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Cell Counting by a Location-Aware Network

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Machine Learning in Medical Imaging (MLMI 2021)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 12966))

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Abstract

The purpose of cell counting is to estimate the number of cells in microscopy images. Most popular methods obtain the cell numbers by integrating the density maps that are generated by deep cell counting networks. However, these cell counting networks that reply on estimated cell density maps may leave cell locations in a black-box. In this paper, we propose a novel cell counting network leveraging cell location information to obtain accurate cell numbers. Evaluated on four widely used cell counting datasets, our method which uses cell locations to boost the cell density map generation and cell counting, achieves superior performances compared to the state-of-the-art. The source codes will be available in our Github.

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References

  1. Cohen, J.P., Boucher, G., Glastonbury, C.A., Lo, H.Z., Bengio, Y.: Count-ception: counting by fully convolutional redundant counting. In: 2017 IEEE International Conference on Computer Vision Workshops, ICCV Workshops 2017, Venice, Italy, 22–29 October 2017, pp. 18–26 (2017)

    Google Scholar 

  2. Falk, T., et al.: U-Net: deep learning for cell counting, detection, and morphometry. Nat. Methods 16(1), 67 (2019)

    Google Scholar 

  3. Guo, Y., Stein, J.L., Wu, G., Krishnamurthy, A.K.: SAU-Net: a universal deep network for cell counting. In: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, Niagara Falls, NY, USA, 7–10 September 2019, pp. 299–306. ACM (2019)

    Google Scholar 

  4. Hagos, Y.B., Narayanan, P.L., Akarca, A.U., Marafioti, T., Yuan, Y.: ConCORDe-Net: cell count regularized convolutional neural network for cell detection in multiplex immunohistochemistry images. In: Shen, D., et al. (eds.) MICCAI 2019, Part I. LNCS, vol. 11764, pp. 667–675. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-32239-7_74

    Chapter  Google Scholar 

  5. Jonker, R., Volgenant, T.: Improving the Hungarian assignment algorithm. Oper. Res. Lett. 5(4), 171–175 (1986)

    Article  MathSciNet  Google Scholar 

  6. Kainz, P., Urschler, M., Schulter, S., Wohlhart, P., Lepetit, V.: You should use regression to detect cells. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015, Part III. LNCS, vol. 9351, pp. 276–283. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24574-4_33

    Chapter  Google Scholar 

  7. Khan, A., Gould, S., Salzmann, M.: Deep convolutional neural networks for human embryonic cell counting. In: Hua, G., Jégou, H. (eds.) ECCV 2016, Part I. LNCS, vol. 9913, pp. 339–348. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46604-0_25

    Chapter  Google Scholar 

  8. Lempitsky, V.S., Zisserman, A.: Learning to count objects in images. In: Lafferty, J.D., Williams, C.K.I., Shawe-Taylor, J., Zemel, R.S., Culotta, A. (eds.) Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010. Proceedings of a meeting held, 6–9 December 2010, Vancouver, British Columbia, Canada, pp. 1324–1332 (2010)

    Google Scholar 

  9. Li, Y., Zhang, X., Chen, D.: CSRNet: dilated convolutional neural networks for understanding the highly congested scenes. In: Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, pp. 1091–1100 (2018)

    Google Scholar 

  10. Lucidi, M., Marsan, M., Visaggio, D., Visca, P., Cincotti, G.: Microscopy direct escherichia coli live/dead cell counting. In: 2018 20th International Conference on Transparent Optical Networks (ICTON), pp. 1–4. IEEE (2018)

    Google Scholar 

  11. Marsden, M., McGuinness, K., Little, S., Keogh, C.E., O’Connor, N.E.: People, penguins and petri dishes: adapting object counting models to new visual domains and object types without forgetting. In: 2018 IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2018, Salt Lake City, UT, USA, 18–22 June 2018, pp. 8070–8079. IEEE Computer Society (2018)

    Google Scholar 

  12. Paszke, A., et al.: Pytorch: an imperative style, high-performance deep learning library. In: Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, NeurIPS 2019, Vancouver, BC, Canada, 8–14 December 2019, pp. 8024–8035 (2019)

    Google Scholar 

  13. Shah, M.A., Wang, D., Rubadue, C., Suster, D., Beck, A.H.: Deep learning assessment of tumor proliferation in breast cancer histological images. In: 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, MO, USA, 13–16 November 2017, pp. 600–603. IEEE Computer Society (2017)

    Google Scholar 

  14. Simonyan, K., Zisserman, A.: Very deep convolutional networks for large-scale image recognition. In: Bengio, Y., LeCun, Y. (eds.) 3rd International Conference on Learning Representations, ICLR 2015, San Diego, CA, USA, 7–9 May 2015, Conference Track Proceedings (2015)

    Google Scholar 

  15. Xia, T., Jiang, R., Fu, Y., Jin, N.: Automated blood cell detection and counting via deep learning for microfluidic point-of-care medical devices. CoRR abs/1909.05393 (2019)

    Google Scholar 

  16. Xie, W., Noble, J.A., Zisserman, A.: Microscopy cell counting and detection with fully convolutional regression networks. CMBBE Imaging Vis. 6(3), 283–292 (2018)

    Google Scholar 

  17. Xue, Y., Ray, N., Hugh, J., Bigras, G.: Cell counting by regression using convolutional neural network. In: Hua, G., Jégou, H. (eds.) ECCV 2016, Part I. LNCS, vol. 9913, pp. 274–290. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46604-0_20

    Chapter  Google Scholar 

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Acknowledgment

This project was supported by Stony Brook University - Brookhaven National Laboratory (SBU-BNL) seed grant on annotation-efficient deep learning.

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Correspondence to Zhaozheng Yin .

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Wang, Z., Yin, Z. (2021). Cell Counting by a Location-Aware Network. In: Lian, C., Cao, X., Rekik, I., Xu, X., Yan, P. (eds) Machine Learning in Medical Imaging. MLMI 2021. Lecture Notes in Computer Science(), vol 12966. Springer, Cham. https://doi.org/10.1007/978-3-030-87589-3_13

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  • DOI: https://doi.org/10.1007/978-3-030-87589-3_13

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