Additional tools

This page contains links to useful tools/scripts that provide additional functionality on top of elastix.

Contributions of users are very much welcomed!

1. Python interfaces

   • itk-elastix
     https://github.com/InsightSoftwareConsortium/ITKElastix
     Provides an ITK Python interface to elastix, including binary Python packages.
     pip install itk-elastix
registered_image = itk.elastix_registration_method(fixed_image, moving_image)

   • SimpleElastix
     https://github.com/SuperElastix/SimpleElastix and http://simpleelastix.github.io/
     SimpleElastix is an extension of SimpleITK that offers user-friendly access to the popular image registration algorithms of the elastix C++ library. This makes state-of-the-art medical image registration really easy to do in languages like Python, Java, R, Ruby, C# and Lua.

2. Interfaces to other scripting languages
   In addition to Python, SimpleElastix also offers interfaces to languages like Java, R, Ruby, C# and Lua.

3. 3DSlicer extension
   Thanks to Andras Lasso, elastix is now available as a plug-in for 3DSlicer. If you download and install 3DSlicer then you can install the elastix extension from Slicer's extension manager by a few clicks.

4. Matlab interfaces

   • ElastixFromMatlab toolbox
     https://sourcesup.renater.fr/elxfrommatlab/

   • ElastixToolbox at project Gerardus
     https://github.com/rcasero/gerardus/tree/master/matlab/ElastixToolbox
     Read/write parameter files, Matlab interfaces to elastix and transformix, 2D grayscale/colour images, concatenation of transforms.

   • MelastiX by Rob Campbell
     http://www.mathworks.com/matlabcentral/fileexchange/52982-melastix
     MelastiX at the Matlab File Exchange, which also contains a GitHub link: Call elastix directly on MATLAB matrices from within MATLAB. Facility for performing inverse transforms, concatenation of transforms, YML preferences file, examples.

5. MeVisLab interface
   https://github.com/MeVisLab/communitymodules
   A set of MeVisLab modules have been created for configuration and execution of elastix and transformix from within MeVisLab, see the MeVisLab interface wiki.
   Contributed by Marijn van Stralen, Image Sciences Institute, UMC Utrecht, the Netherlands.

6. ITKTools
   https://github.com/ITKTools https://github.com/ITKTools
   A collection of general purpose image processing programs, based on ITK. Includes a program to compute overlap between segmentations (which is often used to evaluate image registrations).

7. Atlas generation example
   This example shows how to generate an atlas using non-rigid registration in elastix, based on artificial population data.
   The parameter files, python scripts, and data can be found on the atlas generation example wiki page.
   Contributed by Roy van Pelt, Biomedical Image Analysis group, Eindhoven University of Technology, the Netherlands.

8. statismo-elastix
   https://github.com/statismo/statismo-elastix
   A small elastix user component that provides an interface to statismo, an open source library for statistical shape modeling.
   This allows to perform statistically constrained registration and atlas-based segmentation in elastix.

=== Add your own tools here! ===