Scalable and interactive segmentation and visualization of neural processes in em datasets

Won Ki Jeong*, Johanna Beyer, Markus Hadwiger, Amelio Vazquez, Hanspeter Pfister, Ross T. Whitaker

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

Abstract

Recent advances in scanning technology provide high resolution EM (Electron Microscopy) datasets that allow neuroscientists to reconstruct complex neural connections in a nervous system. However, due to the enormous size and complexity of the resulting data, segmentation and visualization of neural processes in EM data is usually a difficult and very time-consuming task. In this paper, we present NeuroTrace, a novel EM volume segmentation and visualization system that consists of two parts: a semi-automatic multiphase level set segmentation with 3D tracking for reconstruction of neural processes, and a specialized volume rendering approach for visualization of EM volumes. It employs view-dependent on-demand filtering and evaluation of a local histogram edge metric, as well as on-the-fly interpolation and ray-casting of implicit surfaces for segmented neural structures. Both methods are implemented on the GPU for interactive performance. NeuroTrace is designed to be scalable to large datasets and data-parallel hardware architectures. A comparison of NeuroTrace with a commonly used manual EM segmentation tool shows that our interactive workflow is faster and easier to use for the reconstruction of complex neural processes.

Original languageEnglish (US)
Article number5290767
Pages (from-to)1505-1514
Number of pages10
JournalIEEE Transactions on Visualization and Computer Graphics
Volume15
Issue number6
DOIs
StatePublished - Nov 1 2009

Keywords

  • Segmentation
  • connectome
  • graphics hardware
  • implicit surface rendering
  • neuroscience
  • volume rendering

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Computer Vision and Pattern Recognition
  • Computer Graphics and Computer-Aided Design

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