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

Mathews JACOB; Thierry BLU; Cedric VAILLANT; John H MADDOCKS; Michael UNSER

doi:10.1109/TIP.2005.860310

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

Journal article

Open access

Peer reviewed

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

Mathews JACOB, Thierry BLU, Cedric VAILLANT, John H MADDOCKS and Michael UNSER

IEEE transactions on image processing, Vol.15(1), pp.214-227

2006

DOI: 10.1109/TIP.2005.860310

PMID: 16435551

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http://infoscience.epfl.ch/record/130310View

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Abstract

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.

Signal Processing

Applied Sciences

Pattern recognition. Digital image processing. Computational geometry

Image processing

Telecommunications and information theory

Exact sciences and technology

Information, signal and communications theory

Artificial intelligence

Computer science; control theory; systems

Details

Title: Subtitle: 3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake
Creators: Mathews JACOB - Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
Thierry BLU - Swiss Federal Institute of Technology, Lausanne, Switzerland
Cedric VAILLANT - Swiss Federal Institute of Technology, Lausanne, Switzerland
John H MADDOCKS - Swiss Federal Institute of Technology, Lausanne, Switzerland
Michael UNSER - Swiss Federal Institute of Technology, Lausanne, Switzerland
Resource Type: Journal article
Publication Details: IEEE transactions on image processing, Vol.15(1), pp.214-227
DOI: 10.1109/TIP.2005.860310
PMID: 16435551
NLM abbreviation: IEEE Trans Image Process
ISSN: 1057-7149
eISSN: 1941-0042
Publisher: Institute of Electrical and Electronics Engineers; New York, NY
Language: English
Date published: 2006
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Radiology; Electrical and Computer Engineering; Iowa Neuroscience Institute; Radiation Oncology
Record Identifier: 9984070562302771

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