DR-MERGE: A Large-Scale Multi-Source Retinal Image Dataset for Diabetic Retinopathy via Systematic Integration and Deduplication
DOI:
https://doi.org/10.29284/mfph5424Keywords:
Diabetic Eye Problem, Medical Picture Collec- tion, Data Joining, Dataset Putting Together, MD5 Codes, Finding Same Pictures, Eye Imaging, Computer Help for Doctors, Deep Learning, Medical AIAbstract
Diabetes can hurt eyes badly, causing what we call diabetic retinopathy. This eye problem is a big reason people lose sight around the world. To make computer programs that help doctors find this eye problem, we need lots of eye pictures. Right now, available picture groups are often too small or not varied enough. This makes building good detection systems tough. Our work introduces DR-MERGE, a new large group of eye pictures we made by joining four public sets: Diabetic Retinopathy- Glaucoma-Mask, Diabetic Retinopathy Dataset, ODIR-5K, and STARE project. We made a careful way to put these together, fixing issues like different file types, finding same pictures using MD5 codes, and organizing everything well. Our method found and joined 17,976 different eye pictures from starting 18,104 pictures, taking out 128 copies that were exactly the same. DR- MERGE is now one of the biggest joined sets of eye pictures made just for diabetes eye problem research. We explain our full method, show numbers about the original sets and joined collection, and talk about how this can help move forward research in finding eye problems using computers. The picture set and our code are out there for others to check our work and keep studying medical pictures.
References
1. Whitmer, R. A., Karter, A. J., Yaffe, K., Quesenberry, C. P., & Selby,
2. J. V. (2009). Global prevalence of diabetes: estimates for the year 2000 and projections for 2030. Diabetes Care, 32(5), 1043-1045.
3. Saeedi, P., Petersohn, I., Salpea, P., Malanda, B., Karuranga, S., Unwin, N., ... & Williams, R. (2019). Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: Results from the International Diabetes Federation Diabetes Atlas. Diabetes Research and Clinical Practice, 157, 107843.
4. Yau, J. W., Rogers, S. L., Kawasaki, R., Lamoureux, E. L., Kowalski,
5. J. W., Bek, T., ... & Chen, S. J. (2012). Global prevalence and major risk factors of diabetic retinopathy. Diabetes Care, 35(3), 556-564.
6. Galanis, G., & Papakostas, G. A. (2021). Deep learning for diabetic retinopathy detection and classification based on fundus images: A review. Computers in Biology and Medicine, 135, 104599.
7. Ting, D. S. W., Pasquale, L. R., Peng, L., Campbell, J. P., Lee, A. Y., Raman, R., ... & Keane, P. A. (2018). Deep learning in ophthalmology: The technical and clinical considerations. Progress in Retinal and Eye Research, 72, 100759.
8. Voets, M., Møllersen, K., & Bongo, L. A. (2019). Replication study: Development and validation of deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs. PLoS One, 14(6), e0217541.
9. Kowalski, E. J., Liu, T. Y. A., & Lee, A. Y. (2021). Systematic review of publicly available datasets for diabetic retinopathy. Ophthalmology Science, 1(2), 100030.
10. Sun, C., Shrivastava, A., Singh, S., & Gupta, A. (2017). Revisiting unreasonable effectiveness of data in deep learning era. Proceedings of the IEEE International Conference on Computer Vision, 843-852.
11. Benjamens, S., Dhunnoo, P., & Mesko´, B. (2020). The state of artificial intelligence-based FDA-approved medical devices and algorithms: an online database. NPJ Digital Medicine, 3(1), 118.
12. Shamshad, F., Khan, S., Zamir, S. W., Khan, M. H., Hayat, M., Khan,S., & Fu, H. (2023). Transformers in medical imaging: A survey. Medical Image Analysis, 88, 102802.
13. Litjens, G., Kooi, T., Bejnordi, B. E., Setio, A. A. A., Ciompi, F., Ghafoorian, M., ... & Sa´nchez, C. I. (2017). A survey on deep learning in medical image analysis. Medical Image Analysis, 42, 60-88.
14. Wilkinson, C. P., Ferris, F. L., Klein, R. E., Lee, P. P., Agardh, C. D., Davis, M., ... & Gradings, D. (2003). Proposed international clinical diabetic retinopathy and diabetic macular edema disease severity scales. Ophthalmology, 110(9), 1677-1682.
15. Agarwal, A., Soliman, M. K., Sepah, Y. J., Do, D. V., & Nguyen, Q. D. (2021). Diabetic retinopathy: variations in patient therapeutic outcomes and pharmacogenomics. Pharmacogenomics and Personalized Medicine, 14, 1.
16. Klein, R., Klein, B. E., Moss, S. E., Davis, M. D., & DeMets, D. L. (1984). The Wisconsin epidemiologic study of diabetic retinopathy: II. Prevalence and risk of diabetic retinopathy when age at diagnosis is less than 30 years. Archives of Ophthalmology, 102(4), 520-526.
17. Nezhad, M. Z., Zhu, D., Li, X., Yang, K., & Levy, P. (2016). Context- aware diabetic retinopathy detection. Proceedings of the IEEE Interna- tional Conference on Bioinformatics and Biomedicine, 589-594.
18. Decencie`re, E., Zhang, X., Cazuguel, G., Lay, B., Cochener, B., Trone, C., ... & Gain, P. (2014). Feedback on a publicly distributed database: the Messidor database. Image Analysis & Stereology, 33(3), 231-234.
19. Cuadros, J., & Bresnick, G. (2021). EyePACS: An open-source platform for diabetic retinopathy screening and research. Journal of Diabetes Science and Technology, 15(1), 15-22.
