Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging

Suhas Somnath, Christopher R. Smith, Sergei V. Kalinin, Miaofang Chi, Albina Borisevich, Nicholas Cross, Gerd Duscher, Stephen Jesse

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

We develop an algorithm for feature extraction based on structural similarity and demonstrate its application for atom and pattern finding in high-resolution electron and scanning probe microscopy images. The use of the combined local identifiers formed from an image subset and appended Fourier, or other transform, allows tuning selectivity to specific patterns based on the nature of the recognition task. The proposed algorithm is implemented in Pycroscopy, a community-driven scientific data analysis package, and is accessible through an interactive Jupyter notebook available on GitHub.

Original languageEnglish
Article number3
JournalAdvanced Structural and Chemical Imaging
Volume4
Issue number1
DOIs
StatePublished - Dec 1 2018

Funding

This research was sponsored by the Division of Materials Sciences and Engineering, Basic Energy Sciences, US Department of Energy (SVK and SS). This research was conducted and partially supported (CRS) at the Center for Nanophase Materials Sciences, which is an US DOE Office of Science User Facility. This research was supported by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC for the US Department of Energy (S.J.). We gratefully acknowledge Ondrej Dyck’s assistance in identifying the filtering parameters for an atomically resolved image. Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC0500OR22725 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a nonexclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for the United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). This research was sponsored by the Division of Materials Sciences and Engineering, Basic Energy Sciences, US Department of Energy. Part of this research was funded by Center for Nanophase Materials Sciences, which is an US DOE Office of Science User Facility. This research was supported by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC for the US Department of Energy.

Keywords

  • Atom finding
  • Clustering
  • Electron microscopy
  • Image denoising
  • Scanning transmission electron microscopy
  • Scanning tunneling microscopy
  • Singular value decomposition
  • Statistics

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