Gene Myers

Kira Vinogradova, Alexandr Dibrov, Gene Myers

Convolutional neural networks have become state-of-the-art in a wide range of image recognition tasks. The interpretation of their predictions, however, is an active area of research. Whereas various interpretation methods have been suggested for image classification, the interpretation of image segmentation still remains largely unexplored. To that end, we propose SEG-GRAD-CAM, a gradient-based method for interpreting semantic segmentation. Our method is an extension of the widely-used Grad-CAM method, applied locally to produce heatmaps showing the relevance of individual pixels for semantic segmentation.

Martin Weigert, Loic Royer, Florian Jug et al.

Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconvolution methods and other techniques to address this problem exist, they are either time consuming to apply or limited in their ability to remove anisotropy. We propose a method to recover isotropic resolution from readily acquired anisotropic data. We achieve this using a convolutional neural network that is trained end-to-end from the same anisotropic body of data we later apply the network to. The network effectively learns to restore the full isotropic resolution by restoring the image under a trained, sample specific image prior. We apply our method to $3$ synthetic and $3$ real datasets and show that our results improve on results from deconvolution and state-of-the-art super-resolution techniques. Finally, we demonstrate that a standard 3D segmentation pipeline performs on the output of our network with comparable accuracy as on the full isotropic data.

Dmitrij Schlesinger, Florian Jug, Gene Myers et al.

We propose a novel label fusion technique as well as a crowdsourcing protocol to efficiently obtain accurate epithelial cell segmentations from non-expert crowd workers. Our label fusion technique simultaneously estimates the true segmentation, the performance levels of individual crowd workers, and an image segmentation model in the form of a pairwise Markov random field. We term our approach image-aware STAPLE (iaSTAPLE) since our image segmentation model seamlessly integrates into the well-known and widely used STAPLE approach. In an evaluation on a light microscopy dataset containing more than 5000 membrane labeled epithelial cells of a fly wing, we show that iaSTAPLE outperforms STAPLE in terms of segmentation accuracy as well as in terms of the accuracy of estimated crowd worker performance levels, and is able to correctly segment 99% of all cells when compared to expert segmentations. These results show that iaSTAPLE is a highly useful tool for crowd sourcing image segmentation.