Araştırma Makalesi
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Automatic Cell Nucleus Segmentation Using Superpixels and Clustering Methods in Histopathological Images

Yıl 2021, Cilt: 9 Sayı: 3, 304 - 309, 30.07.2021
https://doi.org/10.17694/bajece.864266

Öz

It is seen that there is an increase in cancer and cancer-related deaths day by day. Early diagnosis is vital for the early treatment of the cancerous area. Computer-aided programs allow for early diagnosis of unhealthy cells that specialist pathologists diagnose as a result of efforts. In this study, kMeans and Fuzzy C Means methods, which are among the global segmentation methods, and SLIC, Quickshift, Felzenszwalb, Watershed and ERS algorithms, which are among the superpixel segmentation methods, were used for automatic cell nucleus detection in high resolution histopathological images with computer aided programs. As a result of the study, the success performances of the segmentation algorithms were analyzed and evaluated. It is seen that better success is obtained in watershed and FCM algorithms in high resolution histopathological images used. Quickshift and SLIC methods gave better results in terms of precision. It is seen that there are k-Means and FCM algorithms that provide the best performance in F measure (F-M) and the true negative rate (TNR) is more successful in Quickshift, k-Means and SLIC methods.

Kaynakça

  • Anonim,2017. Erken Teşhis Hayat Kurtarır [Online] https://www.saglik.gov.tr/Eklenti/8635,kanser-istatistikleridocx.docx?0
  • Albayrak, A., & Bilgin, G. (2017, May). Superpixel approach in high resolution histopathological image segmentation. In 2017 25th Signal Processing and Communications Applications Conference (SIU) (pp. 1-4). IEEE.
  • Xu, J., Xiang, L., Liu, Q., Gilmore, H., Wu, J., Tang, J., & Madabhushi, A. (2015). Stacked sparse autoencoder (SSAE) for nuclei detection on breast cancer histopathology images. IEEE transactions on medical imaging, 35(1), 119-130.
  • Aksebzeci, B. H., & Kayaalti, Ö. (2017, October). Computer-aided classification of breast cancer histopathological images. In 2017 Medical Technologies National Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Albayrak, A., & Bilgin, G. (2018, November). Segmentation of cellular structures with encoder-decoder based deep learning algorithm in histopathological images. In 2018 Medical Technologies National Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Albayrak, A., Ünlü, A., Çalık, N., Bilgin, G., Türkmen, İ., Çakır, A., ... & Ata, L. D. (2017, May). Segmentation of precursor lesions in cervical cancer using convolutional neural networks. In 2017 25th Signal Processing and Communications Applications Conference (SIU) (pp. 1-4). IEEE.
  • Turan, S., & Bilgin, G. (2019, April). Semantic nuclei segmentation with deep learning on breast pathology images. In 2019 Scientific Meeting on Electrical-Electronics & Biomedical Engineering and Computer Science (EBBT) (pp. 1-4). IEEE.
  • Li, B., Niessen, W. J., Klein, S., de Groot, M., Ikram, M. A., Vernooij, M. W., & Bron, E. E. (2019, October). A hybrid deep learning framework for integrated segmentation and registration: Evaluation on longitudinal white matter tract changes. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 645-653). Springer, Cham.
  • Ronneberger, O., Fischer, P., & Brox, T. (2015, October). U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention (pp. 234-241). Springer, Cham.
  • Bagdigen, M. E., & Bilgin, G. (2019, October). Detection and Grading of Breast Cancer via Spatial Features in Histopathological Images. In 2019 Medical Technologies Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Feng-Ping, A., & Zhi-Wen, L. (2019). Medical image segmentation algorithm based on feedback mechanism convolutional neural network. Biomedical Signal Processing and Control, 53, 101589.
  • Xia, K., Yin, H., Qian, P., Jiang, Y., & Wang, S. (2019). Liver semantic segmentation algorithm based on improved deep adversarial networks in combination of weighted loss function on abdominal CT images. IEEE Access, 7, 96349-96358.
  • Feng, Y., Zhao, H., Li, X., Zhang, X., & Li, H. (2017). A multi-scale 3D Otsu thresholding algorithm for medical image segmentation. Digital Signal Processing, 60, 186-199
  • Farag, T. H., Hassan, W. A., Ayad, H. A., AlBahussain, A. S., Badawi, U. A., & Alsmadi, M. K. (2017). Extended absolute fuzzy connectedness segmentation algorithm utilizing region and boundary-based information. Arabian Journal for Science and Engineering, 42(8), 3573-3583.
