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3D Reconstruction of DNA Filaments

Investigator: Mathews Jacob

Summary: We developed a parametric active-contour algorithm for reconstructing the 3D shape of DNA filaments from a matched pair of tilted cryo-electron micrographs.

Main Contributions

We proposed a model-based algorithm the 3-D reconstruction of DNA filaments from a pair of stereo cryo-electron micrographs. The underlying principle is to specify a 3-D model of a filament—described as a spline curve—and to fit it to the 2-D data using a snake-like algorithm. To drive the snake, we specify a ridge-enhancing vector field for each of the images based on the maximum output of a bank of rotating matched filters. The magnitude of the field gives a confidence measure for the presence of a filament and the phase indicates its direction. The snake algorithm starts with an initial curve (input by the user) and evolves it so that its projections on the viewing plane are in maximal agreement with the corresponding vector fields.

To accelerate the computation of the rotating matched filter, we introduced the concept of projection-steerable filtering. Specifically, we consider an elongated blob-like template whose projection in any direction can be expressed as a linear combination of a few basis functions (derivatives of Gaussians). The weights are simple functions of the 3-D orientation and the required inner-products between the basis functions and the micrographs are evaluated by separable filtering.

Collaborations: Prof. Michael Unser and Dr. Thierry Blu; Prof. John Maddocks and Cédrick Vaillant (EPFL); Prof. Jacques Dubochet (LAU, Uni Lausanne)

Period: 2001-2005

Funding: Grants 2000-061420.00 and 200020-101821 from the Swiss National Science Foundation

Major Publications

[1] 

A. Amzallag, C. Vaillant, M. Jacob, M. Unser, J. Bednar, J.D. Kahn, J. Dubochet, A. Stasiak, J.H. Maddocks, "3D Reconstruction and Comparison of Shapes of DNA Minicircles Observed by Cryo-Electron Microscopy," Nucleic Acids Research, vol. 34, no. 18, pp. e125, September 29, 2006.

[2] 

M. Jacob, T. Blu, C. Vaillant, J.H. Maddocks, M. Unser, "3-D Shape Estimation of DNA Molecules from Stereo Cryo-Electron Micro-Graphs Using a Projection-Steerable Snake," IEEE Transactions on Image Processing, vol. 15, no. 1, pp. 214-227, January 2006.

[3] 

M. Jacob, T. Blu, M. Unser, "3-D Reconstruction of DNA Filaments from Stereo Cryo-Electron Micrographs," Proceedings of the First IEEE International Symposium on Biomedical Imaging: Macro to Nano (ISBI'02), Washington DC, USA, July 7-10, 2002, vol. II, pp. 597-600.

[4] 

M. Jacob, "Parametric Shape Processing in Biomedical Imaging," Swiss Federal Institute of Technology Lausanne, EPFL Thesis no. 2857 (2003), 192 p., September 30, 2003.

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