Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images

Z.H. Shah, M. Müller, T.-C. Wang, P.M. Scheidig, A. Schneider, M. Schüttpelz, T. Huser, W. Schenck, BioRxiv (2020).

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Preprint | Veröffentlicht | Englisch
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Shah, Zafran HussainFH Bielefeld; Müller, Marcel; Wang, Tung-Cheng; Scheidig, Philip Maurice; Schneider, AxelFH Bielefeld ; Schüttpelz, Mark; Huser, Thomas; Schenck, WolframFH Bielefeld
Abstract
Abstract - Super-resolution structured illumination microscopy (SR-SIM) provides an up to two-fold enhanced spatial resolution of fluorescently labeled samples. The reconstruction of high quality SR-SIM images critically depends on patterned illumination with high modulation contrast. Noisy raw image data, e.g. as a result of low excitation power or low exposure times, result in reconstruction artifacts. Here, we demonstrate deep-learning based SR-SIM image denoising that results in high quality reconstructed images. A residual encoding-decoding convolution neural network (RED-Net) was used to successfully denoise computationally reconstructed noisy SR-SIM images. We also demonstrate the entirely deep-learning based denoising and reconstruction of raw SIM images into high-resolution SR-SIM images. Both image reconstruction methods prove to be very robust against image reconstruction artifacts and generalize very well over various noise levels. The combination of computational reconstruction and subsequent denoising via RED-Net shows very robust performance during inference after training even if the microscope settings change.
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bioRxiv
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Shah, Zafran Hussain ; Müller, Marcel ; Wang, Tung-Cheng ; Scheidig, Philip Maurice ; Schneider, Axel ; Schüttpelz, Mark ; Huser, Thomas ; Schenck, Wolfram: Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images. In: bioRxiv, Cold Spring Harbor Laboratory (2020)
Shah ZH, Müller M, Wang T-C, et al. Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images. bioRxiv. 2020.
Shah, Z. H., Müller, M., Wang, T.-C., Scheidig, P. M., Schneider, A., Schüttpelz, M., … Schenck, W. (2020). Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images. BioRxiv. Cold Spring Harbor Laboratory.
@article{Shah_Müller_Wang_Scheidig_Schneider_Schüttpelz_Huser_Schenck_2020, title={Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images}, journal={bioRxiv}, publisher={Cold Spring Harbor Laboratory}, author={Shah, Zafran Hussain and Müller, Marcel and Wang, Tung-Cheng and Scheidig, Philip Maurice and Schneider, Axel and Schüttpelz, Mark and Huser, Thomas and Schenck, Wolfram}, year={2020} }
Shah, Zafran Hussain, Marcel Müller, Tung-Cheng Wang, Philip Maurice Scheidig, Axel Schneider, Mark Schüttpelz, Thomas Huser, and Wolfram Schenck. “Deep-Learning Based Denoising and Reconstruction of Super-Resolution Structured Illumination Microscopy Images.” BioRxiv. Cold Spring Harbor Laboratory, 2020.
Z. H. Shah et al., “Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
Shah, Zafran Hussain, et al. “Deep-Learning Based Denoising and Reconstruction of Super-Resolution Structured Illumination Microscopy Images.” BioRxiv, Cold Spring Harbor Laboratory, 2020.

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