  • Salazar-Reque, I. F., Huamán, S. G., Kemper, G., Telles, J., & Diaz, D. (2019). An algorithm for plant disease visual symptom detection in digital images based on superpixels. Int. J. Adv. Sci. Eng. Inf. Technol, 9(1), 194-203.
  • Qin, W., Wu, J., Han, F., Yuan, Y., Zhao, W., Ibragimov, B., ... & Xing, L. (2018). Superpixel-based and boundary-sensitive convolutional neural network for automated liver segmentation. Physics in Medicine & Biology, 63(9), 095017.
  • Kar, O. F., Güngör, A., Ilbey, S., & Güven, H. E. (2018, May). An efficient parallel algorithm for single-pixel and fpa imaging. In Computational Imaging III (Vol. 10669, p. 106690J). International Society for Optics and Photonics.
  • Yu, H., Jiang, M., Chen, H., Feng, J., Wang, Y., & Lu, Y. (2017). Super-pixel algorithm and group sparsity regularization method for compressed sensing MR image reconstruction. Optik, 140, 392-404.
  • Kaur, S., Bansal, R. K., Mittal, M., Goyal, L. M., Kaur, I., & Verma, A. (2019). Mixed pixel decomposition based on extended fuzzy clustering for single spectral value remote sensing images. Journal of the Indian Society of Remote Sensing, 47(3), 427-437.
  • Kanungo, T., Mount, DM, Netanyahu, NS, Piatko, CD, Silverman, R., & Wu, AY (2002). An effective k-mean clustering algorithm: Analysis and application. IEEE processes on model analysis and machine intelligence, 24 (7), 881-892.
  • Likas, A., Vlassis, N., & Verbeek, J. J. (2003). The global k-means clustering algorithm. Pattern recognition, 36(2), 451-461.
  • Tripathy, B. K., Basu, A., & Govel, S. (2014, December). Image segmentation using spatial intuitionistic fuzzy C means clustering. In 2014 IEEE International Conference on Computational Intelligence and Computing Research (pp. 1-5). IEEE.
  • Zhang, S., Ma, Z., Zhang, G., Lei, T., Zhang, R., & Cui, Y. (2020). Semantic Image Segmentation with Deep Convolutional Neural Networks and Quick Shift. Symmetry, 12(3), 427.
  • Achanta, R., Shaji, A., Smith, K., Lucchi, A., Fua, P., & Süsstrunk, S. (2012). SLIC superpixels compared to state-of-the-art superpixel methods. IEEE transactions on pattern analysis and machine intelligence, 34(11), 2274-2282.
  • Zhang, S., Ma, Z., Zhang, G., Lei, T., Zhang, R., & Cui, Y. (2020). Semantic Image Segmentation with Deep Convolutional Neural Networks and Quick Shift. Symmetry, 12(3), 427.
  • Osman, F. M., & Yap, M. H. (2020). Adjusted Quick Shift Phase Preserving Dynamic Range Compression method for breast lesions segmentation. Informatics in Medicine Unlocked, 100344.
  • Levinshtein, A., Stere, A., Kutulakos, K. N., Fleet, D. J., Dickinson, S. J., & Siddiqi, K. (2009). Turbopixels: Fast superpixels using geometric flows. IEEE transactions on pattern analysis and machine intelligence, 31(12), 2290-2297.
  • Felzenszwalb, P. F., & Huttenlocher, D. P. (2004). Efficient graph-based image segmentation. International journal of computer vision, 59(2), 167-181.
  • Yao, L., & Muhammad, S. (2019). A novel technique for analysing histogram equalized medical images using superpixels. Computer Assisted Surgery, 24(sup1), 53-61.
  • Machairas, V., Decencière, E., & Walter, T. (2014, October). Waterpixels: Superpixels based on the watershed transformation. In 2014 IEEE International Conference on Image Processing (ICIP) (pp. 4343-4347
  • Schönberger, J., Siqueira A.,Mueller A., Gouillart E., Lee G., Harfouche M., Warner J., Iglesias J.N., Grüter L., Corvellec M., Fezzani R., Boulogne F., Panfilov E., & Walt S., (2014) https://scikit-image.org/ [Online]
  • Benson, CC, Deepa, V., Lajish, VL, & Rajamani, K. (2016, September). Brain tumor segmentation from MR brain images using advanced fuzzy c-averaged clustering and watershed algorithm. In the 2016 International Conference on Informatics, Communication and Informatics Advances (ICACCI) (p.187-192).
  • Roerdink, J. B., & Meijster, A. (2000). The watershed transform: Definitions, algorithms and parallelization strategies. Fundamenta informaticae, 41(1, 2), 187-228.
  • Albayrak, A., & Bilgin, G. (2019). Automatic cell segmentation in histopathological images via two-staged superpixel-based algorithms. Medical & biological engineering & computing, 57(3), 653-665.
Yıl 2021, Cilt: 9 Sayı: 3, 304 - 309, 30.07.2021
https://doi.org/10.17694/bajece.864266

