Open-Source Automatic Segmentation of Ocular Structures and Biomarkers of Microbial Keratitis on Slit-Lamp Photography Images Using Deep Learning

• Published in: IEEE journal of biomedical and health informatics Vol. 25; no. 1; pp. 88 - 99
• Main Authors: Loo, Jessica, Kriegel, Matthias F., Tuohy, Megan M., Kim, Kyeong Hwan, Prajna, Venkatesh, Woodward, Maria A., Farsiu, Sina
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.01.2021; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithms; Annotations; Artificial neural networks; Automatic segmentation; Biomarkers; Cornea; Datasets; Deep Learning; Edema; Eye; Eye (anatomy); Feature extraction; Humans; Image Processing, Computer-Assisted; Image segmentation; Keratitis; Keratitis - diagnostic imaging; Leukocytes; Machine learning; Manuals; Medical services; Metric space; microbial keratitis; Microorganisms; Neural networks; Pathology; Photography; Reflexes; slit-lamp imaging; White light
• ISSN: 2168-2194; 2168-2208; 2168-2208
• DOI: 10.1109/JBHI.2020.2983549

We propose a fully-automatic deep learning-based algorithm for segmentation of ocular structures and microbial keratitis (MK) biomarkers on slit-lamp photography (SLP) images. The dataset consisted of SLP images from 133 eyes with manual annotations by a physician, P1. A modified region-based convolutional neural network, SLIT-Net, was developed and trained using P1's annotations to identify and segment four pathological regions of interest (ROIs) on diffuse white light images (stromal infiltrate (SI), hypopyon, white blood cell (WBC) border, corneal edema border), one pathological ROI on diffuse blue light images (epithelial defect (ED)), and two non-pathological ROIs on all images (corneal limbus, light reflexes). To assess inter-reader variability, 75 eyes were manually annotated for pathological ROIs by a second physician, P2. Performance was evaluated using the Dice similarity coefficient (DSC) and Hausdorff distance (HD). Using seven-fold cross-validation, the DSC of the algorithm (as compared to P1) for all ROIs was good (range: 0.62-0.95) on all 133 eyes. For the subset of 75 eyes with manual annotations by P2, the DSC for pathological ROIs ranged from 0.69-0.85 (SLIT-Net) vs. 0.37-0.92 (P2). DSCs for SLIT-Net were not significantly different than P2 for segmenting hypopyons (p > 0.05) and higher than P2 for WBCs (p < 0.001) and edema (p < 0.001). DSCs were higher for P2 for segmenting SIs (p < 0.001) and EDs (p < 0.001). HDs were lower for P2 for segmenting SIs (p = 0.005) and EDs (p < 0.001) and not significantly different for hypopyons (p > 0.05), WBCs (p > 0.05), and edema (p > 0.05). This prototype fully-automatic algorithm to segment MK biomarkers on SLP images performed to expectations on an exploratory dataset and holds promise for quantification of corneal physiology and pathology.