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Instance Segmentation Model Created from Three Semantic Segmentations of Mask, Boundary and Centroid Pixels Verified on GlaS Dataset

Wybrane pełne teksty z tego czasopisma
Identyfikatory
Warianty tytułu
Konferencja
Federated Conference on Computer Science and Information Systems (15 ; 06-09.09.2020 ; Sofia, Bulgaria)
Języki publikacji
EN
Abstrakty
EN
Segmentation is the key computer vision task in modern medicine applications. Instance segmentation became the prevalent way to improve segmentation performance in recent years. This work proposes a novel way to design an instance segmentation model that combines 3 semantic segmentation models dedicated for foreground, boundary and centroid predictions. It contains no detector so it is orthogonal to a standard instance segmentation design and can be used to improve the performance of a standard design. The presented custom designed model is verified on the Gland Segmentation in Colon Histology Images dataset.
Rocznik
Tom
Strony
569--576
Opis fizyczny
Bibliogr. 27 poz., tab., wykr., il.
Twórcy
autor
  • Institute of Informatics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 07 Bratislava, Slovakia
  • Institute of Informatics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 07 Bratislava, Slovakia
  • Faculty of Informatics and Information Technologies, Slovak University of Technology, Ilkovičova 2, 842 16 Bratislava, Slovakia
Bibliografia
  • 1. T. Adams, J. Dörpinghaus, M. Jacobs, and V. Steinhage, “Automated lung tumor detection and diagnosis in ct scans using texture feature analysis and svm,” in Communication Papers of the 2018 Federated Conference on Computer Science and Information Systems, ser. Annals of Computer Science and Information Systems, M. Ganzha, L. Maciaszek, and M. Paprzycki, Eds., vol. 17. PTI, 2018, pp. 13–20. [Online]. Available: http://dx.doi.org/10.15439/2018F176
  • 2. M. Li, Q. Yin, and M. Lu, “Retinal blood vessel segmentation based on multi-scale deep learning,” in Proceedings of the 2018 Federated Conference on Computer Science and Information Systems, ser. Annals of Computer Science and Information Systems, M. Ganzha, L. Maciaszek, and M. Paprzycki, Eds., vol. 15. IEEE, 2018, pp. 117–123. [Online]. Available: http://dx.doi.org/10.15439/2018F127
  • 3. K. Simonyan and A. Zisserman, “Very deep convolutional networks for large-scale image recognition,” in 3rd International Conference on Learning Representations, ICLR 2015, San Diego, CA, USA, May 7–9, 2015, Conference Track Proceedings, Y. Bengio and Y. LeCun, Eds., 2015. [Online]. Available: http://arxiv.org/abs/1409.1556
  • 4. C. Szegedy, W. Liu, Y. Jia, P. Sermanet, S. E. Reed, D. Anguelov, D. Erhan, V. Vanhoucke, and A. Rabinovich, “Going deeper with convolutions,” in IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2015, Boston, MA, USA, June 7–12, 2015. IEEE Computer Society, 2015, pp. 1–9. [Online]. Available: https://doi.org/10.1109/CVPR.2015.7298594
  • 5. J. Kang and J. Gwak, “Ensemble of instance segmentation models for polyp segmentation in colonoscopy images,” IEEE Access, vol. 7, pp. 26 440–26 447, 2019. [Online]. Available: http://dx.doi.org/10.1109/ACCESS.2019.2900672
  • 6. A. O. Vuola, S. U. Akram, and J. Kannala, “Mask-rcnn and u-net ensembled for nuclei segmentation,” in 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Venice, Italy, April 2019, pp. 208–212. [Online]. Available: http://dx.doi.org/10.1109/ISBI.2019.8759574
  • 7. L. Podlodowski, S. Roziewski, and M. Nurzyński, “An ensemble of deep convolutional neural networks for marking hair follicles on microscopic images,” in Position Papers of the 2018 Federated Conference on Computer Science and Information Systems, ser. Annals of Computer Science and Information Systems, M. Ganzha, L. Maciaszek, and M. Paprzycki, Eds., vol. 16. PTI, 2018, pp. 23–28. [Online]. Available: http://dx.doi.org/10.15439/2018F389
  • 8. B. D. Brabandere, D. Neven, and L. V. Gool, “Semantic instance segmentation with a discriminative loss function,” CoRR, vol. abs/1708.02551, 2017. [Online]. Available: http://arxiv.org/abs/1708.02551
  • 9. J. Dai, K. He, Y. Li, S. Ren, and J. Sun, “Instance-sensitive fully convolutional networks,” in Computer Vision – ECCV 2016, B. Leibe, J. Matas, N. Sebe, and M. Welling, Eds. Cham: Springer International Publishing, 2016, pp. 534–549. [Online]. Available: http://dx.doi.org/10.1007/978-3-319-46466-4_32
  • 10. F. A. Guerrero-Peña, P. D. Marrero Fernandez, T. Ing Ren, M. Yui, E. Rothenberg, and A. Cunha, “Multiclass weighted loss for instance segmentation of cluttered cells,” in 2018 25th IEEE International Conference on Image Processing (ICIP), Athens, October 2018, pp. 2451–2455. [Online]. Available: http://dx.doi.org/10.1109/ICIP.2018.8451187
  • 11. L. Chen, G. Papandreou, I. Kokkinos, K. Murphy, and A. L. Yuille, “Deeplab: Semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 4, pp. 834–848, April 2018. [Online]. Available: http://dx.doi.org/10.1109/TPAMI.2017.2699184
  • 12. S. Liu, L. Qi, H. Qin, J. Shi, and J. Jia, “Path aggregation network for instance segmentation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, June 2018, pp. 8759–8768. [Online]. Available: http://dx.doi.org/10.1109/CVPR.2018.00913
