SimpleElastix – Image registration made easy


Kasper Marstal1, Floris Berendsen2, Stefan Klein1 and Marius Staring2

Estimated cost



Alpha version- Apache 2.0 License

SimpleElastix is a user-friendly medical image registration program. It aims to bring the high-performance of elastix [1], a powerful medical image registration library, to a wider audience by streamlining its routines. SimpleElastix makes state-of-the-art image registration available through languages like C++, Python, Java, R, Ruby, Octave, Lua, Tcl and C#.

SimpleElastix is:

  • Versatile: As it inherits the functionality of elastix, it supports diverse registration methods based on various transform models (rigid, affine, nonrigid), similarity measures (e.g., mutual information), optimisation methods (for example gradient descent), interpolation methods (nearest neighbour, linear, cubic), and multi-resolution schemes.
  • Powerful: It exploits efficient C++ libraries like ITK and elastix.
  • Convenient: SimpleElastix can be used as a native library in Python, Java, R, Octave, Lua, Tcl and C# on Linux, Mac and Windows and integrates naturally with many development environments.
  • User-friendly: The registrations can be done in few code lines.

[1] 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.



1Erasmus Medical Center, Biomedical Imaging Group Rotterdam, Rotterdam, the Netherlands

2Leiden University Medical Center, Division of Image Processing, Leiden, the Netherlands