Skip to main content
SpringerLink
Log in

Automated Reconstruction of Neurovascular Networks in Knife-Edge Scanning Microscope Rat Brain Nissl Data Set

  • Conference paper
  • First Online:
Advances in Visual Computing (ISVC 2016)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 10072))

Included in the following conference series:

Abstract

Analyzing mammalian brain image can help to understand the interaction between cerebral blood flow and its surrounding tissue. However, extracting the geometry of the vasculature and the cells is difficult because of the complexity of the brain. In this paper, we propose an approach for reconstructing the neurovascular networks from Knife-Edge Scanning Microscope (KESM) rat Nissl data set. The proposed method includes the following steps. First, we enhanced the raw image data using homomorphic filtering, fast Fourier transform, and anisotropic diffusion. Next, we initially extracted the vessel cross section from the image using dynamic global thresholding. Subsequently, we computed local properties of the connected components to remove various sources of noise. Finally, the proposed method connected small and large discontinuities in the vascular traces. To validate the performance of the proposed method, we compared reconstruction results of the proposed method with an existing method (Lim’s method [1, 2]). The comparison results show that the proposed method outperforms the previous method: faster and robust to noise.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Lim, S., Nowak, M., Choe, Y.: Automated neurovascular tracing and analysis of the knife-edge scanning microscope rat nissl data set using a computing cluster. In: Proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2016, in press)

    Google Scholar 

  2. Lim, S.: Automated neurovascular tracing and analysis of the knife-edge scanning microscope rat nissl data set using ADA computing cluster. MS thesis, Department of Computer Science and Engineering, Texas A&M University, College Station, Texas (2015)

    Google Scholar 

  3. Wang, H., Hitron, I.M., Iadecola, C., Pickel, V.M.: Synaptic and vascular associations of neurons containing cyclooxygenase-2 and nitric oxide synthase in rat somatosensory cortex. 15, 1250–1260 (2005). Oxford University Press

    Google Scholar 

  4. Wells, J.A., Holmes, H.E., O’Callaghan, J.M., Colgan, N., Ismail, O., Fisher, E.M., Siow, B., Murray, T.K., Schwarz, A.J., O’Neill, M.J.: Increased cerebral vascular reactivity in the tau expressing rTg4510 mouse: evidence against the role of tau pathology to impair vascular health in Alzheimer’s disease. J. Cereb. Blood Flow Metab. 35, 359–362 (2015)

    Article  Google Scholar 

  5. Girouard, H., Iadecola, C.: Neurovascular coupling in the normal brain and in hypertension, stroke, and Alzheimer disease. Am. Physiol. Soc. 100, 328–335 (2006)

    Google Scholar 

  6. Choe, Y., Mayerich, D., Kwon, J., Miller, D.E., Chung, J.R., Sung, C., Keyser, J., Abbott, L.C.: Knife-edge scanning microscopy for connectomics research. In: The 2011 International Joint Conference on Neural Networks (IJCNN), pp. 2258–2265. IEEE press (2011)

    Google Scholar 

  7. Kádár, A., Wittmann, G., Liposits, Z., Fekete, C.: Improved method for combination of immunocytochemistry and nissl staining. 184, 115–118 (2009). Elsevier

    Google Scholar 

  8. De Jonge, N., Peckys, D.B., Kremers, G., Piston, D.: Electron microscopy of whole cells in liquid with nanometer resolution. Natl. Acad. Sci. 106, 2159–2164 (2009)

    Article  Google Scholar 

  9. Roebroeck, A., Galuske, R., Formisano, E., Chiry, O., Bratzke, H., Ronen, I., Kim, D.s., Goebel, R.: High-resolution diffusion tensor imaging and tractography of the human optic chiasm at 9.4 T. 39, 157–168 (2008). Elsevier

    Google Scholar 

  10. Mayerich, D., Abbott, L., McCormick, B.: Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain. Library 231, 134–143 (2008). Wiley Online

    MathSciNet  Google Scholar 

  11. Chung, J.R., Sung, C., Mayerich, D., Kwon, J., Miller, D.E., Huffman, T., Keyser, J., Abbott, L.C., Choe, Y.: Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas. 5, 84–100 (2011). Program No. 516.3

    Google Scholar 

  12. Gonzalez, R.C., Woods, R.E.: Digital Image Processing. Pearson, New York City (2002)

    Google Scholar 

  13. Perona, P., Malik, J.: Scale space and edge detection for visual scene analysis. In: Proceedings of IEEE Computer Society Workshop on Computer Vision, pp. 16–22 (1987)

    Google Scholar 

  14. An, W.: Automated reconstruction of neurovascular networks in knife-edge scanning microscope mouse and rat brain nissl stained data sets. MS thesis, Department of Computer Science and Engineering, Texas A&M University, College Station, Texas (2016)

    Google Scholar 

Download references

Acknowledgments

Part of this research was funded by National Science Foundation, under grants #0905041, #1208174, and #1256086. This paper is largely based on the first author’s master’s thesis [14]. Lim’s method’s results were obtained from original Matlab code.

Author information

Authors and Affiliations

  1. Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, 77843-3112, USA

    Wookyung An & Yoonsuck Choe

Authors
  1. Wookyung An
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yoonsuck Choe
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wookyung An .

Editor information

Editors and Affiliations

  1. University of Nevada , Reno, Nevada, USA

    George Bebis

  2. NASA Ames Research Center , Moffett Field, California, USA

    Richard Boyle

  3. Lawrence Berkeley National Laboratory , Berkeley, California, USA

    Bahram Parvin

  4. Desert Research Institute , Reno, Nevada, USA

    Darko Koracin

  5. The Australian National University , O'Malley, Aust Capital Terr, Australia

    Fatih Porikli

  6. Pilot AI Labs , Redwood City, California, USA

    Sandra Skaff

  7. University of Florida , Gainesville, Florida, USA

    Alireza Entezari

  8. Google Inc. , Mountain View, California, USA

    Jianyuan Min

  9. Osaka University , Osaka, Japan

    Daisuke Iwai

  10. The MOVES Institute , Monterey, California, USA

    Amela Sadagic

  11. University of Arizona , Tucson, Arizona, USA

    Carlos Scheidegger

  12. Université Paris-Sud , Orsay, France

    Tobias Isenberg

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing AG

About this paper

Cite this paper

An, W., Choe, Y. (2016). Automated Reconstruction of Neurovascular Networks in Knife-Edge Scanning Microscope Rat Brain Nissl Data Set. In: Bebis, G., et al. Advances in Visual Computing. ISVC 2016. Lecture Notes in Computer Science(), vol 10072. Springer, Cham. https://doi.org/10.1007/978-3-319-50835-1_40

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-50835-1_40

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-50834-4

  • Online ISBN: 978-3-319-50835-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation