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Joint Denoising and Super-Resolution for Fluorescence Microscopy Using Weakly-Supervised Deep Learning

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Medical Optical Imaging and Virtual Microscopy Image Analysis (MOVI 2022)

Abstract

Recent studies have shown that joint denoising and super-resolution (JDSR) approach is capable of producing high-quality medical images. The training process requires noise-free ground truth or multiple noisy captures. However, these extra training datasets are often unavailable in fluorescence microscopy. This paper presents a new weakly-supervised method, in which different from other approaches, the JDSR model is trained with a single noisy capture alone. We further introduce a novel training framework to approximate the supervised JDSR approach. In this paper, we present both theoretical explanation and experimental analysis for our method validation. The proposed method can achieve an approximation accuracy of \(98.11\%\) compared to the supervised approach. The source code is available at https://github.com/colinsctsang/weakly_supervised_JDSR.

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References

  1. Anwar, S., Barnes, N.: Real image denoising with feature attention. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 3155–3164 (2019)

    Google Scholar 

  2. Belthangady, C., Royer, L.A.: Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction. Nat. Methods 16(12), 1215–1225 (2019)

    Article  Google Scholar 

  3. Chakrova, N., Canton, A.S., Danelon, C., Stallinga, S., Rieger, B.: Adaptive illumination reduces photo-bleaching in structured illumination microscopy. Biomed. Opt. Express 7(10), 4263–4274 (2016)

    Article  Google Scholar 

  4. Choi, J.H., Zhang, H., Kim, J.H., Hsieh, C.J., Lee, J.S.: Evaluating robustness of deep image super-resolution against adversarial attacks. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 303–311 (2019)

    Google Scholar 

  5. El Helou, M., Süsstrunk, S.: Blind universal Bayesian image denoising with gaussian noise level learning. IEEE Trans. Image Process. 29, 4885–4897 (2020)

    Article  Google Scholar 

  6. Goncharova, A.S., Honigmann, A., Jug, F., Krull, A.: Improving blind spot denoising for microscopy. In: Bartoli, A., Fusiello, A. (eds.) ECCV 2020. LNCS, vol. 12535, pp. 380–393. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-66415-2_25

    Chapter  Google Scholar 

  7. Gustafsson, M.G.: Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy. J. Microsc. 198(2), 82–87 (2000)

    Article  Google Scholar 

  8. Huang, T., Li, S., Jia, X., Lu, H., Liu, J.: Neighbor2Neighbor: self-supervised denoising from single noisy images. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 14781–14790 (2021)

    Google Scholar 

  9. Khademi, W., Rao, S., Minnerath, C., Hagen, G., Ventura, J.: Self-supervised poisson-gaussian denoising. In: Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, pp. 2131–2139 (2021)

    Google Scholar 

  10. Krull, A., Buchholz, T., Jug, F.: Noise2Void: learning denoising from single noisy images. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 2129–2137 (2019)

    Google Scholar 

  11. Krull, A., Vičar, T., Prakash, M., Lalit, M., Jug, F.: Probabilistic Noise2Void: unsupervised content-aware denoising. Front. Comput. Sci. 2, 5 (2020)

    Article  Google Scholar 

  12. Lai, W.S., Huang, J.B., Ahuja, N., Yang, M.H.: Deep laplacian pyramid networks for fast and accurate super-resolution. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 624–632 (2017)

    Google Scholar 

  13. Laine, S., Karras, T., Lehtinen, J., Aila, T.: High-quality self-supervised deep image denoising. In: Advances in Neural Information Processing Systems, vol. 32 (2019)

    Google Scholar 

  14. Lehtinen, J., et al.: Noise2Noise: learning image restoration without clean data. In: International Conference on Machine Learning, pp. 2965–2974 (2018)

    Google Scholar 

  15. Li, Y., Sixou, B., Peyrin, F.: A review of the deep learning methods for medical images super resolution problems. IRBM 42, 120–133 (2021)

    Article  Google Scholar 

  16. Peng, C., Zhou, S.K., Chellappa, R.: DA-VSR: domain adaptable volumetric super-resolution for medical images. In: de Bruijne, M., et al. (eds.) MICCAI 2021. LNCS, vol. 12906, pp. 75–85. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87231-1_8

