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Comparative Analysis of Data Augmentation for Retinal OCT Biomarker Segmentation

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Ophthalmic Medical Image Analysis (OMIA 2024)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 15188))

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Abstract

Data augmentation plays a crucial role in addressing the challenge of limited expert-annotated datasets in deep learning applications for retinal Optical Coherence Tomography (OCT) scans. This work exhaustively investigates the impact of various data augmentation techniques on retinal layer boundary and fluid segmentation. Our results reveal that their effectiveness significantly varies based on the dataset’s characteristics and the amount of available labeled data. While the benefits of augmentation are not uniform-being more pronounced in scenarios with scarce data, particularly for transformation-based methods-the findings highlight the necessity of a strategic approach to data augmentation. It is essential to note that the effectiveness of data augmentation varies significantly depending on the characteristics of the dataset. The findings emphasize the need for a nuanced approach, considering factors like dataset characteristics, the amount of labelled data, and the choice of model architecture.

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References

  1. Bar-David, D., Bar-David, L., Shoudry, S., Fischer, A.: Impact of data augmentation on retinal oct image segmentation for diabetic macular edema analysis. In: Ophthalmic Medical Image Analysis: 8th International Workshop, OMIA 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings 8. pp. 148–158. Springer (2021)

    Google Scholar 

  2. Bogunovic, H., Venhuizen, F., Klimscha, S., Apostolopoulos, S., Bab-Hadiashar, A., Bagci, U., Beg, M.F., Bekalo, L., Chen, Q., Ciller, C., Gopinath, K., Gostar, A.K., Jeon, K., Ji, Z., Kang, S.H., Koozekanani, D.D., Lu, D., Morley, D., Parhi, K.K., Park, H.S., Rashno, A., Sarunic, M., Shaikh, S., Sivaswamy, J., Tennakoon, R., Yadav, S., De Zanet, S., Waldstein, S.M., Gerendas, B.S., Klaver, C., Sánchez, C.I., Schmidt-Erfurth, U.: RETOUCH: The Retinal OCT Fluid Detection and Segmentation Benchmark and Challenge. IEEE Transactions on Medical Imaging 38(8), 1858–1874 (Aug 2019). 10.1109/TMI.2019.2901398

    Article  Google Scholar 

  3. Buslaev, A., Iglovikov, V.I., Khvedchenya, E., Parinov, A., Druzhinin, M., Kalinin, A.A.: Albumentations: fast and flexible image augmentations. Information 11(2),  125 (2020)

    Article  Google Scholar 

  4. Chlap, P., Min, H., Vandenberg, N., Dowling, J., Holloway, L., Haworth, A.: A review of medical image data augmentation techniques for deep learning applications. Journal of Medical Imaging and Radiation Oncology 65(5), 545–563 (2021)

    Article  Google Scholar 

  5. He, Y., Carass, A., Liu, Y., Calabresi, P.A., Saidha, S., Prince, J.L.: Longitudinal deep network for consistent oct layer segmentation. Biomedical Optics Express 14(5), 1874–1893 (2023)

    Article  Google Scholar 

  6. He, Y., Carass, A., Liu, Y., Jedynak, B.M., Solomon, S.D., Saidha, S., Calabresi, P.A., Prince, J.L.: Fully convolutional boundary regression for retina oct segmentation. In: Medical Image Computing and Computer Assisted Intervention–MICCAI 2019: 22nd International Conference, Shenzhen, China, October 13–17, 2019, Proceedings, Part I 22. pp. 120–128. Springer (2019)

    Google Scholar 

  7. He, Y., Carass, A., Liu, Y., Jedynak, B.M., Solomon, S.D., Saidha, S., Calabresi, P.A., Prince, J.L.: Structured layer surface segmentation for retina oct using fully convolutional regression networks. Medical image analysis 68, 101856 (2021)

    Article  Google Scholar 

  8. Johnson, D.H.: Signal-to-noise ratio. Scholarpedia 1(12),  2088 (2006)

    Google Scholar 

  9. Kepp, T., Ehrhardt, J., Heinrich, M.P., Hüttmann, G., Handels, H.: Topology-preserving shape-based regression of retinal layers in oct image data using convolutional neural networks. In: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019). pp. 1437–1440. IEEE (2019)

