Sept. 30, 2016


SmartAlign for DigitalMicrograph


Higashimatsuyama, Saitama, Japan (Sept. 30, 2016): HREM Research Inc. introduced SmartAlign for DigitalMicrograph. The SmartAlign corrects slow instability of probe scanning system (scan distortion) from fast-acquisition multi-frame images using rigid and non-rigid image alignment. Thus, SmartAlign restores resolution before degradation, and improves image quality.


Procedures of SmartAlign have been developed by Lewys Jones and Peter Nellist of University of Oxford [1], and may be well applied for a scanning system, such as a scanning transmission electron microscope (STEM), or scanning tunneling microscope (STM). In these instruments, low frequency instabilities, such as stage drift and scan distortion, change from image to image, and degrade resolution even when we add these images after rigid alignment (simple overall translation alignment). SmartAlign performs non-rigid alignment (pixel level alignment) of each image, and thus restores resolution before degradation. Using the alignment information the other data set obtained at the same time will be aligned. This will be well applied for spectrum image (SI) data obtained with annular dark field (ADF).


[1] L. Jones, et al., "Smart Align a new tool for robust non-rigid registration of scanning microscope data", Advanced Structural & Chemical Imaging 1:8 (2015) doi:10.1186/s40679-015-0008-4.

About HREM Research Inc.

Founded in 2001, HREM Research Inc. specializes in developing products and services that enhance High-Resolution Electron Microscopy (HREM). Dr. Kazuo Ishizuka, the founder of a company has established the whole technique for HREM image simulation. Thus, a company's flagship product, Mac/WinHREM, is a world leading HREM image simulation software. Currently, HREM Research Inc. is actively working on making useful techniques to be available for the HREM community. For more information, visit or contact



Kazuo Ishizuka (

HREM Research Inc.

14-48 Matsukazedai, Higashimatsuyama

355-0055 JAPAN






Supplementary materials




Single raw STEM ADF image

(Bottom Left)

Image after SmartAlign

(Bottom Right)

Strain map obtained from the aligned image