  • 13. J. Respondek and W. Westwańska, “Counting instances of objects specified by vague locations using neural networks on example of honey bees,” in Proceedings of the 2019 Federated Conference on Computer Science and Information Systems, ser. Annals of Computer Science and Information Systems, M. Ganzha, L. Maciaszek, and M. Paprzycki, Eds., vol. 18. IEEE, 2019, pp. 87–90. [Online]. Available: http://dx.doi.org/10.15439/2019F94
  • 14. K. He, G. Gkioxari, P. Dollár, and R. Girshick, “Mask r-cnn,” in 2017 IEEE International Conference on Computer Vision (ICCV), Oct 2017, pp. 2980–2988. [Online]. Available: http://dx.doi.org/10.1109/ICCV.2017.322
  • 15. Y. Xu, Y. Li, Y. Wang, M. Liu, Y. Fan, M. Lai, and E. I. Chang, “Gland instance segmentation using deep multichannel neural networks,” IEEE Transactions on Biomedical Engineering, vol. 64, no. 12, pp. 2901–2912, December 2017. [Online]. Available: http://dx.doi.org/10.1109/TBME.2017.2686418
  • 16. A. Böhm, A. Ücker, T. Jäger, O. Ronneberger, and T. Falk, “Isoodl: Instance segmentation of overlapping biological objects using deep learning,” in 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Washington, DC, April 2018, pp. 1225–1229. [Online]. Available: http://dx.doi.org/10.1109/ISBI.2018.8363792
  • 17. K. Sirinukunwattana, J. P. Pluim, H. Chen, X. Qi, P.-A. Heng, Y. B. Guo, L. Y. Wang, B. J. Matuszewski, E. Bruni, U. Sanchez, A. Böhm, O. Ronneberger, B. B. Cheikh, D. Racoceanu, P. Kainz, M. Pfeiffer, M. Urschler, D. R. Snead, and N. M. Rajpoot, “Gland segmentation in colon histology images: The glas challenge contest,” Medical Image Analysis, vol. 35, pp. 489 – 502, January 2017. [Online]. Available: http://www.sciencedirect.com/science/article/pii/S1361841516301542
  • 18. O. Ronneberger, P. Fischer, and T. Brox, “U-net: Convolutional networks for biomedical image segmentation,” in Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015, N. Navab, J. Hornegger, W. M. Wells, and A. F. Frangi, Eds. Cham: Springer International Publishing, 2015, pp. 234–241. [Online]. Available: http://dx.doi.org/10.1007/978-3-319-24574-4_28
  • 19. K. He, X. Zhang, S. Ren, and J. Sun, “Deep residual learning for image recognition,” in 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Las Vegas, NV, June 2016, pp. 770–778. [Online]. Available: http://dx.doi.org/10.1109/CVPR.2016.90
  • 20. F. Chollet, “Xception: Deep learning with depthwise separable convolutions,” in 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Honolulu, HI, July 2017, pp. 1800–1807. [Online]. Available: http://dx.doi.org/10.1109/CVPR.2017.195
  • 21. S. Manivannan, W. Li, J. Zhang, E. Trucco, and S. J. McKenna, “Structure prediction for gland segmentation with hand-crafted and deep convolutional features,” IEEE Transactions on Medical Imaging, vol. 37, no. 1, pp. 210–221, January 2018. [Online]. Available: http://dx.doi.org/10.1109/TMI.2017.2750210
  • 22. J. Yi, P. Wu, D. J. Hoeppner, and D. Metaxas, “Pixel-wise neural cell instance segmentation,” in 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Washington, DC, April 2018, pp. 373–377. [Online]. Available: http://dx.doi.org/10.1109/ISBI.2018.8363596
  • 23. S. Graham and N. M. Rajpoot, “Sams-net: Stain-aware multi-scale network for instance-based nuclei segmentation in histology images,” in 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Washington, DC, April 2018, pp. 590–594. [Online]. Available: http://dx.doi.org/10.1109/ISBI.2018.8363645
  • 24. G. Payyavula, “Nuclei segmentation in microscope cell images,” 2018. [Online]. Available: https://www.kaggle.com/gangadhar/nuclei-segmentation-in-microscope-cell-images/
  • 25. S. Graham, H. Chen, Q. Dou, P.-A. Heng, and N. M. Rajpoot, “Mild-net: Minimal information loss dilated network for gland instance segmentation in colon histology images,” Medical Image Analysis, vol. 52, pp. 199–211, 2019. [Online]. Available: http://dx.doi.org/10.1016/j.media.2018.12.001
  • 26. A. Khvostikov, A. Krylov, I. Mikhailov, O. Kharlova, N. Oleynikova, and P. Malkov, “Automatic mucous glands segmentation in histological images,” ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, vol. XLII-2/W12, pp. 103–109, 2019. [Online]. Available: https://www.int-arch-photogramm-remote-sens-spatial-inf-sci.net/XLII-2-W12/103/2019/
  • 27. N. Oleynikova, A. Khvostikov, A. Krylov, I. Mikhailov, O. Kharlova, N. Danilova, P. G. Mal’kov, N. Ageykina, and E. Fedorov, “Automatic glands segmentation in histological images obtained by endoscopic biopsy from various parts of the colon,” Endoscopy, vol. 51, 04 2019. [Online]. Available: http://dx.doi.org/10.1055/s-0039-1681188
Uwagi
1. Track 4: Information Systems and Technology
2. Technical Session: 2nd Special Session on Data Science in Health, Ecology and Commerce
3. Opracowanie rekordu ze środków MNiSW, umowa Nr 461252 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2021).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-15afcc7c-3d28-4314-ad67-cd150622c748
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