AutoMorph: Automated Retinal Vascular Morphology Quantification via a Deep Learning Pipeline

Purpose To externally validate a deep learning pipeline (AutoMorph) for automated analysis of retinal vascular morphology on fundus photographs. AutoMorph has been made publicly available ( https://github.com/rmaphoh/AutoMorph ), facilitating widespread research in ophthalmic and systemic diseases. Methods AutoMorph consists of four functional modules: image pre-processing, image quality grading, anatomical segmentation (including binary vessel, artery/vein, and optic disc/cup segmentation), and vascular morphology feature measurement. Image quality grading and anatomical segmentation use the most recent deep learning techniques. We employ a model ensemble strategy to achieve robust results and analyse the prediction confidence to rectify false gradable cases in image quality grading. We externally validate each module’s performance on several independent publicly available datasets. Results The EfficientNet-b4 architecture used in the image grading module achieves comparable performance to the state-of-the-art for EyePACS-Q, with an F1-score of 0.86. The confidence analysis reduces the number of images incorrectly assessed as gradable by 76%. Binary vessel segmentation achieves an F1-score of 0.73 on AV-WIDE and 0.78 on DR-HAGIS. Artery/vein scores 0.66 on IOSTAR-AV, and disc segmentation achieves 0.94 in IDRID. Vascular morphology features measured from AutoMorph segmentation map and expert annotation show good to excellent agreement. Conclusions AutoMorph modules perform well even when external validation data shows domain differences from training data, e.g., with different imaging devices. This fully automated pipeline can thus allow detailed, efficient and comprehensive analysis of retinal vascular morphology on colour fundus photographs. Translational Relevance By making AutoMorph publicly available and open source, we hope to facilitate ophthalmic and systemic disease research, particularly in the emerging field of ‘oculomics’.