Ingrained: An Automated Framework for Fusing Atomic-Scale Image Simulations into Experiments

Eric Schwenker, Venkata Surya Chaitanya Kolluru, Jinglong Guo, Rui Zhang, Xiaobing Hu, Qiucheng Li, Joshua T. Paul, Mark C. Hersam, Vinayak P. Dravid, Robert Klie, Jeffrey R. Guest, Maria K.Y. Chan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy, 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, “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, is introduced. 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 are described.

Original languageEnglish (US)
Article number2102960
Issue number19
StatePublished - May 12 2022


  • image registration
  • materials image simulations
  • microscopy automation

ASJC Scopus subject areas

  • Engineering (miscellaneous)
  • Chemistry(all)
  • Materials Science(all)
  • Biotechnology
  • Biomaterials


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