    Chapter  Google Scholar 

  17. Prakash, M., Lalit, M., Tomancak, P., Krul, A., Jug, F.: Fully unsupervised probabilistic Noise2Void. In: IEEE 17th International Symposium on Biomedical Imaging, pp. 154–158 (2020)

    Google Scholar 

  18. Qiu, B., et al.: N2NSR-OCT: Simultaneous denoising and super-resolution in optical coherence tomography images using semisupervised deep learning. J. Biophotonics 14(1), e202000282 (2021)

    Article  Google Scholar 

  19. Ronneberger, O., Fischer, P., Brox, T.: U-Net: convolutional networks for biomedical image segmentation. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9351, pp. 234–241. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24574-4_28

    Chapter  Google Scholar 

  20. Shocher, A., Cohen, N., Irani, M.: “zero-shot” super-resolution using deep internal learning. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 3118–3126 (2018)

    Google Scholar 

  21. Sui, Y., Afacan, O., Gholipour, A., Warfield, S.K.: MRI super-resolution through generative degradation learning. In: de Bruijne, M., et al. (eds.) MICCAI 2021. LNCS, vol. 12906, pp. 430–440. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87231-1_42

    Chapter  Google Scholar 

  22. Wang, Z., Bovik, A.C., Sheikh, H.R., Simoncelli, E.P.: Image quality assessment: from error visibility to structural similarity. IEEE Trans. Image Process. 14(4), 600–612 (2004)

    Article  Google Scholar 

  23. Wang, Z., Chen, J., Hoi, S.: Deep learning for image super-resolution: a survey. IEEE Trans. Pattern Anal. Mach. Intell. 43, 3365–3387 (2020)

    Article  Google Scholar 

  24. Weigert, M., et al.: Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat. Methods 15(12), 1090–1097 (2018)

    Article  Google Scholar 

  25. Wu, Q., et al.: IREM: high-resolution magnetic resonance image reconstruction via implicit neural representation. In: de Bruijne, M., et al. (eds.) MICCAI 2021. LNCS, vol. 12906, pp. 65–74. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87231-1_7

    Chapter  Google Scholar 

  26. Xing, W., Egiazarian, K.: End-to-end learning for joint image demosaicing, denoising and super-resolution. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 3507–3516 (2021)

    Google Scholar 

  27. Xu, J., Adalsteinsson, E.: Deformed2Self: self-supervised denoising for dynamic medical imaging. In: de Bruijne, M., et al. (eds.) MICCAI 2021. LNCS, vol. 12902, pp. 25–35. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-87196-3_3

    Chapter  Google Scholar 

  28. Zhang, K., Zuo, W., Chen, Y., Meng, D., Zhang, L.: Beyond a gaussian denoiser: residual learning of deep CNN for image denoising. IEEE Trans. Image Process. 26(7), 3142–3155 (2017)

    Article  MathSciNet  Google Scholar 

  29. Zhou, R., El Helou, M., Sage, D., Laroche, T., Seitz, A., Süsstrunk, S.: W2S: microscopy data with joint denoising and super-resolution for widefield to SIM mapping. In: Bartoli, A., Fusiello, A. (eds.) ECCV 2020. LNCS, vol. 12535, pp. 474–491. Springer, Cham (2020). https://doi.org/10.1007/978-3-030-66415-2_31

    Chapter  Google Scholar 

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Correspondence to Colin S. C. Tsang .

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Tsang, C.S.C., Mok, T.C.W., Chung, A.C.S. (2022). Joint Denoising and Super-Resolution for Fluorescence Microscopy Using Weakly-Supervised Deep Learning. In: Huo, Y., Millis, B.A., Zhou, Y., Wang, X., Harrison, A.P., Xu, Z. (eds) Medical Optical Imaging and Virtual Microscopy Image Analysis. MOVI 2022. Lecture Notes in Computer Science, vol 13578. Springer, Cham. https://doi.org/10.1007/978-3-031-16961-8_4

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  • DOI: https://doi.org/10.1007/978-3-031-16961-8_4

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