ABSTRACT
Background: Accurate identification of inflammatory cells from mucosal histopathology images is important in diagnosing ulcerative colitis. The identification of eosinophils in the colonic mucosa has been associated with disease course. Cell counting is not only time-consuming but can also be subjective to human biases. In this study we developed an automatic eosinophilic cell counting tool from mucosal histopathology images, using deep learning. Method: Four pediatric IBD pathologists from two North American pediatric hospitals annotated 530 crops from 143 standard-of-care hematoxylin and eosin (H & E) rectal mucosal biopsies. A 305/75 split was used for training/validation to develop and optimize a U-Net based deep learning model, and 150 crops were used as a test set. The U-Net model was then compared to SAU-Net, a state-of-the-art U-Net variant. We undertook post-processing steps, namely, (1) the pixel-level probability threshold, (2) the minimum number of clustered pixels to designate a cell, and (3) the connectivity. Experiments were run to optimize model parameters using AUROC and cross-entropy loss as the performance metrics. Results: The F1-score was 0.86 (95%CI:0.79-0.91) (Precision: 0.77 (95%CI:0.70-0.83), Recall: 0.96 (95%CI:0.93-0.99)) to identify eosinophils as compared to an F1-score of 0.2 (95%CI:0.13-0.26) for SAU-Net (Precision: 0.38 (95%CI:0.31-0.46), Recall: 0.13 (95%CI:0.08-0.19)). The inter-rater reliability was 0.96 (95%CI:0.93-0.97). The correlation between two pathologists and the algorithm was 0.89 (95%CI:0.82-0.94) and 0.88 (95%CI:0.80-0.94) respectively. Conclusion: Our results indicate that deep learning-based automated eosinophilic cell counting can obtain a robust level of accuracy with a high degree of concordance with manual expert annotations.
Subject(s)
Colitis, Ulcerative , Machine Learning , Humans , Colitis, Ulcerative/therapy , Colitis, Ulcerative/diagnosis , Colitis, Ulcerative/pathology , Colitis, Ulcerative/drug therapy , Child , Male , Adolescent , Female , Treatment Outcome , Predictive Value of Tests , Biopsy , Colon/pathology , Colon/diagnostic imaging , Gastrointestinal Agents/therapeutic use , Colonoscopy , Remission InductionABSTRACT
IMPACT: Provide an overview of bronchopulmonary dysplasia, its definitions, and their shortcomings. Explore the areas where machine learning may be used to further our understanding of bronchopulmonary dysplasia.
Subject(s)
Bronchopulmonary Dysplasia , Infant, Newborn , Humans , Artificial IntelligenceABSTRACT
Background. The aim of this work is to present an automatic colorectal polyp detection scheme for capsule endoscopy. Methods. PillCam COLON2 capsule-based images and videos were used in our study. The database consists of full exam videos from five patients. The algorithm is based on the assumption that the polyps show up as a protrusion in the captured images and is expressed by means of a P-value, defined by geometrical features. Results. Seventeen PillCam COLON2 capsule videos are included, containing frames with polyps, flat lesions, diverticula, bubbles, and trash liquids. Polyps larger than 1 cm express a P-value higher than 2000, and 80% of the polyps show a P-value higher than 500. Diverticula, bubbles, trash liquids, and flat lesions were correctly interpreted by the algorithm as nonprotruding images. Conclusions. These preliminary results suggest that the proposed geometry-based polyp detection scheme works well, not only by allowing the detection of polyps but also by differentiating them from nonprotruding images found in the films.
