<a href="https://elastix.dev/">
  <img src="https://github.com/SuperElastix/elastix/blob/main/dox/art/elastix_logo_full_small.bmp" alt="elastix logo" title="elastix" align="right" height="80" />
</a>

# elastix image registration toolbox #

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[![Model Zoo](https://img.shields.io/badge/open-Model%20Zoo-blue.svg)](https://lkeb.ml/modelzoo/)
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[![DOI](https://zenodo.org/badge/91586944.svg)](https://zenodo.org/doi/10.5281/zenodo.13366181)
[![CZI's Essential Open Source Software for Science](https://img.shields.io/badge/funded%20by-EOSS-FF414B)](https://czi.co/EOSS)

Welcome to elastix: a toolbox for rigid and nonrigid registration of images.

elastix is open source software, based on the well-known [Insight Segmentation and Registration Toolkit (ITK)](https://itk.org/). The software consists of a collection of algorithms that are commonly used to perform (medical) image registration: the task of finding a spatial transformation, mapping one image (the _fixed_ image) to another (the _moving_ image), by optimizing relevant image similarity metrics. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting.
Nowadays elastix is accompanied by [ITKElastix](https://github.com/InsightSoftwareConsortium/ITKElastix) making it available in Python ([on Pypi](https://pypi.org/project/itk-elastix/)) and by [SimpleElastix](http://simpleelastix.github.io/), making it available in languages like C++, Python, Java, R, Ruby, C# and Lua. A docker image of the latest elastix build is available as well on [dockerhub](https://hub.docker.com/repository/docker/superelastix/elastix). Several plugins exist for those who wish to use the functionality of elastix in a graphical user interface, among others a [napari](https://github.com/SuperElastix/elastix_napari) and a [3Dslicer](https://github.com/lassoan/SlicerElastix) plugin.

## Authors ##

The lead developers of elastix are [Stefan Klein](https://github.com/stefanklein) and [Marius Staring](https://github.com/mstaring). This software was initially developed at the [Image Sciences Institute](http://www.isi.uu.nl), under supervision of [Josien P.W. Pluim](http://www.isi.uu.nl/People/Josien/). Today, [many](https://github.com/SuperElastix/elastix/graphs/contributors) have contributed to elastix.

If you use this software anywhere we would appreciate if you cite the following articles:
- 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. [download](https://elastix.dev/marius/publications/2010_j_TMI.php) [doi](http://dx.doi.org/10.1109/TMI.2009.2035616)
- 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. [download](https://elastix.dev/marius/publications/2014_j_FNI.php) [doi](http://dx.doi.org/10.3389/fninf.2013.00050)

Specific components of elastix are made by many; The relevant citation can be found [here](https://github.com/SuperElastix/elastix/wiki/How-to-cite-elastix-(components)).
In addition, you can use the elastix DOI identifiers from Zenodo to refer to specific software releases: https://zenodo.org/doi/10.5281/zenodo.13366181

## More information ##

More information, including an extensive manual and model zoo, can be found on the [wiki](https://github.com/SuperElastix/elastix/wiki)

Interactive tutorials are available in [Jupyter notebooks](https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKElastix/main?urlpath=lab/tree/examples%2FITK_Example01_SimpleRegistration.ipynb).

You can also subscribe to the [mailing list](https://groups.google.com/forum/#!forum/elastix-imageregistration) for questions. Information on contributing to `elastix` can be found [here](CONTRIBUTING.md).
