Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting

Nord, Magnus; Vullum, Per Erik; MacLaren, Ian; Tybell, Thomas; Holmestad, Randi

doi:10.1186/s40679-017-0042-5

Cited by 207 publications

(152 citation statements)

References 42 publications

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“…3 demonstrates. While the approach used by GPA is advantageous for the analysis of HRTEM images of limited spatial resolution, ideally, the analysis of aberration corrected STEM images should take the advantages of all frequencies, and this can be achieved using real space based methods based on atomic peak finding or template matching (TeMA) [5,6]. In these methods, the position of the atomic columns is determined by the intensity distribution, which utilizes all information recorded in the image.…”

Section: Resultsmentioning

confidence: 99%

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

Vatanparast

Vullum

Nord

et al. 2017

J. Phys.: Conf. Ser.

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Abstract. Geometric phase analysis (GPA), a fast and simple Fourier space method for strain analysis, can give useful information on accumulated strain and defect propagation in multiple layers of semiconductors, including quantum dot materials. In this work, GPA has been applied to high resolution Z-contrast scanning transmission electron microscopy (STEM) images. Strain maps determined from different g vectors of these images are compared to each other, in order to analyze and assess the GPA technique in terms of accuracy. The SmartAlign tool has been used to improve the STEM image quality getting more reliable results. Strain maps from template matching as a real space approach are compared with strain maps from GPA, and it is discussed that a real space analysis is a better approach than GPA for aberration corrected STEM images.

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Section: Resultsmentioning

confidence: 99%

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

Vatanparast

Vullum

Nord

et al. 2017

J. Phys.: Conf. Ser.

Self Cite

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“…Several other specialized algorithms have been designed to quantify atom positions in electron microscope datasets, such as Atomap [33], StatSTEM [34] and oxygen octahedra picker [35]. The Atomap algorithm uses principal component analysis to obtain denoised STEM images and nds the center of mass based on the initial guess of local intensity maxima or minima.…”

Section: Comparisons With Other Algorithmsmentioning

confidence: 99%

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

Mukherjee

Miao

Stone

et al. 2020

Adv Struct Chem Imag

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The standard technique for sub-pixel estimation of atom positions from atomic resolution scanning transmission electron microscopy images relies on fi ing intensity maxima or minima with a two-dimensional Gaussian function. While this is a widespread method of measurement, it can be error prone in images with non-zero aberrations, strong intensity di erences between adjacent atoms or in situations where the neighboring atom positions approach the resolution limit of the microscope. Here we demonstrate mpfit, an atom finding algorithm that iteratively calculates a series of overlapping two-dimensional Gaussian functions to fit the experimental dataset and then subsequently uses a subset of the calculated Gaussian functions to perform sub-pixel refinement of atom positions. Based on both simulated and experimental datasets presented in this work, this approach gives lower errors when compared to the commonly used single Gaussian peak fi ing approach and demonstrates increased robustness over a wider range of experimental conditions.

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“…Each of the atomic columns was fitted with an elliptical 2-D Gaussian. The ellipticity parameter was extracted and defined as the ratio of a long-to-short ellipse axis accordingly to Nord et al 40 . The ellipticity value of "1" corresponds to perfectly circular atomic columns while values greater than "1" indicates displacement of the atoms, within the column, in the x-y plane 39,40 .…”

Section: /31mentioning

confidence: 99%

Towards the understanding of the gold interaction with AIII-BV semiconductors at the atomic level

Jany

Janas²,

Piskorz³

et al. 2020

Nanoscale

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AIII-BV semiconductors have been considered for decades to be a promising material in overcoming the limitations of silicone semiconductor devices. One of the important aspects within AIII-BV semiconductor technology are gold-semiconductor interactions on the nanoscale, since Au is widely used to catalyze the growth of AIII-BV nanostructures.We report on the chemical interactions of Au atoms with AIII-BV semiconductor crystals by an investigation of the nanostructures formation in the process of thermally-induced Au self-assembly on various AIII-BV surfaces, and this by means of atomically resolved HAADF STEM measurements. We have found that the formation of nanostructures is a consequence of the surface diffusion and nucleation of adatoms produced by Au induced chemical reactions on AIII-BV semiconductor surfaces. Only for InSb crystal we have found that there is efficient diffusion of Au atoms into the bulk, which we 2/31 experimentally studied by Machine Learning HAADF STEM image quantification. The process of Au dissolution in InSb lattice has been additionally characterized by DFT calculations with inclusion of finite temperature effects. Furthermore, based on the stoichiometry of nanostructures grown, the effective number of Au atoms needed to release one AIII metal atom has been estimated. The experimental finding reveals a difference in the Au interactions with In-and Ga-based groups of AIII-BV semiconductors. Our comprehensive and systematic studies uncover the details of the Au interactions with the AIII-BV surface at the atomic level with chemical sensitivity.AIII-BV semiconductors due to their unique properties, such as high electron mobility and direct bandgap, are being considered material for the new generation of nanoscale electronic devices 1-4 .Recently, new technologies were developed such as template-assisted selective epitaxy (TASE) by IBM Zurich group 5 and epitaxial lift off (ELO) technique 6 to integrate AIII-BV with Si at the nanoscale. This will allow one to expand the use of AIII-BV crystals by extending the conventional Si-based technology for future AIII-BV/Si nanodevice fabrication 7 . For many applications the arrays of standing, vertically aligned AIII-BV nanowires grown on semiconductor surfaces are desired [8][9][10] . A device for efficient water splitting can be built from such AIII-BV nanowires arrays 11,12 . Also the AIII-BV nanowire LED device integrated on Si has been developed, with 3 orders of magnitude higher efficiency than the conventional device 13 . To control the physico-chemical properties of the devices local information on the atomic arrangement is necessary as has recently been shown by atomic resolution spectrum imaging in STEM 14 .The growth of such monocrystalline AIII-BV nanowires is mainly catalyzed by Au seeded nanoparticles 15 . Studies on the role of Au in the process of nanowires growth, in a closed system being in equilibrium, have been performed by Dick et al. 16 . They have shown that deposited Au is not inert with respect to AIII-BV material and i...

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Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting

Cited by 207 publications

References 42 publications

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

Strategy for reliable strain measurement in InAs/GaAs materials from high-resolution Z-contrast STEM images

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

Towards the understanding of the gold interaction with AIII-BV semiconductors at the atomic level

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