Öz

Kaynakça

  • Anonim,2017. Erken Teşhis Hayat Kurtarır [Online] https://www.saglik.gov.tr/Eklenti/8635,kanser-istatistikleridocx.docx?0
  • Albayrak, A., & Bilgin, G. (2017, May). Superpixel approach in high resolution histopathological image segmentation. In 2017 25th Signal Processing and Communications Applications Conference (SIU) (pp. 1-4). IEEE.
  • Xu, J., Xiang, L., Liu, Q., Gilmore, H., Wu, J., Tang, J., & Madabhushi, A. (2015). Stacked sparse autoencoder (SSAE) for nuclei detection on breast cancer histopathology images. IEEE transactions on medical imaging, 35(1), 119-130.
  • Aksebzeci, B. H., & Kayaalti, Ö. (2017, October). Computer-aided classification of breast cancer histopathological images. In 2017 Medical Technologies National Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Albayrak, A., & Bilgin, G. (2018, November). Segmentation of cellular structures with encoder-decoder based deep learning algorithm in histopathological images. In 2018 Medical Technologies National Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Albayrak, A., Ünlü, A., Çalık, N., Bilgin, G., Türkmen, İ., Çakır, A., ... & Ata, L. D. (2017, May). Segmentation of precursor lesions in cervical cancer using convolutional neural networks. In 2017 25th Signal Processing and Communications Applications Conference (SIU) (pp. 1-4). IEEE.
  • Turan, S., & Bilgin, G. (2019, April). Semantic nuclei segmentation with deep learning on breast pathology images. In 2019 Scientific Meeting on Electrical-Electronics & Biomedical Engineering and Computer Science (EBBT) (pp. 1-4). IEEE.
  • Li, B., Niessen, W. J., Klein, S., de Groot, M., Ikram, M. A., Vernooij, M. W., & Bron, E. E. (2019, October). A hybrid deep learning framework for integrated segmentation and registration: Evaluation on longitudinal white matter tract changes. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 645-653). Springer, Cham.
  • Ronneberger, O., Fischer, P., & Brox, T. (2015, October). U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention (pp. 234-241). Springer, Cham.
  • Bagdigen, M. E., & Bilgin, G. (2019, October). Detection and Grading of Breast Cancer via Spatial Features in Histopathological Images. In 2019 Medical Technologies Congress (TIPTEKNO) (pp. 1-4). IEEE.
  • Feng-Ping, A., & Zhi-Wen, L. (2019). Medical image segmentation algorithm based on feedback mechanism convolutional neural network. Biomedical Signal Processing and Control, 53, 101589.
  • Xia, K., Yin, H., Qian, P., Jiang, Y., & Wang, S. (2019). Liver semantic segmentation algorithm based on improved deep adversarial networks in combination of weighted loss function on abdominal CT images. IEEE Access, 7, 96349-96358.
  • Feng, Y., Zhao, H., Li, X., Zhang, X., & Li, H. (2017). A multi-scale 3D Otsu thresholding algorithm for medical image segmentation. Digital Signal Processing, 60, 186-199
  • Farag, T. H., Hassan, W. A., Ayad, H. A., AlBahussain, A. S., Badawi, U. A., & Alsmadi, M. K. (2017). Extended absolute fuzzy connectedness segmentation algorithm utilizing region and boundary-based information. Arabian Journal for Science and Engineering, 42(8), 3573-3583.
  • Salazar-Reque, I. F., Huamán, S. G., Kemper, G., Telles, J., & Diaz, D. (2019). An algorithm for plant disease visual symptom detection in digital images based on superpixels. Int. J. Adv. Sci. Eng. Inf. Technol, 9(1), 194-203.
  • Qin, W., Wu, J., Han, F., Yuan, Y., Zhao, W., Ibragimov, B., ... & Xing, L. (2018). Superpixel-based and boundary-sensitive convolutional neural network for automated liver segmentation. Physics in Medicine & Biology, 63(9), 095017.
  • Kar, O. F., Güngör, A., Ilbey, S., & Güven, H. E. (2018, May). An efficient parallel algorithm for single-pixel and fpa imaging. In Computational Imaging III (Vol. 10669, p. 106690J). International Society for Optics and Photonics.
  • Yu, H., Jiang, M., Chen, H., Feng, J., Wang, Y., & Lu, Y. (2017). Super-pixel algorithm and group sparsity regularization method for compressed sensing MR image reconstruction. Optik, 140, 392-404.
