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National Energy Research Scientific Computing Center (NERSC) Visualization Highlights Cristina Siegerist NERSC Center Division, LBNL October 4, 2005. Visualization Highlights: Visualization of 3D Reconstructions of Electron Tomography Data Ken Downing, Life Sciences Division, LBNL.

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National Energy Research Scientific Computing Center (NERSC) Visualization Highlights

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National Energy Research

Scientific Computing Center

(NERSC)

Visualization Highlights

Cristina Siegerist

NERSC Center Division, LBNL

October 4, 2005


Visualization

Highlights:

Visualization of 3D Reconstructions of Electron Tomography Data

Ken Downing,

Life Sciences Division, LBNL


The Science

  • Bacteria contain a wealth of mechanisms that organize their internal and external structure. Electron tomography offers the possibility to localize the cell components at a resolution that allows a better understanding of their structure and function. The 3D reconstruction of whole cells should lead to the ability to model spatial and temporal relationships between sub-cellular structures, organelles and macromolecular complexes


The Science

  • Electron Tomography consists of obtaining a three-dimensional reconstruction of an object from a series of projection images. Resolution depends on the resolution of the tilt angles and the dose.


From Images to Volume

  • Reconstruction of dividing Caulobacter Crescentus cells


From Images to Volume

  • Reconstruction of dividing Caulobacter Crescentus cells: isosurface after filtering


From Volumes to Surfaces

AVS/Express Model builder application:

  • Provide an interactive interface to build a model of 2D features (membranes for example) in noisy data.


From Volumes to Surfaces

AVS/Express Model builder application:

  • Select points along a membrane for each slice in the z direction


From Volumes to Surfaces

AVS/Express Model builder application:

  • Add the sets


From Volumes to Surfaces

AVS/Express Model builder application:

  • Build splines for each set and make a polyline field.


From Volumes to Surfaces

AVS/Express Model builder application:

  • Triangulate the surface


From Volumes to Surfaces

AVS/Express Model builder application:

  • Triangulate the surface


From Volumes to Surfaces


From Volumes to Surfaces

  • Start with the points selected on a membrane for each slice along the Z axis.


From Volumes to Surfaces

  • Constructing the splines.


From Volumes to Surfaces

  • Triangulation


From Volumes to Surfaces

  • Triangulation


From Volumes to Surfaces


From Volumes to Surfaces

Journal of Bacteriology October 2005

Cover


From Volumes to Surfaces

Problems:

easy to solve: smoothing the surface.

not so easy: stitching and bifurcations.


Another Approach:Point Clouds to surfaces

  • Reconstruction of surfaces with boundaries from point clouds without the restriction of dense sampling: Normfet, AMLS and Co-Cone software provided by Dr.Tamal Dey, Ohio State University.

  • References:

    • T. K. Dey and J. Sun. Normal and Feature Estimations from Noisy Point Clouds. Technical Report OSU-CISRC-7/50-TR50, July, 2005.

    • T. K. Dey and J. Sun. Adaptive MLS Surfaces for Reconstruction with Guarantees. Proc. Eurographics  Symposium on Geometry Processing (2005), 43--52.

    • N. Amenta, S. Choi, T. K. Dey and N. Leekha. A simple algorithm for homeomorphic surface reconstruction. Intl. J. Comput. Geom. Appl.,  Vol. 12 (2002), 125--141.

    • http://www.cse.ohio-state.edu/~tamaldey/cocone.html


Point Clouds to surfaces

  • Start with the points selected on a membrane for each slice along the Z axis.


Point Clouds to surfaces

  • Estimate the normals


Point Clouds to surfaces

  • Smooth the cloud


Point Clouds to surfaces

  • Smooth the cloud


Point Clouds to surfaces

  • Reconstruct the surface with boundaries


Point Clouds to surfaces


Point Clouds to surfaces

  • Smoothing the point cloud using AMLS, Co-cone rescontruction (T.Dey Ohio State University)


Use of the Model


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