Ink Marker Segmentation in Histopathology Images Using Deep Learning

TL;DR

This paper introduces a deep learning method to accurately segment ink-marked regions in histopathology images, improving the reliability of digital pathology analysis by removing confounding ink artifacts.

Contribution

The study presents a novel deep learning approach using an FPN with EfficientNet-B3 backbone for ink-marked region segmentation in histopathology images, with a new dataset of 4,305 patches.

Findings

F1 score of 94.53% achieved with the proposed model

Created a dataset of 4,305 patches from 79 whole slide images

EfficientNet-B3 backbone outperformed other configurations

Abstract

Due to the recent advancements in machine vision, digital pathology has gained significant attention. Histopathology images are distinctly rich in visual information. The tissue glass slide images are utilized for disease diagnosis. Researchers study many methods to process histopathology images and facilitate fast and reliable diagnosis; therefore, the availability of high-quality slides becomes paramount. The quality of the images can be negatively affected when the glass slides are ink-marked by pathologists to delineate regions of interest. As an example, in one of the largest public histopathology datasets, The Cancer Genome Atlas (TCGA), approximately $12\%$ of the digitized slides are affected by manual delineations through ink markings. To process these open-access slide images and other repositories for the design and validation of new methods, an algorithm to detect the marked regions of the images is essential to avoid confusing tissue pixels with ink-colored pixels for computer methods. In this study, we propose to segment the ink-marked areas of pathology patches through a deep network. A dataset from $79$ whole slide images with $4,305$ patches was created and different networks were trained. Finally, the results showed an FPN model with the EffiecentNet-B3 as the backbone was found to be the superior configuration with an F1 score of $94.53\%$.