You are on page 1of 76

Volume 1, Issue 1, 2007 Lattice-Fringe Fingerprinting: Structural Identication of Nanocrystals Employing High-Resolution Transmission Electron Microscopy Ruben Bjorge,

PhD student, Norwegian University of Science and Technology. Email: ruben.bjorge@ntnu.no Abstract Lattice-fringe ngerprinting is a novel method of identifying nanocrystals on the basis of the Fourier transforms of high-resolution transmission electron microscopy (HRTEM) images. The spacings between lattice fringes and the interfringe angles, measured when nanocrystals show crossed lattice fringes in HRTEM images, are used to initially ngerprint the nanocrystal. The two-dimensional space group symmetry of the projected electrostatic potential can also be used within the range of the validity of the weak phaseobject approximation (and probably also somewhat beyond) for ngerprinting purposes. For an abundance of nanocrystals, the theory of lattice-fringe visibility (Fraundorf et al., 2005) makes it possible to compare the frequency of the observation of any zone axis in a HRTEM image to the theoretical probability of observing that zone axis, providing additional ngerprinting information. Lattice-fringe ngerprinting was applied to three different crystal systems: titania, iron oxide and simulated images of gallium nitride. The titania nanocrystals were found to be rutile in the [111] orientation. For iron oxide, the results were inconclusive because a solid solution between magnetite and maghemite is likely to exist. The majority of the iron oxide nanocrystals showing crossed lattice fringes were oriented close to the [211] orientation. The analysis of simulated images of gallium nitride demonstrated the prospective possibility of using the phases of the Fourier coefcients of HRTEM images in identifying a crystal structure. These phases could in the future be compared directly to calculated structure factor phases for a range of candidate structures in order to make lattice-fringe ngerprinting more discriminative. In this thesis, only the phase restrictions and phase relations due to the projected space group symmetry were used as another component of lattice-fringe ngerprinting. Lattice-fringe ngerprinting requires a comprehensive database of crystallographic information combined with search/match algorithms to be employed for the identication of an unknown nanocrystal out of a range of candidate structures. Such crystallographic information is freely available from the Crystallography Open Database, its mainly inorganic subset at Portland State Universitys research servers, and the emerging Nano-Crystallography Database.

Lattice-fringe ngerprinting: Structural identication of nanocrystals employing high-resolution transmission electron microscopy

by Ruben Bjorge

A thesis submitted in partial fulllment of the requirements for the degree of Master of Science in Physics

Portland State University 2007

Acknowledgments

There are a number of people I would like to acknowledge for their advice and assistance without which this work would not have been possible. First of all, I wish to thank my adviser, prof. Peter Moeck, for all his support over the course of my two years at PSU. It has been invaluable to be able to draw upon his knowledge of electron microscopy and crystallography in my research. I would also like to express my gratitude to prof. Bjoern Seipel for his help with the lattice-fringe ngerprinting, our useful conversations and for his patience with my grading. I must also thank the rest of my thesis committee, prof. Rolf Koenenkamp and prof. Sherry Cady, for their valuable suggestions and our discussions concerning my thesis. I was fortunate to have the opportunity to stay at Technische Universitt Chemnitz over the summer of 2006 and to be able to use the transmission electron microscope there. I thank prof. Michael Hietschold for welcoming me into his group, and Dr. Schulze and Dr. Falke for all their help with using the microscope and writing scripts. I thank Modesto Godinez of Portland State University for the images of the titania nanocrystals and Eric Mandell of the University of Missouri-St. Louis for images of iron oxide nanocrystals. I thank Dr. Klaus Pecher at Pacic Northwest National Laboratory for providing the iron oxide nanocrystals. I am grateful for my fellow graduate students in the physics department who have made my stay at PSU so much more enjoyable and the hard times more bearable. Finally, I am indebted to Amanda, for her unwavering support, encouragement and love.

iv

Table of Contents Page Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv vii

List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii List of Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x 1 1 1 2 3 3 4 5 5 7 9

1.1 Overview of the Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.2 Review of Standard Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3 Overview of Experimental Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chapter 2 High-Resolution Transmission Electron Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2.1 The Fourier Transform 2.2 Kinematical Scattering

2.3 Dynamical Scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.4 Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.5 Lattice-Fringe Visibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2.6 Fourier Coefcients of the Electrostatic Potential . . . . . . . . . . . . . . . . . . . . . . . . . Chapter 3

Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

3.1 Lattice-Fringe Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 3.2 Sub-Pixel Interpolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 3.3 Lattice-Fringe Visibility and Probability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 3.4 Phases of the Fourier Coefcients of Images . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 3.5 Database Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3.6 Search/Match Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Page Chapter 4 Application of Lattice-Fringe Fingerprinting . . . . . . . . . . . . . . . . . . . . . . . . 23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4.1 Computer Implementation

4.2 Titania . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 4.3 Iron Oxide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 4.4 Fourier Coefcient Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 4.4.1 Gallium Nitride . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 4.4.2 Titania . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Chapter 5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

5.1 Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Chapter 6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 Appendix Scripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

vi

List of Tables Table 2.1 3.1 3.2 4.1 Page Reection conditions due to cell centering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

The effect of lattice parameter distortions on rutile . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Phase relations of the 17 two-dimensional space groups . . . . . . . . . . . . . . . . . . . . . . . 21 Calculated structure factor phases and measured Fourier coefcient phases for the reections present in gallium nitride in the [010] orientation . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

vii

List of Figures Figure 2.1 3.1 3.2 Lattice-fringe visibility band Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Lattice-fringe ngerprinting owchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 (a) Simulated HRTEM image of silicon in the [100] orientation. (b) Fourier transform of the HRTEM image. (c) Lattice-fringe ngerprint plot from measurements of the Fourier transform. . . . . . . . 13 (a) Schematic of an M N pixel image. (b) Plot of the one-dimensional Hanning window. . . . . 15 (a) Closeup of a Fourier transform peak. (b) Plot of the intensity of the pixels along the horizontal line through (k, l) (black dots) and the interpolating intensity curve (solid curve). . . . . . . . . . . 16 Simulated image showing sinusoidally varying fringes . . . . . . . . . . . . . . . . . . . . . . . . 18 (a) Fourier transform of a TEM image of amorphous carbon lm showing the dependence of the contrast transfer function on the magnitude of u. (b) Simulated graph of a contrast transfer function at Scherzer defocus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Theoretical lattice-fringe ngerprint plot of anatase . . . . . . . . . . . . . . . . . . . . . . . . . . 24 Theoretical lattice-fringe ngerprint plot of brookite . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Theoretical lattice-fringe ngerprint plot of rutile . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 (a) HRTEM image of a titania nanocrystal. (b) The Fourier transform of the area inside the white square. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Indexed Fourier transform of the region in gure 4.4 assuming [111] rutile. . . . . . . . . . . . . . 26 Lattice-fringe ngerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Averaged lattice-fringe ngerprint plot from titania images . . . . . . . . . . . . . . . . . . . . . . 27 Theoretical lattice-fringe ngerprint plot of magnetite . . . . . . . . . . . . . . . . . . . . . . . . . 29 Theoretical lattice-fringe ngerprint plot of maghemite . . . . . . . . . . . . . . . . . . . . . . . . 30

3.3 3.4

3.5 3.6

4.1 4.2 4.3 4.4

4.5 4.6 4.7 4.8 4.9

viii

Figure

Page

4.10 (a) HRTEM image of iron oxide nanocrystal. (b) Fourier transform of the nanocrystal. . . . . . . . 31 4.11 Lattice-fringe ngerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 32 4.12 Lattice-fringe ngerprint plot of magnetite in the 211 direction . . . . . . . . . . . . . . . . . . . 32 4.13 Indexed Fourier transform of an image of a magnetite nanocrystal . . . . . . . . . . . . . . . . . 33

4.14 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 34 4.15 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 35 4.16 (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image. . . . . . . . 36

4.17 Lattice-fringe ngerprint plot from iron oxide nanocrystal . . . . . . . . . . . . . . . . . . . . . . . 37 4.18 Indexed Fourier transform of the nanocrystal in gure 4.16 . . . . . . . . . . . . . . . . . . . . . . 37 4.19 (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image. . . . . . . . 39

4.20 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 40 4.21 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 41 4.22 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 42 4.23 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 43 4.24 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 44 4.25 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 45 4.26 (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image. . . . 46 4.27 Symmetry elements of the pg two-dimensional space group . . . . . . . . . . . . . . . . . . . . . 47 4.28 (a) Simulated image of GaN, 5 nm thickness oriented along [010]. (b) The indexed Fourier transform of the image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 4.29 Fourier transform with measured phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 4.30 HRTEM image of a titania nanocrystal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

ix

List of Symbols Symbol Page 6 9 6 9 6 4 4 9 9 9 9 3 3 3 5 4 4 5

a aj

Diameter of the objective aperture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Parameter for the t of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

A(u) Aperture function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . bj Cs


Parameter for the t of f e (s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Spherical aberration of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

dhkl Lattice-plane spacing of the (hkl) planes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . e


Elementary charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

f () Atomic scattering factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . f e (s) Atomic scattering factor for electrons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . fX


Atomic scattering factor for x-rays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

F (g ) Structure factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . F
Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

F 1 Inverse Fourier transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . g


Three-dimensional position vector in reciprocal space . . . . . . . . . . . . . . . . . . . . . . . .

g hkl Reciprocal-space vector for the planes with indices hkl . . . . . . . . . . . . . . . . . . . . . . . h


Plancks constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

hkl Miller indices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . I


Intensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Symbol

Page 4 7 4 3 9 7 6 6 6

Relativistic electron mass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Puvw Probability of seeing a family of zone axes uvw

qe (r ) Specimen transmission function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . r s t


Three-dimensional position vector in direct space . . . . . . . . . . . . . . . . . . . . . . . . . .

|g |/2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Crystal thickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

t(r ) Spread function of the objective lens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T (u) Microscope transfer function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . u w
Two-dimensional vector in the back focal plane of the objective lens Weighting factor . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Xkl Complex Fourier coefcient of the pixel at (k, l) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 max Visibility band half-width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (u) Phase-distortion function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Dirac delta function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 6 6

Difference parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

tot Total difference parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 f


Objective lens defocus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 9

obs Observed phase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 res Phase residual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 sym Phase determined from symmetry relations and restrictions . . . . . . . . . . . . . . . . . . . . . 19
xi

Symbol

Page 4 4 6 7 4 7 4 4 6 6 7 6 4 4 3

(r ) Electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . p (r )Projected electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . p 0


Fourier transform of the projected electrostatic potential . . . . . . . . . . . . . . . . . . . . . . . Visibility factor in calculating lattice-fringe visibility band half-widths . . . . . . . . . . . . . . . . . Wavelength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Solid angle subtended by the intersection of two visibility bands . . . . . . . . . . . . . . . . . . . Wave incident on the specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

ex Exit-surface wave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . im Image plane electron wave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ex Fourier transform of ex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . im Fourier transform of im . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sch Scherzer, or point, resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interaction constant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Angle between the incident wave vector and the lattice planes . . . . . . . . . . . . . . . . . . . . Convolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

xii

Chapter 1 Introduction

This thesis deals with a method of identifying nanocrystals using lattice fringes observed in high-resolution transmission electron microscopy (HRTEM) images. Since these lattice fringes are used to uniquely identify a nanocrystal, the method is named lattice-fringe ngerprinting. The interest in nanometer-sized crystals has increased over the last several years. Nanocrystals are appealing for their novel and improved physical, chemical, and biological properties relative to those of the materials in their bulk form. New identication methods are needed for ensuring quality and reproducibility in the production of these particles. Novel methods are particularly desirable for any large-scale commercial manufacturing process. These new identication methods should preferably require minimal operator skill and supervision (Saltiel and Giesche, 2000). The goal of lattice-fringe ngerprinting is to meet these needs using HRTEM.

