Smart Align—a new tool for robust non-rigid registration of scanning microscope data

Jones, Lewys; Yang, Hao; Pennycook, Timothy J.; Marshall, Matthew S. J.; Aert, Sandra Van; Browning, Nigel D.; Castell, Martin R.; Nellist, Peter D.

doi:10.1186/s40679-015-0008-4

Cited by 307 publications

(251 citation statements)

References 40 publications

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“…Digital super-resolution via pixel up-sampling (2x) was applied to exploit the subpixel precision acquired in interpolation. Images and their corresponding EDS volumes were then aligned, non-rigidly registered and summed up using the Smart Align software (Jones et al, 2015). Additional periodic averaging was done spatially over repeating formula units in the projected image (1 or ½ unit cell), along with rotational averaging when appropriate.…”

Section: Methodsmentioning

confidence: 99%

Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy

Wenner

Jones

Marioara

et al. 2017

Micron

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Scanning transmission electron microscopy (STEM) coupled with energy-dispersive X-ray spectroscopy (EDS) is a common technique for chemical mapping in thin samples. Obtaining high-resolution elemental maps in the STEM is jointly dependent on stepping the sharply focused electron probe in a precise raster, on collecting a significant number of characteristic X-rays over time, and on avoiding damage to the sample. In this work, 80 kV aberration-corrected STEM-EDS mapping was performed on ordered precipitates in aluminium alloys. Probe and sample instability problems are handled by acquiring series of annular dark-field (ADF) images and simultaneous EDS volumes, which are aligned and non-rigidly registered after acquisition. The summed EDS volumes yield elemental maps of Al, Mg, Si, and Cu, with sufficient resolution and signal-to-noise ratio to determine the elemental species of each atomic column in a periodic structure, and in some cases the species of single atomic columns. Within the uncertainty of the technique, S and β'' phases were found to have pure elemental atomic columns with compositions Al 2 CuMg and Al 2 Mg 5 Si 4 , respectively. The Q' phase showed some variation in chemistry across a single precipitate, although the majority of unit cells had a composition Al 6 Mg 6 Si 7.2 Cu 2 .

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Section: Methodsmentioning

confidence: 99%

Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy

Wenner

Jones

Marioara

et al. 2017

Micron

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“…Unfortunately, this otherwise superb imaging technique is plagued by scan distortions related to probe flyback, specimen drift, electronic noise and other environmental effects [8,9]. Accurate atomic positions are required for high-resolution strain measurements, and experimenters therefore typically resort to conventional high-resolution TEM imaging [10,11] or only measuring strain along the fast-scan direction in a STEM image when high precision is required.…”

Section: Introductionmentioning

confidence: 99%

“…Images were aligned and non-rigidly registered using Smart Align [9], reducing the flyback distortions by a factor of about 5, when comparing the series average to a typical single frame ADF image. Geometric phase analysis (GPA) [18] was used to find displacement and strain fields by applying a cosine mask to [200]Al and [020]Al Fourier spots.…”

mentioning

confidence: 99%

Accurately measured precipitate–matrix misfit in an Al–Mg–Si alloy by electron microscopy

