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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

National Energy Research

Scientific Computing Center

(NERSC)

Visualization Highlights

Cristina Siegerist

NERSC Center Division, LBNL

October 4, 2005


National energy research scientific computing center nersc visualization highlights

Visualization

Highlights:

Visualization of 3D Reconstructions of Electron Tomography Data

Ken Downing,

Life Sciences Division, LBNL


The science

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 science1

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

From Images to Volume

  • Reconstruction of dividing Caulobacter Crescentus cells


From images to volume1

From Images to Volume

  • Reconstruction of dividing Caulobacter Crescentus cells: isosurface after filtering


From volumes to surfaces

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 surfaces1

From Volumes to Surfaces

AVS/Express Model builder application:

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


From volumes to surfaces2

From Volumes to Surfaces

AVS/Express Model builder application:

  • Add the sets


From volumes to surfaces3

From Volumes to Surfaces

AVS/Express Model builder application:

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


From volumes to surfaces4

From Volumes to Surfaces

AVS/Express Model builder application:

  • Triangulate the surface


From volumes to surfaces5

From Volumes to Surfaces

AVS/Express Model builder application:

  • Triangulate the surface


From volumes to surfaces6

From Volumes to Surfaces


From volumes to surfaces7

From Volumes to Surfaces

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


From volumes to surfaces8

From Volumes to Surfaces

  • Constructing the splines.


From volumes to surfaces9

From Volumes to Surfaces

  • Triangulation


From volumes to surfaces10

From Volumes to Surfaces

  • Triangulation


From volumes to surfaces11

From Volumes to Surfaces


From volumes to surfaces12

From Volumes to Surfaces

Journal of Bacteriology October 2005

Cover


From volumes to surfaces13

From Volumes to Surfaces

Problems:

easy to solve: smoothing the surface.

not so easy: stitching and bifurcations.


Another approach point clouds to surfaces

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

Point Clouds to surfaces

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


Point clouds to surfaces1

Point Clouds to surfaces

  • Estimate the normals


Point clouds to surfaces2

Point Clouds to surfaces

  • Smooth the cloud


Point clouds to surfaces3

Point Clouds to surfaces

  • Smooth the cloud


Point clouds to surfaces4

Point Clouds to surfaces

  • Reconstruct the surface with boundaries


Point clouds to surfaces5

Point Clouds to surfaces


Point clouds to surfaces6

Point Clouds to surfaces

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


Use of the model

Use of the Model


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