1.1

Overview of the Method

To identify nanocrystals, lattice-fringe ngerprinting uses the information contained in crossed lattice fringes that appear in HRTEM images. Lattice fringes are caused by the diffraction of the incident electrons by the specimen and appear as periodic light and dark bands in the image. Crossed lattice fringes are formed by the intersection of two or more sets of lattice fringes. Crossed lattice fringes will be visible when the nanocrystal is oriented close to a zone axis. The primary information used in lattice-fringe ngerprinting is the spacing of the lattice fringes and the angle between intersecting lattice fringes (i. e., the interfringe angle). This information is characteristic of the crystal structure. Instead of working with the actual images, it is more convenient to use the Fourier transform of the HRTEM image, calculated using the fast Fourier transform (FFT) algorithm. When the spacings and angles are not sufcient to identify a nanocrystal, and the nanocrystal is suitably thin, the phase information in the Fourier transform of the image can be used. Determining the phase correctly requires the determination of the origin of a unit cell in the nanocrystal. For an ensemble of nanocrystals another way of making use of lattice fringes is to compare the abundance of visible lattice fringes with calculated probabilities based on the theory of lattice-fringe visibility (Fraundorf et al., 2005).

1.2

Review of Standard Methods

Powder X-ray diffraction is the standard method of identifying crystal structures. This method works best for micrometer-sized crystals and becomes less useful for crystals in the nanometer range, as demonstrated, for example, in Lpez Prez et al. (1997). Powder x-ray diffraction gives the lattice-plane spacings and the corresponding intensities, but does not provide the interplanar angles as in lattice-fringe ngerprinting. X-rays are also much less sensitive than electrons to changes in the electrostatic potential.

Parallel-illumination electron diffraction is also used to identify crystal structures. This can be done by comparing the diffractogram with values calculated from known structures in a database. This process has been automated by, for example, Hart (2002) using the two smallest reciprocal lattice spacings and the angle formed by the intersection of these two planes. The information from electron diffraction patterns is often combined with knowledge of the chemical composition of the material gained using energy-dispersive x-ray spectroscopy or electron energy-loss spectroscopy. Single crystals down to a size of a few tenths of a micrometer can be identied using parallel-illumination electron diffraction. Smaller crystals, on the order of tens of nanometers, can be identied using electron powder diffraction, but these ring patterns only give the lattice-plane spacings. Convergent-beam electron diffraction (CBED) is also used in studying crystals. The ne structure of the CBED disks can be used to identify the crystal. However, CBED patterns of nanocrystals are usually devoid of this ne structure (Williams and Carter, 1996).

1.3

Overview of Experimental Procedures

To study lattice-fringe ngerprinting, HRTEM images of three different materials were examined: titania (titanium dioxide), iron oxide and gallium nitride. The images of titania were taken using an FEI G2 F20 TEM equipped with a eld-emission gun at Portland State University, with a point resolution of 0.24 nm. Some images of iron oxide nanocrystals were taken at the University of Missouri-St. Louis using a Philips EM 430ST, with a LaB6 electron source and a point resolution of 0.19 nm. Other iron oxide images were taken at Technische Universitt Chemnitz on a eld-emission Philips CM20 TEM. Theoretical HRTEM images of gallium nitride were simulated using WebEMAPS (Zuo and Mabon, 2004). Gatan Digital Micrograph was used to process and analyze HRTEM images. The built-in scripting support of Digital Micrograph made it possible to automate parts of the lattice-fringe ngerprinting process.

Chapter 2 High-Resolution Transmission Electron Microscopy

The underlying idea of high-resolution transmission microscopy is using both the direct electron wave and several diffracted electron waves in forming the image. This increases the resolution of the image. The electron waves interfere with one another due to phase differences, creating an interference pattern in the image plane of the objective lens. HRTEM is therefore a type of phase-contrast microscopy. Electron scattering must be treated quantum mechanically. Actually, a 200 keV electron has a speed of approximately 0.7c, where c is the speed of light in vacuum, and should therefore be treated using relativistic quantum mechanics. However, in electron microscopy it is normally sufcient to just replace the mass and wavelength of the electron with corresponding relativistic values (De Graef, 2003, p. 94).

2.1

The Fourier Transform

The Fourier transform plays an important role in HRTEM. It is a convenient tool for analyzing images, but it also plays a more fundamental role in HRTEM theory. There are a number of different conventions when using the Fourier transform. Here the convention most common in crystallography will be used. The Fourier transform of a function f (r ) is then dened as

F (g ) = F [f (r )]

f (r )e2igr dr ,

(2.1)

where r is a three-dimensional position vector in direct space and g is a three-dimensional position vector in Fourier transform, or reciprocal, space. The inverse Fourier transform is dened as

f (r ) = F 1 [F (g )]

F (g )e2igr dg .

(2.2)

When Fourier transforming a set of sampled data, the discrete Fourier transform (DFT) must be used instead of the continuous Fourier transform above. The most common implementation of the DFT on computers is the fast Fourier transform (FFT) algorithm. The convolution is important to understanding HRTEM. The convolution, or folding, of two functions, f (r ) and h(r ), is dened as

f (r ) h(r ) =

f (R)h(r R) dR.

(2.3)

There is a useful theorem relating the convolution in direct space to multiplication in Fourier transform space called the convolution theorem: F [f (r ) h(r )] = F (g ) H (g ). (2.4)

The multiplication theorem relates multiplication in direct space to convolution in Fourier transform space:

F [f (r ) h(r )] = F (g ) H (g ).

(2.5)

2.2

Kinematical Scattering

In one approach to quantum scattering, the wave equation is converted to integral form using the Greens function. This integral equation can then be expanded into the Born series. As a rst-order approximation, only the rst term of the Born series is used, the so-called rst Born approximation. This is equivalent to assuming the electron is scattered no more than once when passing through the specimen. This is called single, or kinematical, scattering. Using only the rst term of the Born series also assumes that the directly transmitted electron wave can be reasonably approximated by the incident wave. In other words, the amplitude of the diffracted waves is negligible compared to the amplitude of the direct wave. The rst Born approximation is equivalent to the Fraunhofer diffraction approximation, where the diffracting object is assumed to be much smaller than the distances to the source and the point of observation (Cowley, 1981). From the expression for Fraunhofer diffraction one can derive the phase-object approximation (POA). The POA gives the specimen transmission function, qe (r ), as

qe (r ) = eip (r) ,

(2.6)

where is the interaction constant and p (r ) is the projection of the electrostatic potential of the specimen, (r ), along the direction of the electron beam. The interaction constant is dened as

2me , h2

(2.7)

where m is the relativistic mass of the electron, e is the elementary charge, is the electron wavelength and h is Plancks constant. As the name implies, the phase-object approximation assumes that only the phase of the complex electron wave is affected when moving through the specimen. If the incident wave is 0 (r ) and the exit-surface wave is ex (r ) then, in the POA, ex (r ) = qe (r ) 0 (r ). Since 0 (r ) is assumed to be constant, we can set it equal to unity. Then, ex (r ) = qe (r ). If we assume that p (r ) is much less than unity we can approximate (2.6) using the rst-degree Taylor polynomial of qe (r ): qe (r ) 1 ip (r ). (2.8) This is called the weak phase-object approximation (WPOA). The assumption that p (r ) is small holds for many thin specimens. However, it fails for an electron passing through the center of even a single uranium atom (Williams and Carter, 1996, p. 462). For specimens that are too thick for the WPOA to hold, Li and Tang (1985) proposed the pseudo-weak phase-object approximation. This approximation takes into account that as the specimen thickness increases beyond the limits of the validity of the WPOA, the heavy atoms start looking more like lighter atoms and vice versa. The specimen is therefore replaced by its imaginary isomorph. The diffraction of electron waves by a crystal can also be understood in terms of Braggs law. Electron waves diffracted by a set of parallel planes with Miller indices hkl will add constructively if the path difference between waves diffracted by separate planes is a multiple of the wavelength. Hence,

2dhkl sin = n,

(2.9)

where dhkl is the lattice-plane spacing of (hkl), is the angle between the incident wave vector and the lattice planes and n is an integer.

A set of parallel lattice planes belongs to a certain zone axis if the planes are parallel to that zone axis. This is known as the Weiss zone law. A set of parallel lattice planes can be described by a three-dimensional reciprocal-space vector g hkl = ha + k b + lc , where |g hkl | = 1/dhkl , that is normal to the set of lattice planes. a , b and c are the basis vectors of reciprocal space. It follows that g must be perpendicular to the zone axis direction [uvw] = ua + v b + wc, where a, b and c are the basis vector of direct space. Using a generalized dot product, this gives hu + kv + lw = 0.

2.3

Dynamical Scattering

If the specimen is so thick or massive that electron waves are scattered more than once, the kinematical approximation no longer holds and we must consider multiple, or dynamical, scattering. The extent of dynamical effects depends on the magnitude of (r ). Since a constant term can be added to the electrostatic potential, it is actually the variation of (r ) that matters. If the crystal is perfectly aligned with the incoming beam parallel to a zone axis, (r ) will change from a relatively large value at the atomic columns to a much smaller value between the columns. If the crystal is tilted slightly away from the zone axis so that the atomic columns appear as lines instead of points, the dynamical effects will be reduced since the variations in (r ) are smaller. Dynamical scattering results in the presence of a kinematically extinct reection h3 k3 l3 that is the result of diffraction of the electron wave by two or more sets of planes. For example, in the case of double diffraction, the wave is rst diffracted by the planes (h1 k1 l1 ) and then by the planes (h2 k2 l2 ) according to the following equations:

h3 k3 l3

= h1 + h2 , = k1 + k2 , = l 1 + l2 .

(2.10)

This means that reections that are kinematically forbidden due to the presence of screw axes or glide planes will be present in the diffraction pattern of a crystal that scatters dynamically. However, kinematically forbidden reections due to unit-cell centering (Sands, 1993) do not appear in dynamical scattering (Denley and Hart, 2002). The reection conditions imposed by the different types of cell centering are listed in table 2.1 Type of centering Condition limiting possible reections

A B C I F

k + l = 2n h + l = 2n h + k = 2n h + k + l = 2n h + k, k + l, l + h = 2n

Table 2.1: Reection conditions due to cell centering. These conditions apply to all reections hkl.

2.4

Imaging

The purpose of HRTEM is the imaging of the electron waves. Using lm, or more commonly a CCD camera, the intensity I (r ) = |im (r )|2 , of the waves is recorded, where im (r ) is the electron wave reaching the

detector. In order to identify a nanocrystal from HRTEM images, these intensities must be related back to the crystal structure. However, before the exit-surface waves reach the recording medium, they are focused by the objective lens and magnied by the projection system. The effect of the projection system on the electron wave is small compared to the effect of the objective lens. im (r ) can therefore be taken to be the electron wave in the image plane of the objective lens. The effect of the objective lens is the convolution of the exit-surface wave with a spread function, t(r ), of the objective lens: ex (r ) t(r ). Using the convolution theorem we can write

im (r ) = ex (r ) t(r ) = F 1 [ex (u) T (u)] ,

(2.11)

where ex (u) is the Fourier transform of ex (r ) and T (u) is called the transfer function of the microscope. u is a two-dimensional vector in the back focal plane of the objective lens. The transfer function of a perfectly coherent microscope can be expressed as the product of an aperture function A(u), due to the objective aperture, and a phase factor exp{i(u)}, due to the defocus and aberrations of the objective lens. The aperture function is a simple step function with a value of unity for u < a/2, where a is the diameter of the objective aperture, and zero everywhere else. The phase factor will depend on the defocus and any aberrations of the objective lens. Assuming the two-fold astigmatism has been corrected for, the spherical aberration, Cs , will be the most signicant aberration of the objective lens. If we only take the defocus and Cs into account, then

1 (u) = f u2 + Cs 3 u4 , 2

(2.12)

where f is the defocus of the objective lens. Williams and Carter (1996) call (u) the phase-distortion function. Following Cowley (1988), we rewrite the spread function as the sum of a real and imaginary part: t(r ) = c(r ) + is(r ), where c(r ) = F [A cos (u)] and s(r ) = F [A sin (u)]. Using this expression we can nd a simple relationship between an image and the projected electrostatic potential in the range of validity of the WPOA. Since ex (r ) = qe (r ) = 1 ip (r ), I (r ) = |[1 ip (r )] [c(r ) + is(r )]|2 . Multiplying this out and ignoring terms of [p (r )]2 since we assume this product is small, we get I (r ) = 1 + 2p (r ) s(r ). Hence, taking the Fourier transform we get

F [I (r )] = (u) + 2p (u) A(u) sin (u),

(2.13)

where p (u) is the Fourier transform of the projected electrostatic potential. The Dirac delta function, , corresponds to the central direct beam. Such a simple linear relationship between the projected electrostatic potential and the image is only possible when the WPOA is valid. From equations (2.12) and (2.13) we see that the presence or absence of information in the image depends on the complicated oscillations of sin (u), often called the contrast transfer function (CTF). Scherzer (1949) showed that these oscillations can be suppressed out to a limit uSch by suitable adjustment of the defocus. The so-called Scherzer defocus is f =
1 4 4 3 Cs .