  • Kaur, S., Bansal, R. K., Mittal, M., Goyal, L. M., Kaur, I., & Verma, A. (2019). Mixed pixel decomposition based on extended fuzzy clustering for single spectral value remote sensing images. Journal of the Indian Society of Remote Sensing, 47(3), 427-437.
  • Kanungo, T., Mount, DM, Netanyahu, NS, Piatko, CD, Silverman, R., & Wu, AY (2002). An effective k-mean clustering algorithm: Analysis and application. IEEE processes on model analysis and machine intelligence, 24 (7), 881-892.
  • Likas, A., Vlassis, N., & Verbeek, J. J. (2003). The global k-means clustering algorithm. Pattern recognition, 36(2), 451-461.
  • Tripathy, B. K., Basu, A., & Govel, S. (2014, December). Image segmentation using spatial intuitionistic fuzzy C means clustering. In 2014 IEEE International Conference on Computational Intelligence and Computing Research (pp. 1-5). IEEE.
  • Zhang, S., Ma, Z., Zhang, G., Lei, T., Zhang, R., & Cui, Y. (2020). Semantic Image Segmentation with Deep Convolutional Neural Networks and Quick Shift. Symmetry, 12(3), 427.
  • Achanta, R., Shaji, A., Smith, K., Lucchi, A., Fua, P., & Süsstrunk, S. (2012). SLIC superpixels compared to state-of-the-art superpixel methods. IEEE transactions on pattern analysis and machine intelligence, 34(11), 2274-2282.
  • Zhang, S., Ma, Z., Zhang, G., Lei, T., Zhang, R., & Cui, Y. (2020). Semantic Image Segmentation with Deep Convolutional Neural Networks and Quick Shift. Symmetry, 12(3), 427.
  • Osman, F. M., & Yap, M. H. (2020). Adjusted Quick Shift Phase Preserving Dynamic Range Compression method for breast lesions segmentation. Informatics in Medicine Unlocked, 100344.
  • Levinshtein, A., Stere, A., Kutulakos, K. N., Fleet, D. J., Dickinson, S. J., & Siddiqi, K. (2009). Turbopixels: Fast superpixels using geometric flows. IEEE transactions on pattern analysis and machine intelligence, 31(12), 2290-2297.
  • Felzenszwalb, P. F., & Huttenlocher, D. P. (2004). Efficient graph-based image segmentation. International journal of computer vision, 59(2), 167-181.
  • Yao, L., & Muhammad, S. (2019). A novel technique for analysing histogram equalized medical images using superpixels. Computer Assisted Surgery, 24(sup1), 53-61.
  • Machairas, V., Decencière, E., & Walter, T. (2014, October). Waterpixels: Superpixels based on the watershed transformation. In 2014 IEEE International Conference on Image Processing (ICIP) (pp. 4343-4347
  • Schönberger, J., Siqueira A.,Mueller A., Gouillart E., Lee G., Harfouche M., Warner J., Iglesias J.N., Grüter L., Corvellec M., Fezzani R., Boulogne F., Panfilov E., & Walt S., (2014) https://scikit-image.org/ [Online]
  • Benson, CC, Deepa, V., Lajish, VL, & Rajamani, K. (2016, September). Brain tumor segmentation from MR brain images using advanced fuzzy c-averaged clustering and watershed algorithm. In the 2016 International Conference on Informatics, Communication and Informatics Advances (ICACCI) (p.187-192).
  • Roerdink, J. B., & Meijster, A. (2000). The watershed transform: Definitions, algorithms and parallelization strategies. Fundamenta informaticae, 41(1, 2), 187-228.
  • Albayrak, A., & Bilgin, G. (2019). Automatic cell segmentation in histopathological images via two-staged superpixel-based algorithms. Medical & biological engineering & computing, 57(3), 653-665.
Toplam 34 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Elektrik Mühendisliği
Bölüm Araştırma Makalesi
Yazarlar

Gamze Mendi 0000-0003-4295-0410

Cafer Budak 0000-0002-8470-4579

Yayımlanma Tarihi 30 Temmuz 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 9 Sayı: 3

Kaynak Göster

APA Mendi, G., & Budak, C. (2021). Automatic Cell Nucleus Segmentation Using Superpixels and Clustering Methods in Histopathological Images. Balkan Journal of Electrical and Computer Engineering, 9(3), 304-309. https://doi.org/10.17694/bajece.864266

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