Wenner

Holmestad

2016

Scripta Materialia

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The age-hardenable Al-Mg-Si alloy system is strengthened by needle-shaped coherent β'' phase precipitates. Using distortion-corrected high-resolution scanning transmission electron microscopy images, we measure the considerable misfit between β'' particles and the Al matrix. The β'' phase is found to adapt its lattice parameters to the particle shape, distributing the strain in the Al matrix evenly in its cross-sectional plane. The measured misfits give a good match to reported atomistic simulations for a β'' phase with composition Mg5Al2Si4.Keywords: electron microscopy, aluminium alloys, precipitation, misfit strain 2 Coherent precipitates in age hardenable alloys and the misfit strain fields they induce in the surrounding matrix have been text book material for many decades [1]. Such precipitates form by thermally activated diffusion, nucleation and growth. A precipitate particle stays coherent until it grows too large for the matrix to accommodate all its misfit. After this, precipitates experience a loss of coherency, and the strain fields diminish, weakening the material. This can happen through several mechanisms:(i) a phase transformation to a less coherent phase (ii) formation of an incoherent surface layer at the matrix-precipitate interface (iii) introduction of interface (misfit) dislocations The precipitate phase can also relieve the system of some strain before coherency loss occurs by less drastic modifications:(iv) generation of stacking faults in the precipitate phase (v) chemical adjustments, including an increased vacancy density in or outside the precipitate phase All five effects can be studied using theoretical calculations such as density functional theory (DFT) or continuum mechanics through the finite element method (FEM). However, calculations need support by experiments at the atomic scale. Experimental studies require that we can both observe the causes (e.g. a single stacking fault) and quantify the resulting change in lattice strain. It is equally important to ensure the absence of faults, if the strain around a perfectly coherent particle is of interest.In this study, we focus on measuring the misfit of perfectly coherent β'' precipitates of the Al-Mg-Si system [2-4] through scanning transmission electron microscopy (STEM). This phase is described by the monoclinic C2/m space group and was initially thought to have composition Mg5Si6, but Mg5Al2Si4 is probably closer to the truth [5,6]. Its lattice parameters have been measured to a = 1.516 nm, b = 0.405 nm, c = 0.674 nm, and its monoclinic angle is 105.3° [2,3]. The phase was chosen since it is one of few fully coherent phases in aluminium alloys, and the main hardening phase of an industrially important alloy system. It is also needle-shaped with a long main coherency direction, often extending through the TEM specimen in which it resides. The lattice strain is therefore uniform through the specimen, and can be measured reliably in a projected image of a precipitate cross-section.When corrected for spherical aberratio...

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“…Beam damage, drift distortion, and scan distortion are inherent issues that hinder quantitative interpretation of scanning transmission electron microscopy (STEM) imaging [1][2][3][4][5][6]. Beam damage occurs when the electron beam used to form the image transfers a critical amount of energy to the sample being examined, potentially causing damage or otherwise changing the subject of the experiment.…”

Section: Introductionmentioning

confidence: 99%

Dynamic scan control in STEM: spiral scans

Sang

Lupini

Unocic

et al. 2016

Adv Struct Chem Imag

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Scanning transmission electron microscopy (STEM) has emerged as one of the foremost techniques to analyze materials at atomic resolution. However, two practical difficulties inherent to STEM imaging are: radiation damage imparted by the electron beam, which can potentially damage or otherwise modify the specimen and slow-scan image acquisition, which limits the ability to capture dynamic changes at high temporal resolution. Furthermore, due in part to scan flyback corrections, typical raster scan methods result in an uneven distribution of dose across the scanned area. A method to allow extremely fast scanning with a uniform residence time would enable imaging at low electron doses, ameliorating radiation damage and at the same time permitting image acquisition at higher frame-rates while maintaining atomic resolution. The practical complication is that rastering the STEM probe at higher speeds causes significant image distortions. Non-square scan patterns provide a solution to this dilemma and can be tailored for low dose imaging conditions. Here, we develop a method for imaging with alternative scan patterns and investigate their performance at very high scan speeds. A general analysis for spiral scanning is presented here for the following spiral scan functions: Archimedean, Fermat, and constant linear velocity spirals, which were tested for STEM imaging. The quality of spiral scan STEM images is generally comparable with STEM images from conventional raster scans, and the dose uniformity can be improved.

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Smart Align—a new tool for robust non-rigid registration of scanning microscope data

Cited by 307 publications

References 40 publications

Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy

Atomic-resolution chemical mapping of ordered precipitates in Al alloys using energy-dispersive X-ray spectroscopy

Accurately measured precipitate–matrix misfit in an Al–Mg–Si alloy by electron microscopy

Dynamic scan control in STEM: spiral scans

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