The rst crossover of sin (u) will then occur at uSch =

1.51(Cs 3 ) . Taking the reciprocal of this gives the Scherzer or point resolution of the microscope: Sch = 1 0.66(Cs 3 ) 4 . Images with spacings greater than Sch are said to be directly interpretable.
A real microscope will not have a perfectly coherent electron source. This means that there will be a range of values for the kinetic energy of the electrons and there will be a certain spread of angles from the source. These imprecisions will affect the transfer function, T (u), of the microscope. There is no simple way of expressing this effect in general. However, in the case of the WPOA these effects can be represented by envelope damping functions that are multiplied by the transfer function. The most important of these are the envelope functions due to chromatic aberration and the angular spread of the source.

The envelope functions put an absolute limit on the information obtainable from a specimen. In an eld emission gun (FEG) TEM the information-limit resolution is often much greater than the Scherzer resolution of the microscope. This makes it important to be careful when interpreting an image from such a microscope. It is possible to dene a third type of resolution in HRTEM that is due to dynamical scattering effects. This is called fringe resolution (OKeefe, 1992). This name is derived from the fact that it is the smallest spacing between lattice fringes visible in the image. In dynamical scattering the diffracted beams are not necessarily much weaker than the direct beam. These diffracted beams can therefore interfere with one another creating peaks in the image intensity spectrum (i. e., Fourier transform of the image) beyond spatial frequencies passed by the transfer function. This non-linear interference might be understood from the general equation for the image intensity spectrum, I (u) = F [im (r )im (r )] = F [im (r )] F [im (r )] = im (u) im (u), where in this case denotes the complex conjugate and im is the Fourier transform of im . The convolution of one diffracted beam with another diffracted beam will give an intensity spectrum peak with a spatial frequency |u|, possibly larger than the spatial frequencies of the diffracted beams.

2.5

Lattice-Fringe Visibility

The theory of lattice-fringe visibility developed by Fraundorf et al. (2005) is potentially useful for the identication of nanocrystals. This theory calculates the probability of seeing a set of lattice fringes for a randomly oriented nanocrystal using the concept of lattice-fringe visibility bands. A visibility band is the solid angle consisting of the ensemble of electron beam incident directions for which a set of parallel lattice planes is visible (gure 2.1). Assuming a spherical crystal, this visibility band will be symmetric about a great circle. The visibility-band half-width is given as

max = arcsin d

+ 1 d t 2d t

(2.14)

where t is the crystal thickness and is a visibility factor taking into account non-ideal imaging conditions. /2+max 2 The solid angle subtended by a visibility band with half-width max is /2max sin dd = 4 sin max . 0 The probability of seeing a family of symmetrically equivalent planes {hkl} with spacing d is therefore sin max times the multiplicity of the planes. The solid angle, , subtended by the intersection of two visibility bands with half-widths max and max intersecting at an angle is approximately given by the equation

2(2max )(2max ) . sin

(2.15)

The probability, Puvw , of seeing a family of zone axes uvw is therefore

Puvw =

2max max (multiplicity) . sin

(2.16)

Figure 2.1: Lattice-fringe visibility band (shaded) for a set of lattice planes parallel to the great circle shown passing through A. The sphere represents all possible electron beam directions incident on the specimen (converging on O). The lattice fringes are visible when the electron beam passes through the visibility band. The visibility-band half-width, AOB , is equal to max in (2.14). The solid angle subtended by the visibility band is 4 sin max (Fraundorf et al., 2005).

2.6

Fourier Coefcients of the Electrostatic Potential

The atomic scattering factor, f (), gives the probability of scattering by a single atom at a certain angle . By using Braggs law (2.9), we can relate this scattering angle to a set of parallel planes with normal vector g . For the scattering of electrons by atoms, the atomic scattering factor, f e , is dened as the Fourier transform of the electrostatic potential (Cowley, 1981):

f e (g ) =

(r )e2igr dr .

(2.17)

From this one can derive the Mott-Bethe formula as given by De Graef (2003):

f e (s) =

|e| 16 2
2 0 |s|

Z f X (s) ,

(2.18)

where s = |g |/2, e is the elementary charge and f X is the atomic scattering factor for x-rays. Instead of using (2.18) directly, this equation is typically parametrized with a set of Gaussians. One such parametrization, by Doyle and Turner (1968), gives the scattering factors as
4

f (s) = 0.04787 801


j =1

aj ebj s ,

(2.19)

where aj and bj are listed for each element in a table. From the atomic scattering factors for single atoms, one can calculate the scattering due to a whole unit cell assuming kinematical (i. e., single) scattering. This is called the structure factor, F (g ), and is a summation of f e (g ) over all the atoms in the unit cell located at positions ri :

F (g ) =
i

fie eii =
i

fie e2igri .

(2.20)

The different positions of the atoms in the unit cell give a path difference between contributions from different scattering centers. These path differences give rise to the phase, , of the structure factor. It is apparent from (2.20) that the structure factor of a centrosymmetric unit cell will be real since the contribution to the imaginary part from an atom at r will be canceled by the contribution from the symmetrically equivalent atom at r : f e e2igr + f e e2ig(r) = 2f e cos(2 g r ). (2.21) In the weak phase-object approximation, the structure factor corresponding to a set of parallel planes (hkl), F (g hkl ), is proportional to p (u) in equation (2.13), the Fourier transform of the projected electrostatic potential, p (r ). This means that the structure factor amplitudes should, in theory, be obtainable from the amplitudes of the peaks in the Fourier transform of an HRTEM image. However, the amplitudes are strongly affected by oscillations of the transfer function and crystal tilt (Zou and Hovmller, 2002). The phase of p (u) is much more reliable though. Oscillations of the transfer function and zone axis misalignment only lead to phase shifts in jumps of 180 (Zou, 1995). For small tilts, the phases are unaffected. Hence, the Fourier coefcient phases will either equal the structure factor phases or differ by 180 . The phases of peaks in the Fourier transform of HRTEM images can therefore assist in the identication of nanocrystals. The fact that the structure factor phases are preserved in a TEM image was rst noted by De Rosier and Klug (1968).

Chapter 3 Lattice-Fringe Fingerprinting

Lattice-fringe ngerprinting is the name given to the method of identifying nanocrystals using high-resolution phase-contrast TEM images. There are different pieces of information that can be used in this method. These different pieces are lattice-fringe vectors, lattice-fringe probability, in the case of studying many nanocrystals, and phases of the Fourier coefcients of the image. The identication of an unknown nanocrystal becomes more likely if more of the available information in the image is used. Identifying an unknown nanocrystal using lattice-fringe ngerprinting is only possible with a database of lattice-fringe ngerprinting information. A crystallographic database containing lattice-fringe ngerprint information combined with search/match algorithms is therefore a work in progress in the Nanocrystallography Group at Portland State University. A owchart outlining the steps involved in lattice-fringe ngerprinting is shown in gure 3.1.

3.1

Lattice-Fringe Vectors

The main component of lattice-fringe ngerprinting is using the characteristic spacing between lattice fringes and the angles at which different sets of lattice fringes intersect. Areas showing crossed lattice fringes are used since lattice-fringe spacings are more reliable when the nanocrystal is oriented close to a zone axis (Malm and OKeefe, 1997). The measurements can be made by directly inspecting the high-resolution image, but it is much more convenient to work in reciprocal space by means of the Fourier transform. A fast Fourier transform (FFT) is therefore computed of a region showing crossed lattice fringes after appropriate lters have been applied to the image (gure 3.2). Any periodicity in the image will show up as peaks in a plot of the modulus of the Fourier transform, also called the power spectrum. Each set of lattice fringes is transformed into two diametrically opposed peaks in the power spectrum. The radial positions of the peaks can then be measured. The distance from each peak to the center of the Fourier space corresponds to the inverse spacing between the lattice fringes. The angles between the different sets of lattice fringes, the interfringe angle, can also be found by measuring the central angle between the peaks of the power spectrum. Fourier coefcients on opposite sides of the center are conjugate pairs. Therefore, not all of the peaks and angles in the power spectrum need to be measured. The lattice-fringe spacing corresponds to the reciprocal lattice spacing, ghkl , of a set of parallel planes (hkl). The reciprocal lattice spacing and interfringe angles can be displayed in a lattice-fringe ngerprint plot, in which interfringe angle is plotted versus reciprocal spacing (Fraundorf et al., 2005). Intersections between two lattice fringes of different spacing appear as two data points in the lattice-fringe ngerprint plot, whereas intersections between two symmetrically equivalent lattice fringes give only a single data point in the plot. The lattice-fringe ngerprint plot provides a convenient way of displaying recorded data and facilitates the comparison between experimental data and theoretical lattice-fringe ngerprint plots calculated from lattice parameters. Measuring the reciprocal lattice vectors using the power spectrum is a common method in high-resolution electron microscopy. In fact, before the widespread use of computers a diffractogram of an image was

10

HRTEM image

Find crossed lattice-fringes

Run hanning_FFT script

Select rectangular region

Select Fourier transform peaks

Run measure_FT script

Measure relative abundance of zone axes

Find origin and measure phases

Match

Compare with calculated data

Figure 3.1: Lattice-fringe ngerprinting owchart.

11

created by using a light source and the image on a transparent lm as a diffraction grating on an optical bench. Using the FFT, one can make much more precise measurements. This precision can be increased through so-called sub-pixel interpolation.

12

004
Interfringe angle

0 22

022 45 000

0 40

0 40

0 2 2 00 4
(a) (b)

02 2

90 80

Interfringe angle (degrees)

70 60 50 40 30 20 10 0 5.0

Intersection of symmetrically equivalent {022} planes

Intersection of symmetrically equivalent {004} planes

Intersection of {022} and {004} planes

5.5

6.0

6.5

7.0

7.5

g (nm )
(c)

-1

Figure 3.2: (a) Simulated HRTEM image of silicon in the [100] orientation (Zuo and Mabon, 2004). (b) Fourier transform of the HRTEM image. The contrast has been inverted for clarity. The dashed lines represent reciprocal lattice vectors. We see, for example, that the (022) and (004) lattice fringes intersect at an interfringe angle of 45 . (c) Lattice-fringe ngerprint plot based on measurements of the Fourier transform.

