Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas
- 1 Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
- 2 Beckman Institute of Advanced Science and Technology, University of Illinois, Urbana-Champaign, IL, USA
- 3 Department of Electrical and Computer Engineering, Kettering University, Flint, MI, USA
- 4 Research and Development, 3Scan, Bryan, TX, USA
- 5 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions.
Keywords: mouse brain, Golgi, web-based brain atlas, multiscale, connectomics, Knife-Edge Scanning Microscopy
Citation: Chung JR, Sung C, Mayerich D, Kwon J, Miller DE, Huffman T, Keyser J, Abbott LC and Choe Y (2011) Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas. Front. Neuroinform. 5:29. doi: 10.3389/fninf.2011.00029
Received: 16 March 2011;
Accepted: 01 November 2011;
Published online: 22 November 2011.
Reviewed by:
Claus Hilgetag, Jacobs University Bremen, Germany
Tao Ju, Washington University in St. Louis, USA
Copyright: © 2011 Chung, Sung, Mayerich, Kwon, Miller, Huffman, Keyser, Abbott and Choe. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.
*Correspondence: Yoonsuck Choe, Department of Computer Science and Engineering, Texas A&M University, 3112 TAMU, College Station, TX 77843-3112, USA. e-mail: choe@tamu.edu
†Ji Ryang Chung and Chul Sung have contributed equally to this work.