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NanoSIMS Stabilizer: a tool to resolve distortions in elemental and isotopic imaging

NanoSIMS has revolutionized the chemical imaging capability in many research fields and catalyzed numerous breakthroughs in the past decades. Nonetheless, we have experienced significant limitations, particularly, scanning distortions during multiple frame acquisition impeded data analysis and interpretation. 

In this work, we introduce NanoSIMS Stabilizer, a plugin and algorithm that addresses these limitations. NanoSIMS Stabilizer is provided as either an easy-to-use ImageJ plugin or a GPU server.


Please refer to the published paper for more details. 

NanoSIMS Stabilizer Demonstration

Comparisons between NanoSIMS Stabilizer with translation-counterbalancing algorithm-based method (Auto Track)

Synchronized Multiple Channels Registration








​Multiple Channel Registration and Composites

​S (blue) +


Br (red)


​S (purple) +


Au (green) +


Dy   O (yellow)



Code and Plugin Avaliability

The ImageJ plugin, code, and operation manual can be accessed at
The Python code (acceleration mode on GPU) can be accessed at


This work is supported by the Hong Kong Research Grant Council General Research Fund (17102722, 17300523), Australian Research Council (LP190100433), and National Natural Science Foundation of China (32271445) to H.J. The authors acknowledge the facilities, and the scientific and technical assistance of Microscopy Australia at the Centre for Microscopy, Characterisation & Analysis, The University of Western Australia, a facility funded by the University, State and Commonwealth Governments. The work was conducted in the JC STEM Lab of Molecular Imaging, funded by The Hong Kong Jockey Club Charities Trust.

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