13

3.2

Sub-Pixel Interpolation

Precision is an obvious concern when measuring reciprocal lattice vectors. Measuring the reciprocal lattice vectors is equivalent to determining the peaks of the power spectrum. Sub-pixel interpolation, as applied by de Ruijter (1994) to two-dimensional lattice-fringe images, was used to make these measurements. This method determines a more precise position of each individual peak. It is also possible to rene the positions of all the peaks in the power spectrum by using a least-squares method to t the peaks to a periodic grid. This could perhaps be used in conjunction with sub-pixel interpolation, but has not been implemented in this thesis. To use sub-pixel interpolation, the average intensity must rst be subtracted from the image. There will usually be artifacts caused by the edges of the Fourier transformed region because the Fourier transform assumes the transformed region repeats indenitely. This edge effect appears as streaking of the power spectrum peaks. This causes the intensity of the peaks to decrease. To reduce this effect, the image selection should be multiplied by a circular window function before Fourier transforming. The two-dimensional hanning window

Wh (m, n) = 1 cos 2

m M

1 cos 2

n N

(3.1)

is suitable for this purpose. Here M and N are the total number of pixels in the m and n direction, respectively (gure 3.3). Sub-pixel interpolation starts with the brightest pixel of a power spectrum peak as a rst-order approximation. A more accurate position of the power spectrum peak is determined by interpolating between the nearestneighbor pixels under the assumption that the intensity in the image varies sinusoidally (gure 3.4). If the position of the brightest pixel is (k, l), fractions of a pixel, k and l , are added in each direction. Thus, the interpolated power spectrum peak will be located at (k + k , l + l ). k and l are given by the expressions (de Ruijter, 1994)

c1 |Xk+,l | c2 |Xkl | , c3 |Xk+,l | + |Xkl | c1 |Xk,l+ | c2 |Xkl | , c3 |Xk,l+ | + |Xkl |


(3.2)

where Xkl is the complex Fourier coefcient of the pixel located at (k, l), and = 1 and = 1 indicated the positions of the brightest neighbors of the brightest pixel. c1 , c2 and c3 depend on the window function used. For the Hanning window, c1 = 2 and c2 = c3 = 1. Sub-pixel interpolation can be used for more than just determining the position of power spectrum peaks. Interpolated values can also be found for the amplitude and the phase of the complex Fourier coefcients. These are given by

A = =

l 2|Xkl | k M N sin k sin l arg (Xkl ) + k + l ,

1k2

1l2 ,

(3.3) (3.4)

where arg(Xkl ) is the argument, or phase, of the complex Fourier coefcient. The terms involving in (3.4) are due to the position of the real-space origin in the upper left-hand corner ((0, 0) in gure 3.3) instead of in the center (de Ruijter, 1994, p. 200). To make use of sub-pixel interpolation, Digital Micrograph scripts were written that allow lattice-fringe spacings, angles, amplitudes and phases to be found for any number of selected power spectrum peaks (Appendix). Sub-pixel interpolation improves the precision of lattice-fringe measurements. The exact precision and accuracy of measurements of nanocrystals have been investigated in several papers. De Ruijter et al. (1995)

14

0 0

M 1

N 1
(a)

1.5

Wh

1 1

0.5

4
(b)

10 M

Figure 3.3: (a) Schematic of an M N pixel image. (b) Plot of the one-dimensional Hanning window m Wh (m) = 1 cos 2 M .

15

4 10

3 10

2 I10

1 10

l k 4 k 3 k -2 2 k 1 k 0.34
(a) (b)

0 k

2 2 k 3 k 4 4 k 1 k

Figure 3.4: (a) Closeup of a Fourier transform peak (without inverted contrast). The brightest pixel is at (k, l). (b) Plot of the intensity of the pixels along the horizontal line through (k, l) (black dots) and the interpolating intensity curve (solid curve) using the pixel values at k and k 1 to t the curve to the experimental data. k is found to be 0.34 using (3.2). In this case, = 1. The same method is applied in the vertical direction to determine l .

16

found for a 15x15 region of a reduced oxide phase a precision of 1 %3 % for the spacing and 0.5 2 for the angle. They concluded that the accuracy, i. e., deviation from expected values, in the measurements for such small crystals would depend more on thickness variations and misorientation than statistical deviations, such as shot noise. It is well-known that for nanocrystals the lattice parameters are dependent on the grain size. Tonejc et al. (2002) studied anatase nanocrystals with a grain size down to about 5 nm. They reported a deviation from the x-ray powder diffraction values of up to 1.4 % for the lattice parameter a, and up to 4.1 % for c. Lu and Zhao (1999) summarize results on lattice distortions found in the literature for various inorganic materials down to a grain size of 4 nm. None of the lattice parameters were distorted by more than 0.30 %. Table 3.1 shows the effect of a pessimistic distortion of 4.1 % of c in the case of rutile. Using more calculations like the ones shown, the average angle difference was found to be 0.7 , with a maximum angle difference of 2.4 .

hkl 110 110 101 10 1 110 101

g (nm1 ) 3.08 3.08 4.02 4.02 3.08 4.02

g (nm1 ) 3.08 3.08 4.14 4.14 3.08 4.14

hkl 1 10 011 011 101 020 200

g (nm1 ) 3.08 4.02 4.02 4.02 4.35 4.35

g (nm1 ) 3.08 4.14 4.14 4.14 4.35 4.35

Angle ( )

Angle ( )

Angle difference ( )

90.0 67.5 45.0 65.6 45.0 57.2

90.0 68.2 43.6 63.4 45.0 58.3

0.0 0.7 1.4 2.2 0.0 1.1

Table 3.1: The effect of lattice parameter distortions on rutile shown by comparing reciprocal lattice spacings, g , and interplanar angles. Values calculated using c decreased by 4.1 %. In an HRTEM image, there may also be a foreshortening of the lattice-fringe spacings when tilting away, perpendicular to the lattice fringes (i. e., perpendicular to the visibility band in gure 2.1 on page 8), from the edge-on view of the lattice fringes. The spacings will be shrunk by a factor of cos , where is the amount of tilt perpendicularly away from the edge-on view. The maximum foreshortening is therefore equal to cos max . This projection effect depends on the lattice-plane spacing and the thickness of the crystal, but calculations using (2.14) show that this effect will usually be less than half of one percent. For example, the {111} spacings of magnetite (d111 = 4.80 ) will be decreased by 0.49 %, assuming a visibility factor, , equal to unity and a crystal thickness of 5 nm. These calculations show that lattice parameter distortions due to nanocrystallinity will not make identication through lattice-fringe ngerprinting impossible.

3.3

Lattice-Fringe Visibility and Probability

The theory of lattice-fringe visibility, as described in section 2.5, can serve as the basis of an additional method of identifying nanocrystals. The solid angle subtended by crossed lattice fringes, multiplied by the multiplicity and divided by 4 , can be interpreted as the probability of seeing crossed lattice fringes in a randomly oriented spherical nanocrystal. This probability can be calculated using (2.15). The probability gives an idea of which zone axes are most likely to be observed. Experimental data on the visibility of crossed lattice fringes from a collection of many nanocrystals, such as a nanopowder, can then be compared with theoretical values. Combined with lattice-fringe vectors, this information can be used to conrm the identication of a crystal phase. The abundance of certain crossed

17

lattice fringes obtained from a limited set of nanocrystals cannot serve as a method of determining the crystal phase by itself, but it might serve as a check. The lattice-fringe visibility can also be included in a lattice-fringe ngerprint plot (Fraundorf et al., 2005).

3.4

Phases of the Fourier Coefcients of Images

The fast Fourier transform is a convenient tool for extracting information from high-resolution images. All the information contained in the image is contained in the complex Fourier coefcients of the FFT. The positions of the peaks can be used to measure the lattice-fringe vectors, whereas the Fourier coefcient amplitudes have been shown to be unreliable (Zou and Hovmller, 2002). The only other piece of information is the phase of the Fourier coefcients. The phase of a Fourier coefcient corresponding to a set of lattice fringes determines the position of the bright lines in the image. Equivalently, the phase determines the relative intensity of the lattice fringes at the origin of the FFT (gure 3.5). This is analogous to the oscillations of a spring, f (t) = A cos(t + ), where the phase, , determines the amplitude at t = 0.

origin

Figure 3.5: Simulated image showing sinusoidally varying fringes. If the upper left-hand corner is chosen as the origin, the phase of the fringes will be 180 , since the brightness is at a minimum at that point. This dependence on origin means that before phases measured from the FFT of an image can be compared with theoretical values, the origin of the image must be determined. The origin of the crystal is chosen to correspond to the unit cell origin given in the International Tables for X-ray Crystallography (Henry and Lonsdale, 1952). An HRTEM image is in the WPOA a two-dimensional projection of the crystal structure, therefore it is the origin of the projected symmetry that must be used. In order to nd the unit cell origin of a high-resolution image we adopt the method developed by Zou and Hovmller (2002) which is implemented in the computer program CRISP (Hovmller, 1992). In this approach the origin is found by minimizing the so-called phase residual, res . The phase residuals are calculated by using phase relations and restrictions present in each of the 17 two-dimensional space groups (table 3.2 on page 21). Each observed phase, obs , is compared to a phase determined from symmetry relations and

18

restrictions, sym , using the formula

[w(hk )|obs (hk ) sym (hk )|] res =


hk

w(hk )
hk

(3.5)

where w(hk ) is the weighting factor given to the reection (hk ).1 In the case of a centrosymmetric space group for example, sym is set to either 0 or 180 . For non-centrosymmetric space groups, the phases can take on any value (from 180 to 180 ). If there are no symmetry relations or restrictions for a given reection, sym is set equal to obs . Hence, this reection is not used in calculating the phase residual. The phase residual is calculated for each possible unit cell origin for each of the 17 two-dimensional space groups since the phase relations and restrictions are different for each of these space groups, giving different sym . Hence, the projected symmetry is determined in addition to the unit cell origin. After the FFT of the image is calculated using the correct two-dimensional space group origin, the symmetrized phases, sym , can be compared to theoretical values. However, if the two-dimensional space group origin is not a unique point, but for example a line, it is not useful in general to compare the symmetrized and theoretical phases. This is the case only for the two-dimensional point groups 1 and m. The phases of Fourier transform peaks corresponding to planes parallel to the mirror or glide line are not affected by this limitation though. The defocus of the objective lens is important when using the phases. A change in sign of the contrast transfer function will result in a 180 phase shift. There are two general ways of dealing with this. Either full-edged CTF correction can be applied to the high-resolution image using software such as CRISP before measuring the phases, or the measured phases in bands of reversed contrast are simply shifted 180 . The spatial frequencies for which the contrast is reversed is in practice found by looking at the Fourier transform of an amorphous region. The contrast reversal, that is sin = 0, will coincide with the middle of the dark circular bands in the power spectrum (gure 3.6). In the case of simulations, the CTF is known and can be used to shift the phases of the peaks in the regions of reversed contrast. When the CTF is negative, such as in the large band at Scherzer defocus, the phases are shifted 180 from the theoretical phases. Another parameter one might think would affect the phases, is crystal tilt. When a crystal zone axis is not perfectly aligned along the incident direction of the electron beam the atomic columns appear as lines instead of points in the image. Being off the axis will decrease the intensity of some of the diffracted beams, this makes the amplitude of Fourier coefcients sensitive to tilt. The phases, however, are not as sensitive to tilt. Zou (1995, pp. 5054) show using a simple model that the phases of thin crystals are not severely affected by crystal tilt. If the tilt of the crystal is known, it can be corrected for. The tilt can be determined from the amplitudes of the peaks in the Fourier transform.

1 The indices hk are only used to index the two-dimensional Fourier transform and are not necessarily related to the Miller indices of the lattice planes.

