Ingrained -- An automated framework for fusing atomic-scale image simulations into experiments

TL;DR

Ingrained is an open-source automated framework that aligns atomic-scale image simulations with experimental microscopy images, enabling high-throughput analysis and improved interpretation of atomic structures.

Contribution

The paper introduces a novel automated framework, ingrained, for fusing atomic-scale simulations with experimental images, streamlining high-accuracy analysis and interpretation.

Findings

Successfully automates correspondence between simulations and experiments.

Facilitates high-throughput atomic structure analysis.

Develops a rationalized forward model for STM simulation.

Abstract

To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy (e.g., electron and scanning probe), an initial correspondence between the simulation and experimental image must be established at the outset of further high accuracy simulations or calculations. Furthermore, if simulation is to be used in context of highly automated processes or high-throughput optimization, the process of finding this correspondence itself must be automated. In this work, we introduce ingrained, an open-source automation framework which solves for this correspondence and fuses atomic resolution image simulations into the experimental images to which they correspond. We describe herein the overall ingrained workflow, focusing on its application to interface structure approximations, and the development of an experimentally rationalized forward model for scanning tunneling microscopy simulation.