    Google Scholar 

  10. Koch, V., Holmberg, O., Spitzer, H., Schiefelbein, J., Asani, B., Hafner, M., Theis, F.J.: Noise transfer for unsupervised domain adaptation of retinal oct images. In: International Conference on Medical Image Computing and Computer-Assisted Intervention. pp. 699–708. Springer (2022)

    Google Scholar 

  11. Konidaris, F., Tagaris, T., Sdraka, M., Stafylopatis, A.: Generative adversarial networks as an advanced data augmentation technique for mri data. In: VISIGRAPP (5: VISAPP). pp. 48–59 (2019)

    Google Scholar 

  12. Lazaridis, G., Xu, M., Afgeh, S.S., Montesano, G., Garway-Heath, D.: Bio-inspired attentive segmentation of retinal oct imaging. In: Ophthalmic Medical Image Analysis: 7th International Workshop, OMIA 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 8, 2020, Proceedings 7. pp. 1–10. Springer (2020)

    Google Scholar 

  13. Li, D., Wu, J., He, Y., Yao, X., Yuan, W., Chen, D., Park, H.C., Yu, S., Prince, J.L., Li, X.: Parallel deep neural networks for endoscopic oct image segmentation. Biomedical optics express 10(3), 1126–1135 (2019)

    Article  Google Scholar 

  14. Li, Q., Li, S., He, Z., Guan, H., Chen, R., Xu, Y., Wang, T., Qi, S., Mei, J., Wang, W.: Deepretina: layer segmentation of retina in oct images using deep learning. Translational vision science & technology 9(2), 61–61 (2020)

    Article  Google Scholar 

  15. Ouyang, J., Mathai, T.S., Lathrop, K., Galeotti, J.: Accurate tissue interface segmentation via adversarial pre-segmentation of anterior segment oct images. Biomedical Optics Express 10(10), 5291–5324 (2019)

    Article  Google Scholar 

  16. Pekala, M., Joshi, N., Liu, T.A., Bressler, N.M., DeBuc, D.C., Burlina, P.: Deep learning based retinal oct segmentation. Computers in biology and medicine 114, 103445 (2019)

    Article  Google Scholar 

  17. Rebuffi, S.A., Gowal, S., Calian, D.A., Stimberg, F., Wiles, O., Mann, T.A.: Data augmentation can improve robustness. Advances in Neural Information Processing Systems 34, 29935–29948 (2021)

    Google Scholar 

  18. Ruan, Y., Xue, J., Li, T., Liu, D., Lu, H., Chen, M., Liu, T., Niu, S., Li, D.: Multi-phase level set algorithm based on fully convolutional networks (fcn-mls) for retinal layer segmentation in sd-oct images with central serous chorioretinopathy (csc). Biomedical optics express 10(8), 3987–4002 (2019)

    Article  Google Scholar 

  19. Shorten, C., Khoshgoftaar, T.M.: A survey on image data augmentation for deep learning. Journal of big data 6(1), 1–48 (2019)

    Article  Google Scholar 

  20. Stromer, D., Moult, E.M., Chen, S., Waheed, N.K., Maier, A., Fujimoto, J.G.: Correction propagation for user-assisted optical coherence tomography segmentation: general framework and application to bruch’s membrane segmentation. Biomedical Optics Express 11(5), 2830–2848 (2020)

    Article  Google Scholar 

  21. Xie, H., Xu, W., Wang, Y.X., Wu, X.: Deep learning network with differentiable dynamic programming for retina oct surface segmentation. Biomedical Optics Express 14(7), 3190–3202 (2023)

    Article  Google Scholar 

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Correspondence to Markus Unterdechler .

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Unterdechler, M., Fazekas, B., Aresta, G., Bogunović, H. (2025). Comparative Analysis of Data Augmentation for Retinal OCT Biomarker Segmentation. In: Bhavna, A., Chen, H., Fang, H., Fu, H., Lee, C.S. (eds) Ophthalmic Medical Image Analysis. OMIA 2024. Lecture Notes in Computer Science, vol 15188. Springer, Cham. https://doi.org/10.1007/978-3-031-73119-8_10

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  • DOI: https://doi.org/10.1007/978-3-031-73119-8_10

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  • Online ISBN: 978-3-031-73119-8

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