tags and titlesFeatured Paper: An Open-Source Deep Learning Algorithm for Efficient and Fully Automatic Analysis of the Choroid in Optical Coherence Tomography@SVDResearch @EdinUniImaging Publication date 27 Nov, 2023
