Three-Dimensional
Coordinates of Individual Atoms in Materials Revealed by Electron Tomography
[Data, image reconstruction and data analysis
source codes for R. Xu, C.-C. Chen, L. Wu, M. C. Scott, W. Theis, C. Ophus, M.
Bartels, Y. Yang, H. Ramezani-Dakhel, M. R. Sawaya, H. Heinz, L. D. Marks, P.
Ercius and J. Miao, ¡°Three-Dimensional Coordinates of
Individual Atoms in Materials Revealed by Electron Tomography¡±, Nature Mater. 14, 1099-1103
(2015).]
Posted on September 21, 2015
In 1959, Richard Feynman challenged
the electron microscopy community to locate the positions of individual atoms
in substances. Although significant
progress has been made with electron microscopy over the last 55 years, Feynman¡¯s
challenge - 3D localization of the coordinates of atoms in
substances without averaging or a priori knowledge of crystallinity -
remained elusive. Recently, we reported, for the first time, the determination
of the 3D coordinates of thousands of individual atoms and a point defect in a
material with a precision of ~19 picometer, where the crystallinity of the
sample is not assumed. From the coordinates of these individual atoms, we
measured the atomic displacement field and the full strain tensor with a 3D
resolution of 1 nm and a precision of 10-3, which were further
verified by density functional theory calculations and molecular dynamics
simulations. The ability to precisely localize the 3D coordinates of individual
atoms in materials without assuming crystallinity, identify point defects in
three dimensions, and measure the atomic displacement field and the full strain
tensor is expected to transform our understanding of materials properties and
functionality at the most fundamental scale.
To facilitate those who are
interested in our method, we make the data, image reconstruction and data
analysis source codes in Matlab freely available below.
1) Click here to download 62 raw experimental
projections.
2) Click
here to download the raw experimental data of the 0¡Æ and 180¡Æ
projections before and
after acquisition of the full tilt series.
3) Click here to download the 3D reconstruction of
the 62 raw experimental projections using the EST algorithm.
4) Click here to download 62 denoised
experimental projections by applying a sparsity-based algorithm (termed BM3D).
5) Click here to download the 3D reconstruction of
the 62 denoised experimental projections using the EST algorithm.
6) Click here to download the traced 3D atomic
model.
7) Click here to download the source code (main
function: Position_Refine.m) to refine the atomic
model. (Note: as described in the Methods section, the positions of <1% of
the atoms was manually adjusted during the refinement, which has also been
widely used in the refinement process in protein crystallography.)
8) Click here to download the final 3D atomic model
after refinement.
If you use any of the above data and
source codes in your publications and/or presentations, we request you cite our
paper: R. Xu, C.-C. Chen, L. Wu, M. C. Scott, W. Theis, C. Ophus, M. Bartels,
Y. Yang, H. Ramezani-Dakhel, M. R. Sawaya, H. Heinz, L. D. Marks, P. Ercius and
J. Miao, ¡°Three-Dimensional Coordinates of Individual Atoms in Materials
Revealed by Electron Tomography¡±, Nature
Mater. 14, 1099-1103 (2015).
This document was prepared by Yongsoo
Yang, Rui Xu, Li Wu, and John Miao in the Department of Physics & Astronomy
and California NanoSystems Institute, University of California, Los Angeles,
California, 90095, USA. Email: miao@physics.ucla.edu.