{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/efficient-and-fully-automatic-retinal-choroid","title":"An open-source deep learning algorithm for efficient and fully-automatic analysis of the choroid in optical coherence tomography","arxiv_id":"2307.00904","date":"2023-07-03","proceeding":null,"authors":["Jamie Burke","Justin Engelmann","Charlene Hamid","Megan Reid-Schachter","Tom Pearson","Dan Pugh","Neeraj Dhaun","Stuart King","Tom MacGillivray","Miguel O. Bernabeu","Amos Storkey","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) 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.","url_abs":"https://arxiv.org/abs/2307.00904v3","url_pdf":"https://arxiv.org/pdf/2307.00904v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"efficient-and-fully-automatic-retinal-choroid","repo_url":"https://github.com/jaburke166/deepgpet","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":null,"task_name":"CPU"},{"task_slug":"segmentation","task_name":"Segmentation"}],"methods":[{"method_slug":"1x1-convolution","method_name":"1x1 Convolution"},{"method_slug":"average-pooling","method_name":"Average Pooling"},{"method_slug":"batch-normalization","method_name":"Batch Normalization"},{"method_slug":"convolution","method_name":"Convolution"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"depthwise-convolution","method_name":"Depthwise Convolution"},{"method_slug":"depthwise-separable-convolution","method_name":"Depthwise Separable Convolution"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gaussian-process","method_name":"Gaussian Process"},{"method_slug":"global-average-pooling","method_name":"Global Average Pooling"},{"method_slug":"hard-swish","method_name":"Hard Swish"},{"method_slug":"inverted-residual-block","method_name":"Inverted Residual Block"},{"method_slug":"pointwise-convolution","method_name":"Pointwise Convolution"},{"method_slug":"relu","method_name":"ReLU"},{"method_slug":"relu6","method_name":"ReLU6"},{"method_slug":"sigmoid-activation","method_name":"Sigmoid Activation"},{"method_slug":"squeeze-and-excitation-block","method_name":"Squeeze-and-Excitation Block"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}