Semantic segmentation is the task of classifying each pixel in an image. Training a segmentation model achieves best results using annotated images, where each pixel is annotated with the corresponding class. When obtaining fine annotations is difficult or expensive, it may be possible to acquire coarse annotations, e.g. by roughly annotating pixels in an images leaving some pixels around the boundaries between classes unlabeled. Segmentation with coarse annotations is difficult, in particular when the objective is to optimize the alignment of boundaries between classes. This paper proposes a regularization method for models with an encoder-decoder architecture with superpixel based upsampling. It encourages the segmented pixels in the decoded image to be SLIC-superpixels, which are based on pixel color and position, independent of the segmentation annotation. The method is applied to FCN-16 fully convolutional network architecture and evaluated on the SUIM, Cityscapes, and PanNuke data sets. It is shown that the boundary recall improves significantly compared to state-of-the-art models when trained on coarse annotations.