Robust Slide Cartography in Colon Cancer Histology - Evaluation on a Multi-scanner Database

Petr Kuritcyn, Carol I. Geppert, Markus Eckstein, Arndt Hartmann, Thomas Wittenberg, Jakob Dexl, Serop Baghdadlian, David Hartmann, Dominik Perrin, Volker Bruns, Michaela Benz

Abstract: Robustness against variations in color and resolution of digitized whole-slide images (WSIs) is an essential requirement for any computer-aided analysis in digital pathology. One common approach to encounter a lack of heterogeneity in the training data is data augmentation. We investigate the impact of different augmentation techniques for whole-slide cartography in colon cancer histology using a newly created multi-scanner database of 39 slides each digitized with six different scanners. A state of the art convolutional neural network (CNN) is trained to differentiate seven tissue classes. Applying a model trained on one scanner to WSIs acquired with a different scanner results in a significant decrease in classification accuracy. Our results show that the impact of resolution variations is less than of color variations: the accuracy of the baseline model trained without any augmentation at all is 73% for WSIs with similar color but different resolution against 35% for WSIs with similar resolution but color deviations. The grayscale model shows comparatively robust results and evades the problem of color variation. A combination of multiple color augmentations methods lead to a significant overall improvement (between 33 and 54 percentage points). Moreover, fine-tuning a pre-trained network using a small amount of annotated data from new scanners benefits the performance for these particular scanners, but this effect does not generalize to other unseen scanners.