19

(a)
1

1
k nm
1

1.0

2.0

3.0

4.0

5.0

6.0

7.0

8.0

9.0

10.0

(b)

Figure 3.6: (a) Fourier transform of a TEM image of amorphous carbon lm showing the dependence of the contrast transfer function on the magnitude of u (i. e., distance from the center of the Fourier transform). The arrows point to the rst two zero crossings of the contrast transfer function. (b) Simulated graph of a contrast transfer function at Scherzer defocus. The black areas correspond to a positive contrast transfer function where the structure factor phases are not shifted. The graph was created using the Contrast Transfer Function Explorer by Sidorov (2002)

20

No. 1 2 3 4 5 6 7 8 9 10 11 12 13

Space group p1 p2 pm pg cm pmm pmg pgg cmm p4 p4m p4g p3

Point group 1 2

Origin on 1 at 2 on m

Phase relations -

Phases 0 or

180
All

) (hk ) = (hk ) + k 180 (hk ) = (hk ) (hk ) = (hk ) (hk ) = (hk ) + k 180 (hk ) = (hk ) + (h + k ) 180 (hk ) = (hk ) (hk ) = (hk ) (hk ) = (kh ) = (hk ) (hk ) = (kh )= (hk ) = (kh ) + k 180 (hk +k ) = (hk ) = (k, h + k, h) (h +k ) = (hk ) = (k, h ) (h + k, h) = (k h +k ) = (hk ) = (k, h (h + k, h) = (kh) +k ) = (hk ) = (k, h (h + k, h) +k ) = (hk ) = (k, h (h + k, h) = (kh)

(h0) (h0) (h0)


All All All All All All All -

on g on m at 2mm at 2

2mm

at 2 at 2mm

at 4 at 4mm

4mm

at 4 at 3

14

p3m1 3m

at 3m1

(hh) ) (h2h (2kk ) ) (hh (h2h) (2kk )


All All

15

p31m

at 31m

16 17

p6 p6m

6 6mm

at 6 at 6mm

Table 3.2: Phase relations of the 17 two-dimensional space groups. After Zou (1995).

21

3.5

Database Support

A crucial component of the method of lattice-fringe ngerprinting is comparing experimental data with accepted values in order to identify the unknown structure. This requires a searchable database of known crystal structures. The database must contain the type of information used in lattice-fringe ngerprinting explicitly, or make it possible for such data to be derived. The Crystallographic Information File (CIF) format (Hall et al., 1991) of the International Union of Crystallography provides a convenient way for electronic storage and interchange of crystal structure information. Data on any crystal can be stored as a CIF. The format allows for basic denitions such as chemical composition, space group, equivalent positions and atomic positions. More advanced information can also be stored. The CIF format is used in the Crystallography Open Database (http://www.crystallography.net/). The format is also used in the Nano-Crystallography Database (NCD) being developed at Portland State University, where lattice-fringe ngerprint plots can be generated for an arbitrary resolution using the information contained in the CIFs.

3.6

Search/Match Procedure

The goal of lattice-fringe ngerprinting is to identify an unknown nanocrystal by comparing experimental data with the corresponding theoretical values for a set of candidate structures. There is therefore a need for search/match algorithms. This thesis does not attempt to provide a way to meet this need. However, a simple search algorithm based on pseudo-code given in De Graef (2003, p. 522) was implemented in order to compare lattice-fringe vector data. The simple program, working one zone axis at a time, rst nds the calculated lattice vector that best ts each experimental lattice vector. The best t for a certain experimental lattice vector is the calculated lattice vector that gives the lowest difference parameter, , where
2 2 2

=
i

(gi,exp gi,cal )

+ ((exp cal ) w ) .

(3.6)

The angle is given a weight, w , of 0.1 to take into account the difference in magnitude when lengths are measured in nanometers and angles in degrees. Once the best match for each experimental lattice vector has been found, the total difference parameter, tot , for the zone axis is calculated by simply summing the individual difference parameters together. This procedure is applied to all the different zone axis. The program then selects the zone axis with the lowest tot as the correct match. By expanding the search to zone axes of different crystal structures, this method can be used to nd the best match between measurements from the FFT of an image and one of many known crystal structures in a database. This algorithm was used to nd the best match of measured values to calculated values of magnetite and maghemite. Structure factor phase information can be included in this search by including an extra term in the radicand in (3.6). This algorithm works for a small database containing a limited number of crystal structures. For a database of a reasonable size however, this method is too inefcient. It might be easier to perform a coarse search rst using for example only the largest lattice vectors and angles in order to reduce the search space. More parameters can then be added to the search successively until the actual crystal structure is determined.

22

Chapter 4 Application of Lattice-Fringe Fingerprinting

To determine the possibilities and limitations of lattice-fringe ngerprinting, the method was applied to HRTEM images of three different materials: titania, iron oxide and gallium nitride.

4.1

Computer Implementation

Lattice-fringe ngerprinting HRTEM images was made easier by using Digital Micrograph scripts. Digital Micrograph is a proprietary computer program that is commonly used by electron microscopists for, among other things, analyzing TEM images. Three scripts were created (Appendix). One script calculates the Fourier transform of a selection after subtracting the average and multiplying by a Hanning window. The selection must be rectangular and the number of pixels along each side must be a power of two. The result of the Fourier transform is displayed in an image of the logarithm of the modulus of the Fourier coefcients, but the complex numbers are available and used for all further calculations. A second script nds the peak of the intensity spectrum inside each of several user-made selections using sub-pixel interpolation and measures the lattice-fringe spacings and angles. The lengths are measured in pixels and then divided by the dimensions of the Fourier transform in order to get a spatial frequency independent of the image size. The reciprocal of this spatial frequency will be proportional to the direct space lattice-fringe spacing. This length can then be multiplied by a scale factor, dependent on the magnication, to obtain the actual length. A third script gives the spacing, the amplitude and the phase of each of the intensity spectrum peaks. The amplitude and phase is calculated from the Fourier coefcients using (3.3) and (3.4). The origin of the Fourier transform in Digital Micrograph is always the upper left-hand corner of the selection.

4.2

Titania

The rst set of images that was analyzed was eight images of titanium dioxide, or titania, nanocrystals. These images were taken by Modesto Godinez at Portland State University.1 Titania crystallizes into three different structures, anatase (I 41 /amd, no. 141), brookite (P bca, no. 61) and rutile (P 42 /mnm, no. 136), where the numbers refer to the numbers assigned in the International Tables. Anatase and rutile are tetragonal whereas brookite is orthorhombic. Theoretical lattice-fringe ngerprint plots of these three crystal structures are shown in gures 4.14.3. To lattice-fringe ngerprint titania from the TEM images, areas with crossed lattice fringes were rst located. The appropriate scripts were then applied to measure the lattice-fringe spacing and angles. Six different regions showing crossed lattice fringes were found in three different images. A part of one image and the corresponding Fourier transform are shown in gure 4.4.
1 The

images were taken by Godinez under the supervision of Chunfei Li and Bjoern Seipel.

23

The magnication of the images was not known in advance. This meant that only the angles and the ratios of the lattice-fringe spacings could be used in determining the structure and not the actual spacings. Comparing the measurements from the three largest lattice-fringe spacings with calculated data for anatase, brookite and rutile, we nd two possible candidates for the structure: brookite in the [011] orientation and rutile in the [111] orientation. However, for brookite one would expect to see many more reections due to a larger unit cell, as is indicated by the lattice-fringe ngerprint plot in gure 4.2. This means that the nanocrystal probably is rutile. With this information the image magnication could be determined and the Fourier transform indexed (gure 4.5). None of the other nanocrystals showed the (2 1 1) reection. Using only the (1 10), (10 1) and (01 1) reections, the experimental data gives three clusters of data points in the lattice-fringe ngerprint plot (gure 4.6). These data correspond fairly well to the expected results from rutile oriented close to the [111] direction, as shown in the plot in gure 4.3. Assuming each of the three clusters correspond to three theoretical values, the average and standard deviation can be calculated (gure 4.7). The large spread of the experimental data might be due to the small size of the nanocrystals.
90

80

111 131 100

Interfringe angle (degrees)

70

100 131 100

60

331
50

40

100

30

100
2.8 3.0 3.2 3.4 3.6
-1

100
3.8 4.0 4.2

20

g (nm )

Figure 4.1: Theoretical lattice-fringe ngerprint plot of anatase, assuming kinematic scattering and 0.24 nm microscope resolution. The zone axis corresponding to each data point is indicated.

24

90 80

001 010 012 010

120 123 124 001 241

Interfringe angle (degrees)

70 60

011

124

50 40 30 20 10 2.0

011 001

001 121 001 120

110 123 124 101 231 231 241 011 312 010 213 213 120 011 251 251 102 412 100 011 011 102 102 231 231 120 120 101 101 011 001 110 121 110 231 231 011 124 211 211 120 112 011 100 010

001 100 100 010 201 201 120

012 324 312 412 100 100 124 124

112 100 010

011

010

2.5

3.0

3.5

4.0

4.5

g (nm )

-1

Figure 4.2: Theoretical lattice-fringe ngerprint plot of brookite, assuming kinematic scattering and 0.24 nm microscope resolution. The zone axis, or in some cases the zone axes, corresponding to each data point is indicated.

90

001

Interfringe angle (degrees)

80

70

111

111 100

60

50

111
40 3.0 3.2 3.4 3.6 3.8 4.0

g (nm )

-1

Figure 4.3: Theoretical lattice-fringe ngerprint plot of rutile, assuming kinematic scattering and 0.24 nm microscope resolution. The zone axis corresponding to each data point is indicated.

25

32.5 4.6
(a) (b)

30.2 24.2

Figure 4.4: (a) HRTEM image of a titania nanocrystal. The white square surrounds the Fourier transformed region. (b) The Fourier transform of the area inside the white square. A black circle marks the position of the weakest visible reection. The amplitude of the Fourier transform peaks, calculated using (3.3), is indicated next to the dark spots. The amplitudes of diametrically opposed points are identical, according to Friedels law and the symmetry of the two-dimensional Fourier transform.

10 1 0 1 1

2 1 1 1 10 000

Figure 4.5: Indexed Fourier transform of the region in gure 4.4 assuming [111] rutile.

26

70

Interfringe angle (degrees)

65

60

55

50

45

40 2.8 3.0 3.2 3.4 3.6


-1

3.8

4.0

4.2

4.4

g (nm )

Figure 4.6: Lattice-fringe ngerprint plot from titania images.

70

Interfringe angle (degrees)

65

60

55

50

45

40 2.8 3.0 3.2 3.4 3.6


-1

3.8

4.0

4.2

4.4

g (nm )

Figure 4.7: Averaged lattice-fringe ngerprint plot from titania images. The error bars correspond to one standard deviation in each direction.

