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Elastix is a Fiji plugin that wraps elastix into a graphical user interface. elastix is a collection of algorithms that are commonly used to solve image registration problems. Both 2D and 3D as well as multi-channel registrations are supported. Several rigid (translation, Euler, similarity, and affine) as well as locally deformable (BSpline) registrations are supported. For more information please visit the GitHub README.


Elastix is available from the ImageJ update site:

For details on how to install an update site click here.

To use this plugin you also need to install elastix itself, as described here.

To start Elastix in ImageJ, select PluginsRegistrationElastixElastix from the main menu.


You can cite this plugin like this:

- C. Tischer (2019). ElastixWrapper: Fiji plugin for 3D image registration with elastix. Zenodo.

Please also cite the original elastix software:

- S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, “elastix: a toolbox for intensity based medical image registration,” IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010.

- D.P. Shamonin, E.E. Bron, B.P.F. Lelieveldt, M. Smits, S. Klein and M. Staring, “Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer’s Disease”, Frontiers in Neuroinformatics, vol. 7, no. 50, pp. 1-15, January 2014.