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Self-supervised Denoising via Diffeomorphic Template Estimation: Application to Optical Coherence Tomography

Part of the Lecture Notes in Computer Science book series (LNIP,volume 12069)

Abstract

Optical Coherence Tomography (OCT) is pervasive in both the research and clinical practice of Ophthalmology. However, OCT images are strongly corrupted by noise, limiting their interpretation. Current OCT denoisers leverage assumptions on noise distributions or generate targets for training deep supervised denoisers via averaging of repeat acquisitions. However, recent self-supervised advances allow the training of deep denoising networks using only repeat acquisitions without clean targets as ground truth, reducing the burden of supervised learning. Despite the clear advantages of self-supervised methods, their use is precluded as OCT shows strong structural deformations even between sequential scans of the same subject due to involuntary eye motion. Further, direct nonlinear alignment of repeats induces correlation of the noise between images. In this paper, we propose a joint diffeomorphic template estimation and denoising framework which enables the use of self-supervised denoising for motion deformed repeat acquisitions, without empirically registering their noise realizations. Strong qualitative and quantitative improvements are achieved in denoising OCT images, with generic utility in any imaging modality amenable to multiple exposures.

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Notes

  1. 1.

    http://www.cs.tut.fi/~foi/GCF-BM3D/.

  2. 2.

    http://stnava.github.io/ANTs/.

  3. 3.

    https://github.com/NVlabs/noise2noise.

  4. 4.

    For [18], Algorithm 1 in the paper suggests that lower is better. However, their code negates the final correlation value, thus making higher better. We do the same to maintain consistency with their convention.

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Acknowledgments

This work was supported by NIH grants 1R01EY027948-01 and 2R01EY013178-15. HPC resources used for this research provided by grant NSF MRI-1229185.

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Correspondence to Neel Dey .

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Gisbert, G., Dey, N., Ishikawa, H., Schuman, J., Fishbaugh, J., Gerig, G. (2020). Self-supervised Denoising via Diffeomorphic Template Estimation: Application to Optical Coherence Tomography. In: Fu, H., Garvin, M.K., MacGillivray, T., Xu, Y., Zheng, Y. (eds) Ophthalmic Medical Image Analysis. OMIA 2020. Lecture Notes in Computer Science(), vol 12069. Springer, Cham. https://doi.org/10.1007/978-3-030-63419-3_8

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  • DOI: https://doi.org/10.1007/978-3-030-63419-3_8

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