Enhanced Image Processing Pipeline and Parallel Generation of Multiscale Tiles for Web-based 3D Rendering of Whole Mouse Brain Vascular Networks

Jaerock Kwon

Abstract

Mapping out the complex vascular network in the brain is critical for understanding the transport of oxygen, nutrition, and signaling molecules. The vascular network can also provide us with clues to the relationship between neural activity and blood oxygen-related signals. Advanced high-throughput 3D imaging instruments such as the Knife-Edge Scanning Microscope (KESM) are enabling the imaging of the full vascular network in small animal brains (e.g., the mouse) at sub-micrometer resolution. The amount of data per brain (for KESM) is on the order of 2TB, thus it is a major challenge just to visualize it at full resolution. In this paper, we present an enhanced image processing pipeline for KESM mouse vascular network data set, and a parallel multi-scale tile generation system for web-based pseudo-3D rendering. The system allows full navigation of the data set at all resolution scales. We expect our approach to help in broader dissemination of large-scale, high-resolution 3D microscopy data.

References

  1. D. Mayerich, J. Kwon, C. Sung, L. C. Abbott, J. Keyser, and Y. Choe, “Fast macro-scale transmission imiging of microvascular networks using KESM,” Biomedical Optics Express, vol. 2, pp. 2888-2896, 2011.
  2. J. R. Chung, C. Sung, D. Mayerich, J. Kwon, D. E. Miller, T. Huffman, L. C. Abbott, J. Keyser, and Y. Choe, “Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas,” Frontiers in Neuroinformatics, vol. 5, pp. 29, 2011.
  3. D. Mayerich, L. C. Abbott, and B. H. McCormick, “Knifeedge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain,” Journal of Microscopy, vol. 231, pp. 134-143, 2008.
  4. J. Kwon, D. Mayerich, Y. Choe, and B. H. McCormick, “Lateral sectioning for knife-edge scanning microscopy,” in Proceedings of the IEEE International Symposium on Biomedical Imaging, 2008, pp. 1371-1374.
  5. J. Kwon, D. Mayerich, and Y. Choe, “Automated cropping and artifact removal for knife-edge scanning microscopy,” in Proceedings of the IEEE International Symposium on Biomedical Imaging, 2011, pp. 1366-1369.
Download


Paper Citation


in Harvard Style

Kwon J. (2014). Enhanced Image Processing Pipeline and Parallel Generation of Multiscale Tiles for Web-based 3D Rendering of Whole Mouse Brain Vascular Networks . In Proceedings of the 3rd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM, ISBN 978-989-758-018-5, pages 783-789. DOI: 10.5220/0004926407830789


in Bibtex Style

@conference{icpram14,
author={Jaerock Kwon},
title={Enhanced Image Processing Pipeline and Parallel Generation of Multiscale Tiles for Web-based 3D Rendering of Whole Mouse Brain Vascular Networks},
booktitle={Proceedings of the 3rd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM,},
year={2014},
pages={783-789},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004926407830789},
isbn={978-989-758-018-5},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 3rd International Conference on Pattern Recognition Applications and Methods - Volume 1: ICPRAM,
TI - Enhanced Image Processing Pipeline and Parallel Generation of Multiscale Tiles for Web-based 3D Rendering of Whole Mouse Brain Vascular Networks
SN - 978-989-758-018-5
AU - Kwon J.
PY - 2014
SP - 783
EP - 789
DO - 10.5220/0004926407830789