27

4.3

Iron Oxide

Iron oxide exists in different crystal structures. Two of these are magnetite and maghemite. Magnetite, Fe3 O4 , is face-centered cubic with space group F d 3m (no. 227). Maghemite, -Fe2 O3 , is primitive cubic with space group P 41 32 (no. 213). These crystal structures have very similar lattice constants with a = 8.32 (Bragg, 1915) and a = 8.33 (Pecharromn et al., 1995), for magnetite and maghemite respectively. The only difference between the two crystal structures is a larger number of cation vacancies in maghemite. The iron oxide nanocrystals are known to exist in solid solution between magnetite and maghemite (Lovely et al., 2006). The objective of lattice-fringe ngerprinting was in this case to see whether it would be possible to distinguish between these two crystal phases. The rst set of images were taken by Eric Mandell at the University of Missouri-St. Louis using a Philips EM 430ST with a point resolution of 0.19 nm. This means that spatial frequencies out to 5.26 nm1 are directly interpretable. Kinematic lattice-fringe ngerprint plots of magnetite and maghemite are shown in gures 4.8 and 4.9. These plots are quite a bit more complex than the plots of rutile. In these plots, some lattice planes intersect multiple other lattice planes at the same angle. For example, the (022) planes intersect both (11 1) and (31 1) at 90 , in the [ 21 1] and [ 23 3] zone axis, respectively. Also, many of the data points are very close together. This makes it virtually impossible to identify these nanocrystals only by inspecting these lattice-fringe ngerprint plots. The lattice-fringe ngerprint plots become less crowded, however, if we consider a single zone axis at a time. That is, instead of trying to identify the crystal structure using all possible lattice plane intersections, we identify the crystal structure and the zone axis. Identifying the crystal structure from HRTEM images is then similar to indexing an electron diffraction pattern. Each nanocrystal must be identied separately since the nanocrystals might be oriented differently. First we consider four nanocrystals imaged with the Philips EM 430ST. The nanocrystal shown in gure 4.10 appeared in ve images acquired with slightly different goniometer settings. The lattice-fringe ngerprint plot that was obtained from Fourier transforms like the one in gure 4.10 is shown in gure 4.11. It is not evident from comparing this plot with gures 4.8 and 4.9 what the zone axis orientation is. However, if we consider only the 211 directions, as in gure 4.12, the plots look very similar. We then conclude that this nanocrystal consists mostly of magnetite oriented close to a 211 zone axis. We can then index the Fourier transform of the image of the nanocrystal as shown in gure 4.13. For maghemite in the 211 orientation, we would also expect to see the {110}, {210} and {321} planes. These reections are kinematically and dynamically forbidden in magnetite due to F -centering.2 Several other nanocrystals showing crossed lattice fringes were identied in a similar fashion. However, to make the process less tedious the search/match procedure outlined in section 3.6 was implemented. All the possible lattice-plane intersections were stored together with the zone axis in a data le, one for magnetite and another for maghemite. The experimental lattice-fringe vector measurements were stored in a different data le. A simple program which calculates the difference parameter in equation 3.6 for a measured latticefringe vector and the theoretical calculations was then used. The zone axes with the lowest total difference parameters were then studied more closely to determine the most likely match. This program was used in nding the best match for the nanocrystal pictured in gure 4.14. As it turns out, this nanocrystal is also oriented close to the 211 direction, as shown in the Fourier transform. What is interesting to note in this case though, is the faint presence of the ( 120) reection. As mentioned, this reection should not be seen in magnetite, but is expected in maghemite. The (01 1) reection is not seen, but the ( 120) reection suggests the presence of maghemite in this nanocrystal.
2 Reections that are forbidden due to centering might be present nonetheless due to atomic ordering. Such effects are not considered any further in this thesis.

28

A third nanocrystal is shown in gure 4.15. The corresponding Fourier transform shows three {022} planes intersecting at angles of 59.6 and 63.1 . The closest match is the intersection of three {022} planes at 60 in the 111 zone axis. A fourth nanocrystal is shown in gures 4.16. The lattice-fringe ngerprint plot is shown in gure 4.17. Using the computer program, the best match was found to be maghemite in a 332 orientation. This even though two expected reections are missing in the Fourier transform, as shown in gure 4.18. The (20 3) and ( 110) reections are not expected in magnetite, again due to F -centering. The absence of ( 330) might be due to a damping of the transfer function in this region. The 02 3 reection is also absent.
{111} {133}
5.0 5.5

{022}

{113} {222}

90 80

Interfringe angle (degrees)

70 60 50 40 30 20 10 2.0 2.5 3.0 3.5 4.0


-1

4.5

g (nm )
Figure 4.8: Theoretical lattice-fringe ngerprint plot of magnetite, F d 3m, assuming kinematic scattering and 0.19 nm microscope resolution. The plane family is indicated above the plot.

29

{004}

90 80

Interfringe angle (degrees)

70 60 50 40 30 20 10 0 1.5 2.0 2.5 3.0 3.5


-1

4.0

4.5

5.0

{033} {114} {133}


5.5

{112}

{013} {113} {222} {023} {123}

g (nm )

Figure 4.9: Theoretical lattice-fringe ngerprint plot of maghemite, P 41 32, assuming kinematic scattering and 0.19 nm microscope resolution. The plane family is indicated above the plot.

30

{004}

{011}

{111}

{012}

{022}

(a)

(b)

Figure 4.10: (a) HRTEM image of iron oxide nanocrystal. (b) Fourier transform of the nanocrystal.

31

90

Interfringe angle (degrees)

80

70

60

50

40

30 2.0 2.5 3.0 3.5


-1

4.0

4.5

g (nm )

Figure 4.11: Lattice-fringe ngerprint plot from iron oxide nanocrystal.

90

Interfringe angle (degrees)

80

70

60

50

40

30 2.0 2.5 3.0 3.5


-1

4.0

4.5

g (nm )

Figure 4.12: Lattice-fringe ngerprint plot of magnetite in the 211 direction.

32

0 22

1 13

20 4 3 33

386

1,691 1,062 000 808


111

222 240

39

380

13 1

36

313

Figure 4.13: Indexed Fourier transform of an image of a magnetite nanocrystal assuming it is oriented close to the [211] direction. The amplitude and index is given for each Friedel pair.

33

(a)

222 111 489


1,499

240 120 13 1 02 2 11 3

000

586 77 1,404 50

(b)

Figure 4.14: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming the nanocrystal is oriented close to the [211] direction.

34

02 2 531 2,262 1,022

20 2 2 20

000

(a)

(b)

Figure 4.15: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming the nanocrystal is oriented close to the [111] direction.

35

(a)

(b)

Figure 4.16: (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image.

36

90 80

Interfringe angle (degrees)

70 60 50 40 30 20 10 1.5 2.0 2.5 3.0 3.5 4.0


-1

4.5

5.0

5.5

g (nm )

Figure 4.17: Lattice-fringe ngerprint plot from the iron oxide nanocrystal in gure 4.16.

3 30 2 20 55 59 957 11 0

13 3 02 3 11 3

000
435 140 17

20 3 3 1 3

Figure 4.18: Indexed Fourier transform of the nanocrystal in gure 4.16, assuming [332] orientation. The arrows point to where there are absent reections.

37

We consider next images taken on a Philips CM20 at Technische Universitt Chemnitz, with a theoretical point resolution of 0.24 nm. The HREM AutoTune software by Gatan was used in order to minimize astigmatism and coma. The specimen was not tilted in order to orient the nanocrystals. Instead, nanocrystals that were showing crossed lattice fringes were imaged. The images are therefore more typical, than ideal, HRTEM images. The best match for the nanocrystal in gure 4.19 is magnetite in a 110 orientation. Those reections that correspond to {022}, {222} and {133} planes are missing, but that is because there is no information in that region of reciprocal space. This might be due to specimen drift since the astigmatism has been corrected for. For maghemite we would expect to see the ( 110) reection for example, which is not present. The nanocrystal in gure 4.20 could be maghemite in a 211 orientation. The presence of a (01 1) reection suggests this. The same goes for the (10 2) reection, barely seen in the Fourier transform. The nanocrystal in gure 4.21 is also oriented close to the 211 zone axis. However, in this case all the visible reections that are expected in magnetite are present in this orientation. There is therefore no evidence of maghemite in this nanocrystal. The nanocrystal in gure 4.22 is probably maghemite in a 211 orientation by the same reasoning as above. In this case the (01 1) and ( 120) reections are fairly strong. The nanocrystal in gure 4.23 could also be maghemite close to 211 since the 01 1 reection is visible. Figure 4.24 is a nanocrystal oriented close to the 110 zone axis. The absence of the ( 110) reection suggests that the structure of this nanocrystal is close to that of magnetite. All the expected reections are seen except for the {133} which is probably beyond the resolution of this image. The nanocrystal in gure 4.25 is another nanocrystal in a 211 orientation. Again, the presence of (01 1) and ( 120) suggest the presence of maghemite. Finally, the nanocrystal in gure 4.26 was found to be oriented close to a 310 zone axis. The (004) reection is not visible. Instead, there is a (002) reection. This reection should be absent in the kinematic limit, which suggests that there is dynamical scattering in this case.

38

(a)

004 9.1 3.2 002 000 14.3 3.1 1 11 11 1 11 3

13.0

(b)

Figure 4.19: (a) HRTEM image of iron oxide nanocrystal. (b) The Fourier transform of the image assuming [110] orientation.

39

(a)

1 11 0 1 1 3.9 3.6 000 1.7 23.6

13 1 02 2

(b)

Figure 4.20: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [211] orientation.

40

(a)

0 22 8.4 5.7 000

1 13 1 11 13 1

3.4 12.0

(b)

Figure 4.21: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [211] orientation.

41

(a)

222
0.4 0.3 1 11 0.8 1.5

02 2 000 0 1 1 3.2 1.4 11 3 10 2 1.5 4.3 30.4 20 4 3 7.6 2 1

1 20

13 1

(b)

Figure 4.22: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [211] orientation.

42

(a)

1 13 4.9 8.5 6.4 111 000 02 2

(b)

Figure 4.23: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [211] orientation.

43

(a)

004 17.1 3.5 22.7 28.1 5.8 28.1 002

11 3 222 1 11 2 20 2 2 2

000 22.7

11 1

11 3

17.7

7.9

(b)

Figure 4.24: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [110] orientation.

44

(a)

3 33 222 111 1 20 13 1 2.3 12.7 000 0 1 1 02 2

5.0 9.1 48.8 4.8 3.6

(b)

Figure 4.25: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [211] orientation.

45

(a)

1 3 3 1 3 1 9.3 7.8 1.7 2.2 000 002 1 31

(b)

Figure 4.26: (a) HRTEM image of iron oxide nanocrystal. (b) The indexed Fourier transform of the image assuming [310] orientation.

46

4.4 4.4.1

Fourier Coefcient Phases Gallium Nitride

HRTEM computer simulations were used to further study using Fourier coefcient phases in characterizing nanocrystals. The WebEMAPS program developed by Zuo and Mabon (2004) was utilized to simulate HRTEM images of gallium nitride. The WebEMAPS program uses Bloch waves, and hence takes into account dynamical scattering. Microscope parameters such as spherical and chromatic aberration, energy spread and defocus can be input into the program, in addition to specimen tilt and thickness. Gallium nitride, Ga3+ N3 , has a wurtzite crystal structure (space group P 63 mc, no. 186). In this study, GaN in the [010] orientation was used. As described in section 3.4, to use the phases we must also nd the correct symmetry. The projected symmetry of all three-dimensional point groups can be found from the International Tables (table 3.7.1, Point-group projection symmetry). In a hexagonal crystal system, the [010] direction is perpendicular to the ( 12 10) plane. From the International Tables we then nd that a projection onto the ( 12 10) plane will have m point-group symmetry. This leaves three possible two-dimensional space groups: pm, pg and cm. The screw axis in the crystal structure will result in a glide line. Hence, the two-dimensional space group will be pg , with the origin on the glide line. The symmetry elements in this two-dimensional space group are illustrated in gure 4.27.

Figure 4.27: Symmetry elements of the pg two-dimensional space group. The dashed lines represent glide lines. Lattice planes that are parallel to the glide line will have real structure factors, so the phases will be either 0 or 180 . There is no other restriction on the phases. However, there will be phase relations due to the glide ) + k 180 , where the glide line is in the k -direction and (hk ) means the phase of the line: (hk ) = (hk 11) = 155 . (hk ) reection. So for example, if (11) = 25 , then ( To study the simulated images one can make use of the program CRISP, but Digital Micrograph was also used in order to study the method in more detail. In order to get theoretical values for the structure factor phases, the structure factors were calculated using the values from Doyle and Turner (1968) as described in section 2.5. The aj and bj coefcients were rst converted into the correct units. It was then possible to compare the calculated structure factor phases with the phases measured in the simulated images of GaN. The structure factor phases were calculated in Microsoft Excel, although the complex addition was done in Mathematica. A simulated HRTEM image of gallium nitride with 5 nm thickness is shown in gure 4.28. The screw axis, parallel to the c-axis, causes the (001) and (003) reection to be absent in the Fourier transform. Since the

47

projected symmetry was known, only the unit cell origin had to be determined. This was done by manually shifting the Fourier transform pixel by pixel and checking the phase restrictions and relations at each position. The calculated structure factor phases, together with the measured Fourier coefcient phases with the Fourier transform origin on the glide line, are listed in table 4.1. We see that there is no correlation between the theoretical and measured phases or between different thicknesses, except for the (100) and (200) reections since these are restricted to 0 or 180 . However, the measured phases follow closely the phase relations, 0l) + l 180 (using Miller indices). For example, (20 obeying (h0l) = (h 2) ( 20 2) and (20 1) ( 20 1)+180 . In this case, since the origin is anywhere on the glide line, one could not expect the theoretical and measured values to be the same, except for the case of reections due to lattice planes parallel to the glide line. As the origin of the Fourier transform is shifted along the glide line, all the phases change except for these reections. This means that when the projected symmetry is that of the two-dimensional point group m, only a few measured phases can be compared directly to the theoretical phases.

