  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.
