Image registration of low signal-to-noise cryo-STEM data

Benjamin H Savitzky; Ismail El Baggari; Colin B Clement; Emily Waite; Berit H Goodge; David J Baek; John P Sheckelton; Christopher Pasco; Hari Nair; Nathaniel J Schreiber; Jason Hoffman; Alemayehu S Admasu; Jaewook Kim; Sang-Wook Cheong; Anand Bhattacharya; Darrell G Schlom; Tyrel M McQueen; Robert Hovden; Lena F Kourkoutis

doi:10.1016/j.ultramic.2018.04.008

Image registration of low signal-to-noise cryo-STEM data

Ultramicroscopy. 2018 Aug:191:56-65. doi: 10.1016/j.ultramic.2018.04.008. Epub 2018 Apr 27.

Authors

Benjamin H Savitzky¹, Ismail El Baggari², Colin B Clement², Emily Waite³, Berit H Goodge³, David J Baek⁴, John P Sheckelton⁵, Christopher Pasco⁵, Hari Nair⁶, Nathaniel J Schreiber⁶, Jason Hoffman⁷, Alemayehu S Admasu⁸, Jaewook Kim⁸, Sang-Wook Cheong⁸, Anand Bhattacharya⁹, Darrell G Schlom¹⁰, Tyrel M McQueen⁵, Robert Hovden¹¹, Lena F Kourkoutis¹²

Affiliations

¹ Department of Physics, Cornell University, Ithaca, NY 14853 USA. Electronic address: [email protected].
² Department of Physics, Cornell University, Ithaca, NY 14853 USA.
³ School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA.
⁴ School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA.
⁵ Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218 USA.
⁶ Department of Materials Science and Engineering, Cornell University, Ithaca, NY 14853, USA.
⁷ Center for Nanoscale Materials and Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA; Present Address: Department of Physics, Harvard University, Cambridge, MA 02138, USA.
⁸ Rutgers Center for Emergent Materials and Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.
⁹ Center for Nanoscale Materials and Materials Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
¹⁰ Department of Materials Science and Engineering, Cornell University, Ithaca, NY 14853, USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 USA.
¹¹ School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA; Present Address: Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109 USA.
¹² School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA; Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 USA. Electronic address: [email protected].

PMID: 29843097
DOI: 10.1016/j.ultramic.2018.04.008

Abstract

Combining multiple fast image acquisitions to mitigate scan noise and drift artifacts has proven essential for picometer precision, quantitative analysis of atomic resolution scanning transmission electron microscopy (STEM) data. For very low signal-to-noise ratio (SNR) image stacks - frequently required for undistorted imaging at liquid nitrogen temperatures - image registration is particularly delicate, and standard approaches may either fail, or produce subtly specious reconstructed lattice images. We present an approach which effectively registers and averages image stacks which are challenging due to their low-SNR and propensity for unit cell misalignments. Registering all possible image pairs in a multi-image stack leads to significant information surplus. In combination with a simple physical picture of stage drift, this enables identification of incorrect image registrations, and determination of the optimal image shifts from the complete set of relative shifts. We demonstrate the effectiveness of our approach on experimental, cryogenic STEM datasets, highlighting subtle artifacts endemic to low-SNR lattice images and how they can be avoided. High-SNR average images with information transfer out to 0.72 Å are achieved at 300 kV and with the sample cooled to near liquid nitrogen temperature.

Keywords: Atomic Resolution; Cryogenic STEM (cryo-STEM); Image reconstruction; Low signal-to-noise ratio (SNR); Rigid registration; Scanning Transmission Electron Microscopy (STEM).

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.