48

(a)

00 4 10 3 20 2 20 1 4,162 3,338 1,979 10 2 10 1 5,709 7,970 3,334 6,183 547


(b)

10 3 00 2 10 2 10 1 000 10 0 7,959 9,511 3,332 6,171 20 2 20 1 20 0 3,336 1,978

Figure 4.28: (a) Simulated image of GaN, 5 nm thickness oriented along [010]. Electron potential: 200 kV, x-axis: [100], defocus: 67 nm, energy spread: 1.0 eV, spherical aberration: 1.2 mm, chromatic aberration: 1.2 mm, output limit: 4.5 nm1 . (b) The indexed Fourier transform of the image. The amplitudes are shown for the reections in the bottom half.

49

hkl 100 200 10 1 101 20 1 201 00 2 10 2 102 20 2 202 10 3 103 00 4

Calculated phase

Phase

t = 5 nm 179.1 179.1 124.5 55.9 78.6 101.3 164.0 76.6 77.1 150.0 149.4 4.9 175.2 172.7

Difference -

Phase

t = 10 nm 179.4 179.4 35.3 145.4

Difference -

180 180 68.4 111.6 109.5 70.5 21.7 158.3 158.3 160.4 160.4 77.4 102.6 1.7

180.4

180.7

179.9

137.1 43.3

180.4
-

170.6 8.0 6.9

0.5

1.1

0.6

155.4 155.7

0.3

180.1

108.8 71.4

180.2
-

7.6

Table 4.1: Calculated structure factor phases and measured Fourier coefcient phases (from two images of crystals with different thicknesses, t) for the reections present in gallium nitride in the [010] orientation. The difference columns show the phase difference between reections that have a phase relation. The phase differences are close to the theoretical value of l 180 . Note also that the phases for the (100) and (200) reections are close to the calculated value.

50

4.4.2

Titania

The titania nanocrystal shown in gure 4.4 on page 26 could also be used to study the phases. Since rutile is centrosymmetric, all the phases must be 0 or 180 . The [111] direction is perpendicular to the plane (hhl), where l/h = c2 /a2 . The International Tables give the two-dimensional point group of the projected symmetry as 2mm. From looking at a model of the structure in the [111] direction, it is clear that there are two perpendicular mirror planes in the projection. The two-dimensional space group is therefore pmm. This ). Calculations show that reections due to the {110} and {011} gives the phase relation of (hk ) = (hk lattice planes will have a phase of 0 . In the case of contrast reversal in the image, the phase of the Fourier coefcients of the image should be 180 . To nd the correct origin, the origin of the image selection was shifted pixel by pixel. Using the origin with the lowest phase residual, the phases of the Fourier coefcients were 9 , 22 , and 16 for the three reections, as shown in gure 4.29. The deviation from the theoretical value might be due to the low resolution of the image. The separation between two bright dots in the HRTEM image (gure 4.30) is about seven pixels. This means that shifting the origin by one pixel can change the phases by roughly 360 /7 51 . It might be possible to use sub-pixel interpolation to get more accurate phase measurements. The fact that the phases are not shifted by 180 with respect to the calculated values imply that the contrast transfer function is positive in the corresponding region of reciprocal space, making the atoms appear white.

10 1
=16

0 1 1

=22

1 10

=9

29.9 18.5

28.6

Figure 4.29: Fourier transform with measured Fourier coefcient phases and amplitudes.

51

Figure 4.30: HRTEM image of a titania crystal. The white square surrounds the Fourier transformed region. The real-space origin is in the upper left-hand corner of the white square.

52

Chapter 5 Discussion

The results show that it is possible to identify the crystal structure of a nanocrystal using lattice-fringe ngerprinting. With the support of a comprehensive database and search/match procedures, this method can also be made as automatic as any other microscopic analysis method. The nanocrystals that were known to be titania were determined to have the rutile crystal structure. The crossed lattice fringes that were visible could only be explained with the crystal structure of rutile. Nanocrystals that did not show crossed lattice fringes could, of course, have had a different structure. The results for the iron oxide nanocrystals suggest that some of the nanocrystals had a structure closer to that of magnetite, and others had a structure closer to that of maghemite. This corresponds with the two crystal structures coexisting in a solid solution. The nanocrystals might have been too thick to draw any conclusions from the phases. Under kinematical conditions it should be possible to distinguish between the two crystal structures also using phases of the Fourier coefcients because of the difference in symmetry. Seven out of the 12 nanocrystals studied were oriented along 211 . The analysis of the simulated images of gallium nitride demonstrate how the phases of the Fourier coefcients of HRTEM images can be used to identify a nanocrystal. When the projection of the symmetry element dening the unit cell origin is a point, the exact crystal origin of an imaged nanocrystal can be determined and the measured and calculated phases can be compared directly. This is sometimes not the case, such as with gallium nitride in any other than the [001] orientation, which is parallel to the hexad screw axis. When the phases can not be directly compared to calculated phases the symmetry can still be used, in the form of phase restrictions and phase relations. In either case, the symmetry of the crystal structure must be present in the image. The increase in microscope point resolution through abberation-corrected lenses will make lattice-fringe ngerprinting more viable. First, more lattice fringes will be visible, making more information available. This also makes it more likely for a randomly oriented nanocrystal to have visible lattice fringes. Secondly, by resolving more lattice fringes, more information on the symmetry of the nanocrystal will be present in the image.

5.1

Limitations

Since lattice fringes depend on the structure of the nanocrystal, lattice-fringe ngerprinting cannot easily distinguish between materials of very similar structure. This goes for homologous structures such as gallium nitride and zinc oxide. These two compounds crystallize in the wurtzite structure. To distinguish between such structures one might use X-ray uorescence, in which the chemical composition of the material can be determined without the need of a focused beam. Another factor that affects the applicability of lattice-fringe ngerprinting is the difculty of obtaining good HRTEM images. Aligning the microscope is very important for high-resolution imaging, and this requires some time and experience. However, the alignment and the general operation of TEMs have become simpler over the years with for example auto-alignment software.

53

The Fourier coefcient phases are resistant to small tilts and simply shifted 180 by contrast transfer oscillations. However, the phases are not usable when dynamical scattering is dominant. When the electron waves are diffracted more than once the path length changes and the path differences, and hence phases, are no longer reliable. One caveat when working with nanocrystals is that these crystals often have lattice parameters that are different from that of the bulk crystal. The effect on the lattice spacings and angles when the lattice parameters are perturbed was shown above. When the structure of the nanocrystal varies dramatically from the crystal in its bulk form this structure should be included in a database, with a note on the size range of the nanocrystal.

54

Chapter 6 Conclusion

Lattice-fringe ngerprinting is a novel method of identifying nanocrystals using HRTEM images. In its most basic form, the reciprocal lattice vectors and the interfringe angles are used to ngerprint the crystal structure. For nanocrystals that are sufciently thin it is also possible to use the phases of the Fourier coefcients of the projected electrostatic potential. For an abundance of nanocrystals, such as in a nanopowder, the probability of seeing certain zone axes can be taken into account as well. Lattice-fringe ngerprinting was applied to three different crystal systems: titania, iron oxide and simulated images of gallium nitride. The titania nanocrystals that showed crossed lattice fringes were found to be rutile in the [111] orientation. For iron oxide, the zone axis was determined for each of the nanocrystals showing crossed lattice fringes. The majority of nanocrystals showing crossed lattice fringes were oriented close to the 211 direction. The simulated images of gallium nitride demonstrated the possibility of using the phases of the Fourier coefcients in identifying the crystal structure. These phases can often not be compared directly with calculated structure factor phases, but instead the phase restrictions and phase relations due to the projected symmetry can be used as another component of the lattice-fringe ngerprint.

55

References

W. H. Bragg. The structure of magnetite and the spinels. Nature, 95:561, 1915. J. M. Cowley. Diffraction physics. North-Holland, 2nd edition, 1981. J. M. Cowley. High-resolution transmission electron microscopy and associated techniques, chapter 2, pages 3857. Oxford University Press, 1988. M. De Graef. Introduction to conventional transmission electron microscopy. Cambridge University Press, 2003. D. J. De Rosier and A. Klug. Reconstruction of three dimensional structures from electron micrographs. Nature, 217:130134, 1968. W. J. de Ruijter. Measurement of lattice-fringe vectors from digital HREM images: theory and simulations. Journal of Computer-Assisted Microscopy, 6(4):195212, 1994. W. J. de Ruijter, R. Sharma, M. R. McCartney, and D. J. Smith. Measurement of lattice-fringe vectors from digital HREM images: experimental precision. Ultramicroscopy, 57:409422, 1995. D. R. Denley and H. V. Hart. RINGS: a new search/match database for identication by polycrystalline electron diffraction. Journal of Applied Crystallography, 35:546551, 2002. P. A. Doyle and P. S. Turner. Relativistic Hartree-Fock x-ray and electron scattering factors. Acta Crystallographica, A24:390397, 1968. P. Fraundorf, W. Qin, P. Moeck, and E. Mandell. Making sense of nanocrystal lattice fringes. Journal of Applied Physics, 98:114308, 2005. S. R. Hall, F. H. Allen, and I. D. Brown. The Crystallographic Information File (CIF): a new standard archive le for crystallography. Acta Crystallographica, A47:655685, 1991. H. V. Hart. ZONES: a search/match database for single-crystal electron diffraction. Journal of Applied Crystallography, 35:552555, 2002. N. F. M. Henry and K. Lonsdale, editors. International tables for x-ray crystallography, volume 1. The Kynoch Press, Birmingham, England, 1952. S. Hovmller. CRISP: crystallographic image processing on a personal computer. Ultramicroscopy, 41: 121135, 1992. F. H. Li and D. Tang. Pseudo-weak-phase-object approximation in high-resolution electron microscopy I. Theory. Acta Crystallographica, A41:376382, 1985. J. A. Lpez Prez, M. A. Lpez Quintela, J. Mira, J. Rivas, and S. W. Charles. Advances in the preparation of magnetic nanoparticles by the microemulsion method. Journal of Physical Chemistry B, 101(41):8045 8047, 1997.

56

G. R. Lovely, A. P. Brown, R. Brydson, A. I. Kirkland, R. R. Meyer, L. Chang, D. A. Jefferson, M. Falke, and A. Bleloch. Observation of octahedral cation coordination on the {111} surfaces of iron oxide nanoparticles. Applied Physics Letters, 88:093124, 2006. K. Lu and Y. H. Zhao. Experimental evidences of lattice distortion in nanocrystalline materials. Nanostructured Materials, 12:559562, 1999. J.-O. Malm and M. A. OKeefe. Deceptive lattice spacings in high-resolution micrographs of metal nanoparticles. Ultramicroscopy, 68:1323, 1997. M. A. OKeefe. Resolution in high-resolution electron microscopy. Ultramicroscopy, 47:282297, 1992. C. Pecharromn, T. Gonzles-Carreo, and J. E. Iglesias. The infrared dielectric properties of maghemite, -Fe2 O3 , from reectance measurement on pressed powders. Physics and Chemistry of Minerals, 22(1): 2129, 1995. C. Saltiel and H. Giesche. Needs and opportunities for nanoparticle characterization. Journal of Nanoparticle Research, 2(3):325326, 2000. D. E. Sands. Introduction to crystallography. Dover Publications, 1993. O. Scherzer. The theoretical resolution limit of the electron microscope. Journal of Applied Physics, 20: 2029, 1949. M. V. Sidorov. Contrast transfer function explorer [computer software], 2002. URL http://clik.to/ ctfexplorer. A. M. Tonejc, I. Djerdj, and A. Tonejc. An analysis of evolution of grain size-lattice parameters dependence in nanocrystalline TiO2 anatase. Materials Science and Engineering C, 19:8589, 2002. D. B. Williams and C. B. Carter. Transmission electron microscopy. Plenum Press, 1996. X. Zou. Electron crystallography of inorganic structurestheory and practice. PhD thesis, Stockholm University, 1995. X. Zou and S. Hovmller. Industrial applications of electron microscopy, chapter 22, pages 583614. Marcel Dekker, 2002. J. M. Zuo and J. C. Mabon. Web-based electron microscopy application software: Web-EMAPS. Microscopy and Microanalysis, 10(Suppl 2):10001001, 2004. URL http://emaps.mrl.uiuc.edu/.

