Tracing Tubular Structures from Teravoxel-Sized Microscope Images

Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul:2018:562-565. doi: 10.1109/EMBC.2018.8512288.

Abstract

Tracing vasculature and neurites from teravoxel sized light-microscopy data-sets is a challenge impeding the availability of processed data to the research community. This is because (1) Holding terabytes of data during run-time is not easy for a regular PC. (2) Processing all the data at once would be slow and inefficient. In this paper, we propose a way to mitigate this challenge by Divide Conquer and Combine (DCC) method. We first split the volume into many smaller and manageable sub-volumes before tracing. These sub-volumes can then be traced individually in parallel (or otherwise). We propose an algorithm to stitch together the traced data from these sub-volumes. This algorithm is robust and handles challenging scenarios like (1) sub-optimal tracing at edges (2) densely packed structures and (3) different depths of trace termination. We validate our results using whole mouse brain vasculature data-set obtained from the Knife-Edge Scanning Microscopy (KESM) based automated tissue scanner.

MeSH terms

  • Algorithms
  • Animals
  • Brain / blood supply*
  • Image Processing, Computer-Assisted / methods*
  • Imaging, Three-Dimensional / methods
  • Mice
  • Microscopy*
  • Neurites