Title: Tissue Artifact Segmentation and Severity Analysis for Automated Diagnosis Using Whole Slide Images

Abstract: Traditionally, pathological analysis and diagnosis are performed by manually eyeballing glass slide specimens under a microscope by an expert. The whole slide image is the digital specimen produced from the glass slide. Whole slide image enabled specimens to be observed on a computer screen and led to computational pathology where computer vision and artificial intelligence are utilized for automated analysis and diagnosis. With the current computational advancement, the entire whole slide image can be analyzed autonomously without human supervision. However, the analysis could fail or lead to wrong diagnosis if the whole slide image is affected by tissue artifacts such as tissue fold or air bubbles depending on the severity. Existing artifact detection methods rely on experts for severity assessment to eliminate artifact affected regions from the analysis. This process is time consuming, exhausting and undermines the goal of automated analysis or removal of artifacts without evaluating their severity, which could result in the loss of diagnostically important data. Therefore, it is necessary to detect artifacts and then assess their severity automatically. In this paper, we propose a system that incorporates severity evaluation with artifact detection utilizing convolutional neural networks. The proposed system uses DoubleUNet to segment artifacts and an ensemble network of six fine tuned convolutional neural network models to determine severity. This method outperformed current state of the art in accuracy by 9 percent for artifact segmentation and achieved a strong correlation of 97 percent with the evaluation of pathologists for severity assessment. The robustness of the system was demonstrated using our proposed heterogeneous dataset and practical usability was ensured by integrating it with an automated analysis system.