Advances in deep learning have led to remarkable success in augmented microscopy, enabling us to obtain high-quality microscope images without using expensive microscopy hardware and sample preparation techniques. Current deep learning models for augmented microscopy are mostly U-Net-based neural networks, thus sharing certain drawbacks that limit the performance. In particular, U-Nets are composed of local operators only and lack dynamic non-local information aggregation. In this work, we introduce global voxel transformer networks (GVTNets), a deep learning tool for augmented microscopy that overcomes intrinsic limitations of the current U-Net-based models and achieves improved performance. GVTNets are built on global voxel transformer operators, which are able to aggregate global information, as opposed to local operators like convolutions. We apply the proposed methods on existing datasets for three different augmented microscopy tasks under various settings.
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We thank the teams at CARE and the Allen Institute for Cell Science for making their data and tools publicly available. This work was supported in part by National Science Foundation grants DBI-1922969, IIS-1908166 and IIS-1908220, National Institutes of Health grant 1R21NS102828 and Defense Advanced Research Projects Agency grant N66001-17-2-4031.
The authors declare no competing interests.
Peer review information Nature Machine Intelligence thanks Ruogu Fang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Wang, Z., Xie, Y. & Ji, S. Global voxel transformer networks for augmented microscopy. Nat Mach Intell 3, 161–171 (2021). https://doi.org/10.1038/s42256-020-00283-x