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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.

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Presentation Transcript
slide1

National Energy Research

Scientific Computing Center

(NERSC)

Visualization Highlights

Cristina Siegerist

NERSC Center Division, LBNL

October 4, 2005

slide2
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 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 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 surfaces6
Point Clouds to surfaces
  • Smoothing the point cloud using AMLS, Co-cone rescontruction (T.Dey Ohio State University)