3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake

• Published in: IEEE transactions on image processing 2006-01, Vol.15 (1), p.214-227
• Main Authors: Jacob, M., Blu, T., Vaillant, C., Maddocks, J.H., Unser, M.
• Format: Article
• Language: English
• Subjects: Active contour; Active contours; Algorithms; Applied sciences; Artificial Intelligence; Atomic force microscopy; Cluster Analysis; Computer science; control theory; systems; cryo; Cryoelectron Microscopy - methods; DNA; DNA - ultrastructure; Electrons; Exact sciences and technology; Filtering; Image Enhancement - methods; Image Interpretation, Computer-Assisted - methods; Image processing; Image reconstruction; Imaging, Three-Dimensional - methods; Information Storage and Retrieval - methods; Information, signal and communications theory; Iterative algorithms; Jacobian matrices; microscopy; Nucleic Acid Conformation; Pattern Recognition, Automated - methods; Pattern recognition. Digital image processing. Computational geometry; Photogrammetry - methods; ridge; separable filtering; Shape; Signal processing; Spline; steerable; Studies; Telecommunications and information theory
• ISSN: 1057-7149; 1941-0042
• DOI: 10.1109/TIP.2005.860310

We introduce a three-dimensional (3-D) parametric active contour algorithm for the shape estimation of DNA molecules from stereo cryo-electron micrographs. We estimate the shape by matching the projections of a 3-D global shape model with the micrographs; we choose the global model as a 3-D filament with a B-spline skeleton and a specified radial profile. The active contour algorithm iteratively updates the B-spline coefficients, which requires us to evaluate the projections and match them with the micrographs at every iteration. Since the evaluation of the projections of the global model is computationally expensive, we propose a fast algorithm based on locally approximating it by elongated blob-like templates. We introduce the concept of projection-steerability and derive a projection-steerable elongated template. Since the two-dimensional projections of such a blob at any 3-D orientation can be expressed as a linear combination of a few basis functions, matching the projections of such a 3-D template involves evaluating a weighted sum of inner products between the basis functions and the micrographs. The weights are simple functions of the 3-D orientation and the inner-products are evaluated efficiently by separable filtering. We choose an internal energy term that penalizes the average curvature magnitude. Since the exact length of the DNA molecule is known a priori, we introduce a constraint energy term that forces the curve to have this specified length. The sum of these energies along with the image energy derived from the matching process is minimized using the conjugate gradients algorithm. We validate the algorithm using real, as well as simulated, data and show that it performs well.