National Energy Research Scientific Computing Center (NERSC)

Visualization Highlights

Cristina Siegerist

NERSC Center Division, LBNLOctober 4, 2005

VisualizationHighlights: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 2005Cover

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