Advanced Computing in Electron Microscopy

Preface
	Preface to Third Edition
	Preface to Second Edition
	Preface to First Edition
Contents
1 Introduction
	1.1 Computing in Electron Microscopy
	1.2 Organization of This Book
2 The Transmission Electron Microscope
	2.1 Introduction
	2.2 Modeling the Electron Microscope
	2.3 Relativistic Electrons
	2.4 Reciprocity
	2.5 Confocal Mode
	2.6 Aberrations
	2.7 Aberration Correction
	2.8 More Aberrations
	2.9 Further Reading
3 Some Image Approximations
	3.1 The Weak Phase Object in Bright Field
		3.1.1 BF-CTEM with Aberration Correctors
	3.2 Partial Coherence in BF-CTEM
		3.2.1 Aberration Correctors and Partial Coherence
	3.3 Detector Influence (CTEM)
	3.4 Incoherent Imaging of Thin Specimens (CTEM)
	3.5 Annular Dark Field STEM
		3.5.1 Minimum Probe Conditions
		3.5.2 Source Size
		3.5.3 Defocus Spread
		3.5.4 Aberration Tunning Errors
	3.6 Compensation
		3.6.1 Two Aberrations at a Time
		3.6.2 Three Aberrations at a Time
	3.7 Confocal Mode for Weak Phase Objects
	3.8 Phase and Amplitude Contrast Revisited
4 Sampling and the Fast Fourier Transform
	4.1 Sampling
	4.2 Discrete Fourier Transform
	4.3 The Fast Fourier Transform or FFT
	4.4 Wrap Around Error and Rearrangement
	4.5 Fourier Transforming Real Valued Data
	4.6 Displaying Diffraction Patterns
	4.7 An FFT Subroutine in C
	4.8 Further Reading
5 Calculation of Images of Thin Specimens
	5.1 The Weak Phase Object
	5.2 Single Atom Properties
		5.2.1 Radial Charge Distribution
		5.2.2 Potential
		5.2.3 Atomic Size
		5.2.4 Scattering Factors
	5.3 Total Specimen Potential
	5.4 BF Phase Contrast Image Calculation
		5.4.1 Single Atom Images
		5.4.2 Thin Specimen Images
		5.4.3 Partial Coherence and the Transmission Cross Coefficient
	5.5 ADF STEM Images of Thin Specimens
		5.5.1 Single Atom Images
		5.5.2 Thin Specimen Images
	5.6 Annular Bright Field (ABF)
	5.7 Summary of Sampling Suggestions
6 Theory of Calculation of Images of Thick Specimens
	6.1 Bloch Wave Eigenvalue Solution
		6.1.1 Bloch Waves
		6.1.2 Periodic Potential
		6.1.3 Matrix Equation
		6.1.4 Initial Conditions and the Exit Wave
		6.1.5 Bloch Wave Eigenvalue Summary
		6.1.6 Relative Performance
	6.2 The Wave Equation for Fast Electrons
	6.3 A Bloch Wave Differential Equation Solution
	6.4 The Multislice Solution
		6.4.1 A Formal Operator Solution
		6.4.2 A Finite Difference Solution
		6.4.3 Free Space Propagation
	6.5 Multislice Interpretation
	6.6 The Multislice Method and FFTs
	6.7 Slicing the Specimen
	6.8 Aliasing and Bandwidth
	6.9 Interfaces and Defects
	6.10 Multislice Implementation
		6.10.1 The Propagator Function and Specimen Tilt
		6.10.2 Convergence Tests
		6.10.3 Partial Coherence in BF-CTEM
		6.10.4 Parallel Computing
	6.11 More Accurate Slice Methods
		6.11.1 Operator Solutions
		6.11.2 Finite Difference Solutions
7 Multislice Applications and Examples
	7.1 Gallium Arsenide
		7.1.1 BF-CTEM Simulation
		7.1.2 ADF-STEM Simulation
		7.1.3 Channeling
	7.2 Silicon Nitride
	7.3 Two-Dimensional Materials (MoS2)
	7.4 Reciprocity and Z-Contrast
	7.5 CBED Simulations
	7.6 Thermal Vibrations of the Atoms in the Specimen
		7.6.1 Silicon 111 CBED with TDS
		7.6.2 Silicon 110 ADF-STEM with TDS
	7.7 Specimen Edges or Interfaces
	7.8 Biological Specimens
	7.9 Ronchigrams (in STEM)
	7.10 Aberration Tuning
	7.11 Quantitative Image Matching
	7.12 Troubleshooting (What Can Go Wrong)
8 The Programs
	8.1 TEMSIM Program Organization
		8.1.1 Image Display
		8.1.2 Disk File Format
	8.2 BF-CTEM Sample Calculations for Periodic Specimens
		8.2.1 Atomic Potentials
		8.2.2 Multislice
		8.2.3 Image Formation
		8.2.4 Partial Coherence
	8.3 ADF-STEM Sample Calculations for Periodic Specimens
	8.4 Non-periodic Specimens
		8.4.1 Fixed Beam Calculation
		8.4.2 Scanned Beam Calculation
			8.4.2.1 Atomic Coordinates
			8.4.2.2 Sample Run
	8.5 Program Incostem
	8.6 Program Computem
A Plotting Transfer Functions
	A.1 CTEM
	A.2 STEM
B The Fourier Projection Theorem
C Atomic Potentials and Scattering Factors
	C.1 Atomic Charge Distribution
	C.2 X-ray Scattering Factors
	C.3 Electron Scattering Factors
	C.4 Parameterization
D The Inverse Problem
E Bilinear Interpolation
F 3D Perspective View
References
Author Index
Subject Index