57

Appendix Scripts

A.1

hanning_FFT.s

The following script subtracts the average from the image, applies a Hanning window and then computes the fast Fourier transform. The \ symbol means that the line continues on the following line.

/******************************************************* Digital Micrograph script 'hanning_FFT.s' */ number size, number zoom, image front, compleximage sizeX, sizeY, top, left, bottom, right, ii, posX, posY test hannX, hannY, hann, avg, hannout fft

front := GetFrontImage(); GetSize(front, sizeX, sizeY); GetSelection(front, top, left, bottom, right); GetWindowPosition(front, posX, posY); zoom = GetZoom(front); // Test if image/selection has dimensions of the power of two. test = bottom - top; while( test / 2 >= 1 ) test = test/2; if( test != 1 ) Throw( "Only for images (selections) of the power of two!" ); test = right - left; while( test / 2 >= 1 ) test = test/2; if( test != 1 ) Throw( "Only for images (selections) of the power of two!" ); // Create Hanning window. ii = 1; hannX := CreateFloatImage("", (right-left), (bottom-top)); hannX = 0; hannX[0, 0, 1, (right-left)] = \ 1 - cos( 2 * Pi() * icol / (right-left)); while( ii < (bottom-top) ) { hannX[ii, 0, 2*ii, (right-left)] = \ hannX[0, 0, ii, (right-left)];
58

ii = ii * 2;

ii = 1; hannY := CreateFloatImage("", (right-left), (bottom-top)); hannY = 0; hannY[0, 0, (bottom-top), 1] = \ 1 - cos( 2 * Pi() * irow / (bottom-top)); while( ii < (right-left) ) { hannY[0, ii, (bottom-top), 2*ii] = \ hannY[0, 0, (bottom-top), ii]; ii = ii * 2; } hann = hannX * hannY; // Subtract average from image. avg = front - Average(front); // Multiply with Hanning window. hannout = avg[top, left, bottom, right] * hann; // Do fast Fourier transform and display image. fft = RealFFT(hannout); SetName(fft, GetName(front) + "H"); DisplayAt(fft, posX + 14, posY + 21);
A.2 measure_FT.s

The next script nds the position of selected Fourier transform peaks using sub-pixel interpolation and calculates reciprocal spacing in units of pixel1 and angles between the reciprocal space vectors in degrees.

/******************************************************* Digital Micrograph script 'measure_FT.s' Get image and selections and make sure they are okay. */ ComplexImage img := GetFrontImage() Number xsize, ysize GetSize(img, xsize, ysize) // Find the central bright spot, assuming it is in the middle. Number centerx = xsize / 2 Number centery = ysize / 2 ImageDisplay imgdisp = img.ImageGetImageDisplay(0) Number roinumber = imgdisp.ImageDisplayCountROis() if(roinumber < 2)
59

OkDialog("This script requires at least two \ rectangular selections.") Exit(0)

Number i ROI iroi for(i = 0; i < roinumber; i++) { iroi = ImageDisplayGetROI(imgdisp, i) if(!ROIIsRectangle(iroi)) { OkDialog("Only rectangular selections can \ be used with this script.") Exit(0) } } /******************************************************* Find the interpolated brightest spot in each selection and save thecoordinates as a number note. */ Number top, left, bottom, right Number x, y, maxx, maxy, pixelintensity, maxintensity Number alpha, beta, xx, xa, xb Number kprime, lprime, spotx, spoty for(i = 0; i < roinumber; i++) { iroi = ImageDisplayGetROI(imgdisp, i) ROIGetRectangle(iroi, top, left, bottom, right) maxintensity = 0 for(y = top; y < bottom; y++) { for(x = left; x < right; x++) { pixelintensity = Abs(GetPixel(img,x,y)) if(pixelintensity > maxintensity) { maxintensity = pixelintensity maxx = x maxy = y } } } // Find brightest neighboring pixel horizontally. if(Abs(GetPixel(img,maxx+1,maxy)) > \ Abs(GetPixel(img,maxx-1,maxy))) alpha = 1 else alpha = -1 // Find brightest neighboring pixel vertically. if(Abs(GetPixel(img,maxx,maxy+1)) > \ Abs(GetPixel(img,maxx,maxy-1))) beta = 1
60

else // xx // // xa xb

beta = -1

Absolute value of brightest pixel. = maxintensity Absolute value of brightest neighbor horizontally and vertically. = Abs(GetPixel(img,maxx+alpha,maxy)) = Abs(GetPixel(img,maxx,maxy+beta))

// Calculate sub-pixel interpolation distance. kprime = alpha * (2*xa - xx) / (xa + xx) lprime = beta * (2* xb - xx) / (xb + xx) spotx = maxx + kprime spoty = maxy + lprime // Save the coordinates as number notes. SetNumberNote(img, "Spotx"+i,spotx) SetNumberNote(img, "Spoty"+i,spoty)

/******************************************************* Calculate the lengths of the reciprocal lattice vectors and the angles between them. */ // Open result window and write header. DocumentWindow reswin = GetResultsWindow(1) Result("Angle"+"\t"+"Length"+"\t\t"+"Length"+"\n") Number j, spotx1, spoty1, length1, spotx2, spoty2 Number length2, length3, theta, angle // Loop for the first leg of the angle. for(i = 0; i < roinumber-1; i++) { // Retrieves the coordinates from the number notes. GetNumberNote(img, "Spotx"+i, spotx1) GetNumberNote(img, "Spoty"+i, spoty1) length1 = sqrt( ( (spotx1 - centerx)/xsize )**2 + \ ( (spoty1 - centery)/ysize )**2 ) // Loop for the "second leg". for(j = i+1; j < roinumber; j++) { GetNumberNote(img, "Spotx"+j, spotx2) GetNumberNote(img, "Spoty"+j, spoty2) length2 = sqrt( ( (spotx2 - centerx)/xsize )**2 + \ ( (spoty2 - centery)/ysize )**2 ) // Side opposite angle of interest. length3 = sqrt( ( (spotx2 - spotx1)/xsize )**2 + \ ( (spoty2 - spoty1)/ysize )**2)
61

// Find cos(angle) by cosine rule. theta = (length1**2 + length2**2 - length3**2) / \ (2 * length1 * length2) // Find angle and convert to degrees. angle = ACos(theta) * (180/Pi()) if(angle <= 90 && angle > 0.5) { // Put tab-delimited values in results window. Result(angle+"\t"+length1+"\t"+length2+"\n") }

}
A.3

amplitude.s

This script is similar to the previous script, but instead of giving the angles it returns the reciprocal spacing, the amplitude, and the phase of the Fourier coefcients using 3.3.

/******************************************************* Digital Micrograph script 'amplitude.s' Get image and selections and make sure they are okay. */ ComplexImage img := GetFrontImage() Number xsize, ysize GetSize(img, xsize, ysize) // Find the central bright spot, assuming it is in the middle. Number centerx = xsize / 2 Number centery = ysize / 2 ImageDisplay imgdisp = img.ImageGetImageDisplay(0) Number roinumber = imgdisp.ImageDisplayCountROis() if(roinumber < 1) { OkDialog("This script requires at least one \ rectangular selection.") Exit(0) } Number i ROI iroi for(i = 0; i < roinumber; i++) { iroi = ImageDisplayGetROI(imgdisp, i) if(!ROIIsRectangle(iroi)) { OkDialog("Only rectangular selections can \
62

Exit(0)

be used with this script.")

/******************************************************* Find the interpolated brightest spot in each selection and save the coordinates as a number note. */ Number top, left, bottom, right Number x, y, maxx, maxy, pixelintensity, maxintensity Number alpha, beta, xx, xa, xb Number kprime, lprime, spotx, spoty, amplitude, phase ComplexNumber xxc for(i = 0; i < roinumber; i++) { iroi = ImageDisplayGetROI(imgdisp, i) ROIGetRectangle(iroi, top, left, bottom, right) maxintensity = 0 for(y = top; y < bottom; y++) { for(x = left; x < right; x++) { pixelintensity = Abs(GetPixel(img,x,y)) if(pixelintensity > maxintensity) { maxintensity = pixelintensity maxx = x maxy = y } } } //Find brightest neighboring pixel horizontally. if(Abs(GetPixel(img,maxx+1,maxy)) > \ Abs(GetPixel(img,maxx-1,maxy))) alpha = 1 else alpha = -1 //Find brightest neighboring pixel vertically. if(Abs(GetPixel(img,maxx,maxy+1)) > \ Abs(GetPixel(img,maxx,maxy-1))) beta = 1 else beta = -1 //Complex value of the brightest pixel. xxc = GetPixel(img,maxx,maxy) //Absolute value of brightest pixel. xx = Abs(xxc) //Absolute value of brightest neighbor horizontally // and vertically. xa = Abs(GetPixel(img,maxx+alpha,maxy)) xb = Abs(GetPixel(img,maxx,maxy+beta)) //Calculate sub-pixel interpolation distance.
63

kprime = alpha * (2*xa - xx) / (xa + xx) lprime = beta * (2* xb - xx) / (xb + xx) spotx = maxx + kprime spoty = maxy + lprime amplitude = (2*xx/(xsize * ysize))* \ ((Pi()*kprime)/(Sin(Pi()*kprime)))* \ ((Pi()*lprime)/(Sin(Pi()*lprime)))* \ (1-kprime**2)*(1-lprime**2) phase = ( Phase(xxc) + kprime*Pi() + lprime*Pi() )* \ (180/Pi()) //Save the coordinates as number notes. SetNumberNote(img, "Spotx"+i,spotx) SetNumberNote(img, "Spoty"+i,spoty) SetNumberNote(img, "Amplitude"+i, amplitude) SetNumberNote(img, "Phase"+i, phase) SetNumberNote(img, "kprime"+i, kprime) SetNumberNote(img, "lprime"+i, lprime) } /******************************************************* Calculate the lengths of the reciprocal lattice vectors and the angles between them. */ //Open result window and write header. DocumentWindow reswin = GetResultsWindow(1) Result("Length\t\tAmplitude\tPhase\tk'\t\t\tl'\n") Number spotx1, spoty1, length1 Number amplitude1, phase1, kprime1, lprime1 for(i = 0; i < roinumber; i++) { //Retrieve the coordinates from the number notes. GetNumberNote(img, "Spotx"+i, spotx1) GetNumberNote(img, "Spoty"+i, spoty1) GetNumberNote(img, "Amplitude"+i, amplitude1) GetNumberNote(img, "Phase"+i, phase1) GetNumberNote(img, "kprime"+i, kprime1) GetNumberNote(img, "lprime"+i, lprime1) length1 = sqrt( ( (spotx1 - centerx)/xsize )**2 + \ ( (spoty1 - centery)/ysize )**2 ) //Put tab-delimited values in results window. Result(length1+"\t"+amplitude1+"\t"+phase1+"\t"+ \ kprime1+"\t"+lprime1+"\n")

64

You might also like