Documentation

Project Overview

elastix was originally created as a command line tool to aid image registration, but nowadays many sub-projects and wraps of elastix, that make the toolbox available in other languages or in a GUI, exist. This was done to accommodate users of various programming and non-programming backgrounds within the image registration community. These sub-projects, their programming language and the way of installation are:

• elastix: command tool and c++ library, latest binaries on GitHub Release page
• ITKElastix: Python, available on Pypi
• SimpleElastix: Python, Java, R, Ruby, Octave, Lua, Tcl and C#, for compilation and installation see SimpleElastix docs
• elastix docker image: Docker image, available on DockerHub

and for non-coders:

• elastix_napari: Napari plugin, available on Pypi

Getting Started

To get started with elastix you can do the following:

• Check out the example of usage: elastix-4.9.0-example.zip
• Check out the manual. It will tell you about the technique of image registration and informs about the structure and use of elastix. Chapter 5 gives some general advice on how to tune the registration for a specific application.
• A list of parameters that can be specified in the parameter file can be found here.
• Also check out the Model Zoo. There you can find a growing list of parameter files that were successfully applied in applications of elastix users. Maybe you can find a problem similar to your own!

Mailing list

You can subscribe to the elastix-imageregistration Google forum to stay informed about new developments of elastix, and to communicate with other users and the developers. You can participate via https://groups.google.com/forum/#!forum/elastix-imageregistration.

Useful links

what	link
Website	https://elastix.dev/
GitHub repository (official)	https://github.com/SuperElastix/elastix
Google groups forum	https://groups.google.com/forum/#!forum/elastix-imageregistration
Wiki	https://github.com/SuperElastix/elastix/wiki
Model Zoo	https://elastix.dev/modelzoo/
C++ classes overview	https://elastix.dev/doxygen/classes.html
Dashboard	https://my.cdash.org/index.php?project=elastix
Ohloh	https://www.ohloh.net/p/elastix_
ITKElastix	https://github.com/InsightSoftwareConsortium/ITKElastix
	https://pypi.org/project/itk-elastix/
SimpleElastix	http://simpleelastix.github.io/
	http://simpleelastix.readthedocs.io/
	https://github.com/SuperElastix/SimpleElastix
SuperElastix	http://superelastix.readthedocs.io/
	https://github.com/SuperElastix/SuperElastix
DockerHub	https://hub.docker.com/r/superelastix/elastix
Napari Plugin	https://github.com/SuperElastix/elastix_napari
	https://pypi.org/project/elastix-napari