Introducing Hann windows for reducing edge-effects in patch-based image segmentation

There is a limitation in the size of an image that can be processed using computationally demanding methods such as e.g. Convolutional Neural Networks (CNNs). Furthermore, many networks are designed to work with a pre-determined fixed image size. Some imaging modalities-notably biological and medical-can result in images up to a few gigapixels in size, meaning that they have to be divided into smaller parts, or patches, for processing. However, when performing pixel classification, this may lead to undesirable artefacts, such as edge effects in the final re-combined image. We introduce windowing methods from signal processing to effectively reduce such edge effects. With the assumption that the central part of an image patch often holds richer contextual information than its sides and corners, we reconstruct the prediction by overlapping patches that are being weighted depending on 2-dimensional windows. We compare the results of simple averaging and four different windows: Hann, Bartlett-Hann, Triangular and a recently proposed window by Cui et al., and show that the cosine-based Hann window achieves the best improvement as measured by the Structural Similarity Index (SSIM). We also apply the Dice score to show that classification errors close to patch edges are reduced. The proposed windowing method can be used together with any CNN model for segmentation without any modification and significantly improves network predictions.