20. Porwal, P., Pachade, S., Kamble, R., Kokare, M., Deshmukh, G., Sa- hasrabuddhe, V., ... & Meriaudeau, F. (2018). Indian diabetic retinopathy image dataset (IDRiD): a database for diabetic retinopathy screening research. Data, 3(3), 25.
21. Li, T., Gao, Y., Wang, K., Guo, S., Liu, H., & Kang, H. (2020). Re-
22. thinking diabetic retinopathy image analysis: challenges, opportunities, and prospects. IEEE Reviews in Biomedical Engineering, 14, 185-205.
23. Gan, Y., Wang, M., Chen, J., Huang, Z., Zhang, Y., Li, Q., ... & He,
24. X. (2019). Development and validation of a deep learning system for diabetic retinopathy and related eye diseases using retinal images from multiethnic populations with diabetes. JAMA, 322(11), 1049-1060.
25. Hoover, A. D., Kouznetsova, V., & Goldbaum, M. (2000). Locating blood vessels in retinal images by piecewise threshold probing of a matched filter response. IEEE Transactions on Medical Imaging, 19(3), 203-210.
26. Maier, A., Syben, C., Lasser, T., & Riess, C. (2019). A gentle intro- duction to deep learning in medical image processing. Zeitschrift fu¨r Medizinische Physik, 29(2), 86-101.
27. Rivest, R. (1992). The MD5 message-digest algorithm. RFC 1321.
28. Stevens, M., Sotirov, A., Appelbaum, J., Lenstra, A., Molnar, D., Osvik, A., & de Weger, B. (2012). Attack on MD5 collision resistance. Journal of Cryptology, 25(1), 1-27.
29. Zauner, C. (2010). Implementation and benchmarking of perceptual image hash functions. Master’s thesis, Upper Austria University of Applied Sciences.
30. Ghosh, S., Das, N., Das, I., & Maulik, U. (2019). Understanding deep learning techniques for image segmentation. ACM Computing Surveys, 52(4), 1-35.
31. Lee, C. S., Tyring, A. J., Deruyter, N. P., Wu, Y., Rokem, A., & Lee,Y. (2020). Deep-learning based, automated segmentation of macular edema in optical coherence tomography. Biomedical Optics Express, 8(7), 3440-3446.
32. Bogunovic´, H., Venhuizen, F., Klimscha, S., Apostolopoulos, S., Bab- Hadiashar, A., Bagci, U., ... & Sonka, M. (2019). RETOUCH: The retinal OCT fluid detection and segmentation benchmark and challenge. IEEE Transactions on Medical Imaging, 38(8), 1858-1874.
33. Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J. S., ... & Davatzikos, C. (2017). Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features. Scientific Data, 4(1), 1-13.
34. Dosovitskiy, A., Beyer, L., Kolesnikov, A., Weissenborn, D., Zhai, X., Unterthiner, T., ... & Houlsby, N. (2020). An image is worth 16x16 words: Transformers for image recognition at scale. arXiv preprint arXiv:2010.11929.
35. Salehi, M., Mirzaei, H., Hendrycks, D., Li, Y., Rohban, M. H., & Sabokrou, M. (2021). A unified survey on anomaly, novelty, open-set, and out-of-distribution detection: Solutions and future challenges. arXiv preprint arXiv:2110.14051.
36. Perez, L., & Wang, J. (2017). The effectiveness of data augmen- tation in image classification using deep learning. arXiv preprint arXiv:1712.04621.
37. Koh, P. W., Sagawa, S., Marklund, H., Xie, S. M., Zhang, M., Balsub- ramani, A., ... & Liang, P. (2020). WILDS: A benchmark of in-the-wild distribution shifts. Proceedings of the 37th International Conference on Machine Learning, 5637-5664.
38. Chen, I. Y., Pierson, E., Rose, S., Joshi, S., Ferryman, K., & Ghassemi, M. (2021). Ethical machine learning in healthcare. Annual Review of Biomedical Data Science, 4, 123-144.
39. Abramoff, M. D., Lavin, P. T., Birch, M., Shah, N., & Folk, J. C. (2016). Improved automated detection of diabetic retinopathy on a publicly available dataset through integration of deep learning. Investigative Ophthalmology & Visual Science, 57(13), 5200-5206.
40. Islam, M. M., Yang, H. C., Poly, T. N., Jian, W. S., & Li, Y. C. (2020).
41. Deep learning algorithms for detection of diabetic retinopathy in retinal fundus photographs: A systematic review and meta-analysis. Computer Methods and Programs in Biomedicine, 191, 105320.
42. Rajpurkar, P., Chen, E., Banerjee, O., & Topol, E. J. (2022). AI in health and medicine. Nature Medicine, 28(1), 31-38.
43. Azizi, S., Mustafa, B., Ryan, F., Beaver, Z., Freyberg, J., Deaton, J., ... & Norouzi, M. (2021). Robust and data-efficient generalization of self- supervised machine learning for diagnostic imaging. Nature Biomedical Engineering, 5(8), 836-849.
44. McDermott, M. B. A., Wang, S., Marinsek, N., Ranganath, R., Foschini, L., & Ghassemi, M. (2021). Reproducibility in machine learning for health research: Still a ways to go. Science Translational Medicine, 13(586), eabb1655.
45. Zhou, H. Y., Yu, S., Bian, C., Hu, Y., Ma, K., & Zheng, Y. (2021).
46. Comparing to learn: Surpassing ImageNet pretraining on radiographs by comparing image representations. Medical Image Computing and Computer Assisted Intervention, 12904, 398-407.
47. He, K., Fan, H., Wu, Y., Xie, S., & Girshick, R. (2020). Momentum contrast for unsupervised visual representation learning. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9729-9738.
Downloads
Published
Issue
Section
License

This work is licensed under a Creative Commons Attribution 4.0 International License.
This work is licensed under a Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

