3D Reconstruction of DNA Filaments 
Investigator: Mathews Jacob 

Summary: We developed a parametric activecontour algorithm for reconstructing the 3D shape of DNA filaments from a matched pair of tilted cryoelectron micrographs. 

We proposed a modelbased algorithm the 3D reconstruction of DNA filaments from a pair of stereo cryoelectron micrographs. The underlying principle is to specify a 3D model of a filament—described as a spline curve—and to fit it to the 2D data using a snakelike algorithm. To drive the snake, we specify a ridgeenhancing 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 projectionsteerable filtering. Specifically, we consider an elongated bloblike 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 3D orientation and the required innerproducts 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) 


Funding: Grants 2000061420.00 and 200020101821 from the Swiss National Science Foundation 


[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 CryoElectron 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, "3D Shape Estimation of DNA Molecules from Stereo CryoElectron MicroGraphs Using a ProjectionSteerable Snake," IEEE Transactions on Image Processing, vol. 15, no. 1, pp. 214227, January 2006.

[3]  M. Jacob, T. Blu, M. Unser, "3D Reconstruction of DNA Filaments from Stereo CryoElectron Micrographs," Proceedings of the First IEEE International Symposium on Biomedical Imaging: Macro to Nano (ISBI'02), Washington DC, USA, July 710, 2002, vol. II, pp. 597600.


