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SimpleITK

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SimpleITK is an image analysis toolkit with a large number of components supporting general filtering operations, image segmentation and registration. It is built on top of the Insight Segmentation and Registration Toolkit ITK with the intent of providing a simplified interface to ITK. SimpleITK itself is written in C++ but is available for a large number of programming languages. Currently these include:

Wrapping of the C++ code is accomplished through SWIG, in principle, any language wrapped by SWIG should be applicable to SimpleITK.

Unlike ITK's support of n-dimensional spatio-temporal images, SimpleITK supports 2D, 3D and optionally 3D+time. The dimensionality refers to spatio-temporal dimensions, the voxels can be n-dimensional vectors.

SimpleITK is licensed under the Apache License in the same way as ITK.

Development

SimpleITK uses the Git distributed version control system. The main repository is hosted on itk.org and mirrored to Github.

Contribute

We encourage any contributions from the community!

To submit code to SimpleITK, simply follow the standard GitHub workflow to make a pull request. More information can be found here and here regarding the workflow and getting your computer setup.

After cloning the repository, run ./Utilities/SetupForDevelopment.sh from within the SimpleITK repository to setup Git hooks. Say "no" to setting up access to itk.org as only core developers need access for merging pull requests.

Branches

  • next - An unstable branch which contains future features. These will be tested nightly on CDash. If the tests are passed, then they will be merged into master. Pull requests should never be based on this branch, however this is the default branch you should push changes to.
  • master - Stable branch of the code and suitable for most users when building SimpleITK.
  • release - Branch of the code from the latest release, and patches for the last can be based on and merged to.

The comprehensive regression testing is reported to the CDash Dashboard. This include extensive nightly testing on the next branch, nightly distributions packages on the release or master branch, and continuous integration from Github pull requests.

Documentation

With massive libraries like SimpleITK, good documentation is a must. The documentation for SimpleITK is split up into multiple levels:

  1. API Documentation - This contains class and function documentation. The descriptions for functions and classes are primarily borrowed from the original ITK classes.
  2. SimpleITK Documentation - This contains higher-level guides, installing toolkit's binary distributions, building the toolkit as well as examples specific to SimpleITK. This documentation will be valid for each language that SimpleITK supports. The examples will also include code in each language.
    • SimpleITK Wiki - This is the old SimpleITK documentation page which was replaced by ReadTheDocs. The information may be outdated.
  3. Notebooks Repositories - This documentation is similar to the SimpleITK documentation except it contains examples on how to utilize multiple classes in SimpleITK to facilitate solving a broader image processing problem.

Support

SimpleITK provides access to most of the ITK components, but not all. If you are looking for something specific and can't find it, open an issue on GitHub or ask for support on the forum.

Report an Issue

Help us improve SimpleITK by reporting issues you encounter. When you report an error, you allow us to address your specific problem, but more importantly you are helping all of the SimpleITK community.

Thank you for helping making SimpleITK better!

All issues are reported and managed on the project's GitHub issue tracker. When reporting an issue, please provide as much information as possible to enable us to reproduce the problem.

The following information will allow us to address your issue in a timely manner:

  1. Error message (copy & pasted) and focused description of the problem.
  2. Operating system, and version (e.g. OSX 10.11.6).
  3. Programming language, and version (e.g. Python 2.7.14, R 3.2.3).
  4. Version of SimpleITK (e.g. 1.1.0), just invoke the SimpleITK Version() function.
  5. How did you install SimpleITK, binary distribution (e.g. conda install -c simpleitk simpleitk), or built it from source (e.g. devtools::install_github("SimpleITK/SimpleITKRInstaller")).
  6. A minimal working example which causes the error.
  7. If your code requires input, possibly point to a minimal sized input image.