Skip to main content

Detection of Neurons on Images of the Histological Slices Using Convolutional Neural Network

  • Conference paper
  • First Online:
Advances in Neural Computation, Machine Learning, and Cognitive Research (NEUROINFORMATICS 2017)

Part of the book series: Studies in Computational Intelligence ((SCI,volume 736))

Included in the following conference series:

Abstract

An automatic analysis of images of the histological slices is one of main steps in process of description of structure of neural network in norm and pathology. Understanding of structure and functions of that networks may help to improve neuro-rehabilitation technologies and to translate experimental data to the clinical practice. Main problem of the automatic analysis is complexity of research object and high variance of its parameters, such as thickness and transparency of slice, intensity and type of histological marker, etc. Variance of parameters make every step of neuron detection very hard and complex task. We represent algorithm of neuron detection on images of spinal cord slices using deep neural network. Networks with different parameters are compared to previous algorithm that based on pixels’ filtration by color.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Musienko, P., Heutschi, J., Friedli, L., den Brand, R.V., Courtine, G.: Multi-system neurorehabilitative strategies to restore motor functions following severe spinal cord injury. Exp. Neurol. 235(1), 100–109 (2012)

    Article  Google Scholar 

  2. Musienko, P., van den Brand, R., Maerzendorfer, O., Larmagnac, A., Courtine, G.: Combinatory electrical and pharmacological neuroprosthetic interfaces to regain motor function after spinal cord injury. IEEE Trans. Biomed. Eng. 56(11), 2707–2711 (2009)

    Article  Google Scholar 

  3. Bakhshiev, A.V., Smirnova, E.Y., Musienko, P.E.: Methodological bases of exobalancer design for rehabilitation of people with limited mobility and impaired balance maintenance. Izv. SFedU. Eng. Sci. 10(171), 2011–2013 (2015)

    Google Scholar 

  4. Kolodziejczyk, A., Habrat (Ladniak), M., Piorkowski, A.: Constructing software for analysis of neuron, glial and endothelial cell numbers and density in histological Nissl-stained rodent brain tissue. J. Med. Inform. Technol. 23, 77–86 (2014)

    Google Scholar 

  5. Al-Kofahi, Y., Lassoued, W., Lee, W., Roysam, B.: Improved automatic detection and segmentation of cell nuclei in histopathology images. IEEE Trans. Biomed. Eng. 57(4), 841–852 (2010)

    Article  Google Scholar 

  6. Dong, B., Shao, L., Da Costa, M., Bandmann, O., Frangi, A.F.: Deep learning for automatic cell detection in wide-field microscopy zebrafish images. In: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), pp. 772–776 (2015). ISSN 1945-7928

    Google Scholar 

  7. Karakaya, M., Kerekes, R.A., Gleason, S.S., Martins, R.A., Dyer, M.A.: Automatic detection, segmentation and characterization of retinal horizontal neurons in large-scale 3D confocal imagery. SPIE Med. Imaging (2011). doi:10.1117/12.878029

  8. Lin, G., Chawla, M.K.: A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images. Cytometry Part A 71(9), 724–736 (2007)

    Article  Google Scholar 

  9. Oberlaender, M., Dercksen, V.J., Egger, R., Gensel, M., Sakmann, B., Hege, H.C.: Automated three-dimensional detection and counting of neuron somata. J. Neurosci. Methods 180(1), 147–160 (2009). doi:10.1016/j.jneumeth.2009.03.008. Epub 21 Mar 2009

    Article  Google Scholar 

  10. Ren, S., He, K., Girshick, R., Sun, J.: Faster R-CNN: towards real-time object detection with region proposal networks. In: Advances in Neural Information Processing Systems (NIPS) (2015)

    Google Scholar 

  11. Redmon, J., Farhadi, A.: Yolo9000: better, faster, stronger. arXiv preprint, arXiv:1612.08242 (2016)

  12. Chatfield, K., Simonyan, K., Vedaldi, A., Zisserman, A.: Return of the devil in the details: delving deep into convolutional nets. In: British Machine Vision Conference (2014). arXiv:1405.3531

  13. Isola, P., Zhu, J.-Y., Zhou, T., Efros, A.A.: Image-to-image translation with conditional adversarial networks. In: Computer Vision and Pattern Recognition (cs.CV), submitted 21 Nov 2016. arXiv:1611.07004[cs.CV]

  14. Shelhamer, E., Long, J., Darrell, T.: Fully convolutional models for semantic segmentation. In: PAMI (2016). arXiv:1605.06211

  15. Mikhaylov, V.V., Bakhshiev, A.V.: The system for histopathology images analysis of spinal cord slices. Procedia Comput. Sci. 103, 239–243 (2017)

    Article  Google Scholar 

Download references

Acknowledgements

This work performed with financial support of Russian Science Foundation by Grant â„– 14-15-00788.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ivan Fomin .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this paper

Cite this paper

Fomin, I., Mikhailov, V., Bakhshiev, A., Merkulyeva, N., Veshchitskii, A., Musienko, P. (2018). Detection of Neurons on Images of the Histological Slices Using Convolutional Neural Network. In: Kryzhanovsky, B., Dunin-Barkowski, W., Redko, V. (eds) Advances in Neural Computation, Machine Learning, and Cognitive Research. NEUROINFORMATICS 2017. Studies in Computational Intelligence, vol 736. Springer, Cham. https://doi.org/10.1007/978-3-319-66604-4_13

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-66604-4_13

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-66603-7

  • Online ISBN: 978-3-319-66604-4

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics