National Energy Research Scientific Computing Center (NERSC) Visualization Highlights

1. National Energy Research Scientific Computing Center (NERSC) Visualization Highlights Cristina Siegerist NERSC Center Division, LBNL October 4, 2005

2. Visualization Highlights: Visualization of 3D Reconstructions of Electron Tomography Data Ken Downing, Life Sciences Division, LBNL

3. 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

4. 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.

5. From Images to Volume • Reconstruction of dividing Caulobacter Crescentus cells

6. From Images to Volume • Reconstruction of dividing Caulobacter Crescentus cells: isosurface after filtering

7. 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.

8. From Volumes to Surfaces AVS/Express Model builder application: • Select points along a membrane for each slice in the z direction

9. From Volumes to Surfaces AVS/Express Model builder application: • Add the sets

10. From Volumes to Surfaces AVS/Express Model builder application: • Build splines for each set and make a polyline field.

11. From Volumes to Surfaces AVS/Express Model builder application: • Triangulate the surface

12. From Volumes to Surfaces AVS/Express Model builder application: • Triangulate the surface

13. From Volumes to Surfaces

14. From Volumes to Surfaces • Start with the points selected on a membrane for each slice along the Z axis.

15. From Volumes to Surfaces • Constructing the splines.

16. From Volumes to Surfaces • Triangulation

17. From Volumes to Surfaces • Triangulation

18. From Volumes to Surfaces

19. From Volumes to Surfaces Journal of Bacteriology October 2005 Cover

20. From Volumes to Surfaces Problems: easy to solve: smoothing the surface. not so easy: stitching and bifurcations.

21. 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

22. Point Clouds to surfaces • Start with the points selected on a membrane for each slice along the Z axis.

23. Point Clouds to surfaces • Estimate the normals

24. Point Clouds to surfaces • Smooth the cloud

25. Point Clouds to surfaces • Smooth the cloud

26. Point Clouds to surfaces • Reconstruct the surface with boundaries

27. Point Clouds to surfaces

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

29. Use of the Model