Scalable and Interactive Segmentation and Visualization of Neural Processes in EM Datasets

Won-ki Jeong, Johanna Beyer, Student Member, Markus Hadwiger, Amelio Vazquez, Student Member, Hanspeter Pfister, Senior Member, Ross T. Whitaker
School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
IEEE Transactions on Visualization and Computer Graphics, Vol. 15 no. 6, pp. 1505-1514, 2009


   title={Scalable and interactive segmentation and visualization of neural processes in EM datasets},

   author={Jeong, W.K. and Beyer, J. and Hadwiger, M. and Vazquez, A. and Pfister, H. and Whitaker, R.T.},

   journal={Visualization and Computer Graphics, IEEE Transactions on},








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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.
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