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Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets

Published online by Cambridge University Press:  09 March 2022

Shoucong Ning ,
Wenhui Xu ,
Yinhang Ma ,
Leyi Loh ,
Timothy J. Pennycook ,
Wu Zhou ,
Fucai Zhang ,
Michel Bosman ,
Stephen J. Pennycook  and
Qian He Open the ORCID record for Qian He [Opens in a new window]
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Shoucong Ning
Affiliation:
Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore Center for Bio-Imaging Sciences, National University of Singapore, Singapore 117557, Singapore
Wenhui Xu
Affiliation:
Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen 518055, China Harbin Institute of Technology, Harbin 150001, China
Yinhang Ma
Affiliation:
School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100049, China
Leyi Loh
Affiliation:
Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore
Timothy J. Pennycook
Affiliation:
EMAT, University of Antwerp, Campus Groenenborger, 2020 Antwerp, Belgium
Wu Zhou
Affiliation:
School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100049, China
Fucai Zhang
Affiliation:
Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen 518055, China
Michel Bosman
Affiliation:
Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore
Stephen J. Pennycook
Affiliation:
School of Physical Sciences and CAS Key Laboratory of Vacuum Physics, University of Chinese Academy of Sciences, Beijing 100049, China
Qian He*
Affiliation:
Department of Materials Science and Engineering, National University of Singapore, Singapore 117575, Singapore
N. Duane Loh*
Affiliation:
Center for Bio-Imaging Sciences, National University of Singapore, Singapore 117557, Singapore Department of Physics, National University of Singapore, Singapore 117551, Singapore Department of Biological Sciences, National University of Singapore, Singapore 117557, Singapore
*
*Corresponding authors: Qian He, E-mail: [email protected]; N. Duane Loh, E-mail: [email protected]
*Corresponding authors: Qian He, E-mail: [email protected]; N. Duane Loh, E-mail: [email protected]
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Abstract

Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.

Keywords

4D-STEMatomic resolutioncalibrationptychography
Type
Software and Instrumentation
Information
Microscopy and Microanalysis , Volume 28 , Issue 3 , June 2022 , pp. 622 - 632
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of the Microscopy Society of America

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