Data augmentation based on spatial deformations for histopathology: An evaluation in the context of glomeruli segmentation.

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Abstract

The effective application of deep learning to digital histopathology is hampered by the shortage of high-quality annotated images. In this paper we focus on the supervised segmentation of glomerular structures in patches of whole slide images of renal histopathological slides. Considering a U-Net model employed for segmentation, our goal is to evaluate the impact of augmenting training data with random spatial deformations.The effective application of deep learning to digital histopathology is hampered by the shortage of high-quality annotated images. In this paper we focus on the supervised segmentation of glomerular structures in patches of whole slide images of renal histopathological slides. Considering a U-Net model employed for segmentation, our goal is to evaluate the impact of augmenting training data with random spatial deformations.We show that augmenting training data with spatially deformed images yields an improvement of up to 0.23 in average Dice score, with respect to training with no augmentation. We demonstrate that deformations with relatively strong distortions yield the best performance increase, while previous work only report the use of deformations with low distortions. The selected deformation models yield similar performance increase, provided that their parameters are properly adjusted. We provide bounds on the optimal parameter values, obtained through parameter sampling, which is achieved in a lower computational complexity with our single-parameter method. The paper is accompanied by a framework for evaluating the impact of random spatial deformations on the performance of any U-Net segmentation model.To our knowledge, this study is the first to evaluate the impact of random spatial deformations on the segmentation of histopathological images. Our study and framework provide tools to help practitioners and researchers to make a better usage of random spatial deformations when training deep models for segmentation.Copyright © 2022 Elsevier B.V. All rights reserved.