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Background: Corneal fluorescein sodium staining is a valuable diagnostic method for various ocular surface diseases. However, the examination results are highly dependent on the subjective experience of ophthalmologists. Objectives: To develop an artificial intelligence system based on deep learning to provide an accurate quantitative assessment of sodium fluorescein staining score and the size of cornea epithelial patchy defect. Design: A prospective study. Methods: We proposed an artificial intelligence system for automatically evaluating corneal staining scores and accurately measuring patchy corneal epithelial defects based on corneal fluorescein sodium staining images. The design incorporates two segmentation models and a classification model to forecast and assess the stained images. Meanwhile, we compare the evaluation findings from the system with ophthalmologists with varying expertise. Results: For the segmentation task of cornea boundary and cornea epithelial patchy defect area, our proposed method can achieve the performance of dice similarity coefficient (DSC) is 0.98/0.97 and Hausdorff distance (HD) is 3.60/8.39, respectively, when compared with the manually labeled gold standard. This method significantly outperforms the four leading algorithms (Unet, Unet++, Swin-Unet, and TransUnet). For the classification task, our algorithm achieves the best performance in accuracy, recall, and F1-score, which are 91.2%, 78.6%, and 79.2%, respectively. The performance of our developed system exceeds seven different approaches (Inception, ShuffleNet, Xception, EfficientNet_B7, DenseNet, ResNet, and VIT) in classification tasks. In addition, three ophthalmologists were selected to rate corneal staining images. The results showed that the performance of our artificial intelligence system significantly outperformed the junior doctors. Conclusion: The system offers a promising automated assessment method for corneal fluorescein staining, decreasing incorrect evaluations caused by ophthalmologists’ subjective variance and limited knowledge.

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