Physically motivated global alignment method for electron tomography

Toby Sanders,Cem Akatay,Micah Prange,Peter Binev

doi:10.1186/s40679-015-0005-7

Abstract

AbstractElectron tomography is widely used for nanoscale determination of 3-D structures in many areas of science. Determining the 3-D structure of a sample from electron tomography involves three major steps: acquisition of sequence of 2-D projection images of the sample with the electron microscope, alignment of the images to a common coordinate system, and 3-D reconstruction and segmentation of the sample from the aligned image data. The resolution of the 3-D reconstruction is directly influenced by the accuracy of the alignment, and therefore, it is crucial to have a robust and dependable alignment method. In this paper, we develop a new alignment method which avoids the use of markers and instead traces the computed paths of many identifiable ‘local’ center-of-mass points as the sample is rotated. Compared with traditional correlation schemes, the alignment method presented here is resistant to cumulative error observed from correlation techniques, has very rigorous mathematical justification, and is very robust since many points and paths are used, all of which inevitably improves the quality of the reconstruction and confidence in the scientific results.

Highlights

Electron tomography has been a powerful tool in determining 3-D structures and characterization of nanoparticles in the biological, medical, and materials sciences [1,2,3]
By selecting shifts for individual tilt-series images that globally lead to physically plausible motions for the centers of mass of many cross-sections, our method effectively utilizes the assumption that the sample object is rigid to improve the alignment and the resolution of the final reconstruction
We have shown that conventional alignment procedures, which shift the global center of mass to the origin, may not produce physically plausible motions in other cross-sections

Summary

Introduction

Electron tomography has been a powerful tool in determining 3-D structures and characterization of nanoparticles in the biological, medical, and materials sciences [1,2,3]. The method is carried out by acquiring a series of 2-D projection images of an object and using these 2-D projections to reconstruct the 3-D object. Using the transmission electron microscope, these projections are collected at a number of different orientations, typically by tilting the sample about a fixed tilt axis [4], while other dual axis tilting schemes exist [5]. We will focus only on the case of a single fixed tilt axis in this paper, our methods can be translated to dual axis schemes. Between two consecutive projections acquired at nearby tilts of the sample, one would observe only a small rotation of the projected image.

Methods

Results

Conclusion