Atomap

Atomap analyzes atomic-resolution scanning transmission electron microscopy (STEM) images to extract atomic column positions, sublattice intensities, lattice parameters, and atomic shifts in crystalline materials such as perovskite oxide heterostructures.

Key Features:

• Two-Dimensional Elliptical Gaussian Fitting: Uses 2-D elliptical Gaussian distributions to determine positions and shapes of atomic columns in STEM images.
• Iterative Fitting and Subtraction: Fits the most intense atomic columns and subtracts them to reveal information about all projected sublattices.
• Lattice Parameter and A-cation Shape Extraction: Extracts changes in lattice parameters and the shape of A-cation columns from annular dark field (ADF) images of perovskite oxide heterostructures.
• Quantification of Atomic Shifts: Quantifies shifts in oxygen column positions using annular bright field (ABF) images.
• Sublattice Intensity Handling: Accounts for intensity variations across sublattices composed of different elements.
• Analysis of Large Datasets: Processes STEM datasets containing numerous atomic columns for comprehensive structural characterization.
• Precision Evaluation with Non-rigid Registration: Compares atomic column position precision between standard acquisition and image stacks averaged after non-rigid registration.

Scientific Applications:

• Structural Analysis of Crystalline Materials: Provide atomic-scale structural information from STEM data for crystalline materials, including perovskite oxide heterostructures.
• Sublattice Composition and Intensity Studies: Characterize intensity differences and composition-related contrast across distinct sublattices in STEM images.
• Measurement of Atomic Shifts and Lattice Distortions: Quantify oxygen column shifts and detect changes in lattice parameters and column shapes.
• Evaluation of Imaging and Registration Methods: Assess precision improvements from using image stacks averaged after non-rigid registration versus standard acquisition.

Methodology:

Performs two-dimensional elliptical Gaussian fitting with iterative fitting and subtraction of intense columns; extracts lattice parameters and A-cation shapes from ADF images and oxygen shifts from ABF images; evaluates precision by comparing standard acquisition with image stacks averaged after non-rigid registration.