Difference between revisions of "SimpleITK"

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{{SimpleITKMigrationHeader}}
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[[Image: SimpleITK-SquareTransparentLogo.png|center]]
 
[[Image: SimpleITK-SquareTransparentLogo.png|center]]
  
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SimpleITK captures many of features available in ITK, and is under ongoing development. Earlier in the development process a set of [[SimpleITK/Goals|Specific Goals]] were outlined.
 
SimpleITK captures many of features available in ITK, and is under ongoing development. Earlier in the development process a set of [[SimpleITK/Goals|Specific Goals]] were outlined.
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 +
= How to Cite =
 +
 +
If you find SimpleITK useful in your research, please cite the relevant publications:
 +
 +
* Lowekamp BC, Chen DT, Ibáñez L and Blezek D (2013) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874546/pdf/fninf-07-00045.pdf The Design of SimpleITK]. Front. Neuroinform. 7:45. doi: 10.3389/fninf.2013.00045
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* Z. Yaniv, B. C. Lowekamp, H. J. Johnson, R. Beare, "SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research", J Digit Imaging., https://doi.org/10.1007/s10278-017-0037-8, 2017. (you can freely read the manuscript [http://em.rdcu.be/wf/click?upn=KP7O1RED-2BlD0F9LDqGVeSIWDx8-2B-2B8r81HkSA5fUW53U-3D_kZYp45lAKoeuSXKlMMKnLRu-2FO1jcvtAwo2UFz30PH9bPLAejS1IjjDkfGx8EIWfnvmrgAH2RF3xvrb1fezqultdVNEEAM7Fc2RGY-2BOVhjR-2BAN-2B7Wi6qUoM6BYtn1ZWsTzFdNZQxBXXJ2Nf0BaU5NhQLQVs2hoM2TXsKZ7pnKQXZVJEAOyLbQSvZkJOvdc7Gk36rdNDa3pn5vH17-2FvszYj4mKlZlgROxTE-2Be2yQ-2FOLAYsoDHZNvVuG4vJr4xNpQnmAI16Nz8h3GJi-2F9GKnpBsAg-3D-3D. here])
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= Getting Started =
 
= Getting Started =
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SimpleITK currently provides binary distribution for Python, CSharp and Java language bindings.  
 
SimpleITK currently provides binary distribution for Python, CSharp and Java language bindings.  
You can download the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1/ 0.9.1 release from SourceForge].
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You can download the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/ 1.0.0 release from SourceForge].
  
 
= Documentation =
 
= Documentation =
  
 
* [[SimpleITK/FAQ|Frequently Asked Questions (FAQ)]]
 
* [[SimpleITK/FAQ|Frequently Asked Questions (FAQ)]]
* Nightly generated [http://www.itk.org/SimpleITKDoxygen/html/ Doxygen].
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* Release 0.9 [http://www.itk.org/SimpleITKDoxygen09/html/index.html Doxygen].
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== API ==
* Release 0.8 [http://www.itk.org/SimpleITKDoxygen08/html/index.html Doxygen].
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* Release 0.7 [http://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen].
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* Nightly generated [https://www.itk.org/SimpleITKDoxygen/html/ Doxygen].
* Release 0.6.1 [http://www.itk.org/SimpleITKDoxygen06/html/ Doxygen].
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* Release 1.0 [https://www.itk.org/SimpleITKDoxygen100/html/index.html Doxygen].
 +
* Release 0.10 [https://www.itk.org/SimpleITKDoxygen010/html/index.html Doxygen].
 +
* Release 0.9 [https://www.itk.org/SimpleITKDoxygen09/html/index.html Doxygen].
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* Release 0.8 [https://www.itk.org/SimpleITKDoxygen08/html/index.html Doxygen].
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* Release 0.7 [https://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen].
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* Release 0.6.1 [https://www.itk.org/SimpleITKDoxygen06/html/ Doxygen].
 +
 
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== Short Examples ==
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Concise [https://itk.org/SimpleITKDoxygen/html/examples.html examples] illustrating the usage of various SimpleITK features. Examples are written in a variety of languages including Python, R, C++, Java...
  
 
== SimpleITK Notebooks ==
 
== SimpleITK Notebooks ==
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Additional repositories containing tutorial specific notebooks are listed in the [http://www.itk.org/Wiki/SimpleITK#SimpleITK_Tutorials Tutorials section] below.
 
Additional repositories containing tutorial specific notebooks are listed in the [http://www.itk.org/Wiki/SimpleITK#SimpleITK_Tutorials Tutorials section] below.
 
== Publications ==
 
 
More information about SimpleITK can be found in the following publication:
 
 
* Lowekamp BC, Chen DT, Ibáñez L and Blezek D (2013) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874546/pdf/fninf-07-00045.pdf The Design of SimpleITK]. Front. Neuroinform. 7:45. doi: 10.3389/fninf.2013.00045
 
 
Please cite SimpleITK and ITK when publishing work where it made a significant contribution.
 
  
 
== SimpleITK Tutorials ==
 
== SimpleITK Tutorials ==
  
 
=== Upcoming ===
 
=== Upcoming ===
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* SPIE Medical Imaging 2018, Houston TX, USA: [https://spie.org/MI/course/simpleitk-jupyter-notebooks-biomedical-image-analysis-in-python SimpleITK Jupyter Notebooks: Biomedical Image Analysis in Python].
  
  
 
=== Past ===
 
=== Past ===
 
* The International Symposium on Biomedical Imaging (ISBI) 2016, Prague, Czech republic: [http://biomedicalimaging.org/2016/?page_id=572  SimpleITK: An Interactive, Python-Based Introduction to SimpleITK with the Insight Segmentation and Registration Toolkit (ITK)]
 
* The International Symposium on Biomedical Imaging (ISBI) 2016, Prague, Czech republic: [http://biomedicalimaging.org/2016/?page_id=572  SimpleITK: An Interactive, Python-Based Introduction to SimpleITK with the Insight Segmentation and Registration Toolkit (ITK)]
* SPIE Medical Imaging 2016, San Diego, USA: [http://spie.org/MI/course/itk-in-biomedical-research-and-commercial-applications ITK in Biomedical Research and Commercial Applications]
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* SPIE Medical Imaging 2016, San Diego, USA: ITK in Biomedical Research and Commercial Applications
 
: Tutorial material: [https://github.com/InsightSoftwareConsortium/SimpleITKTutorialSPIE2016 git repository] [https://hdl.handle.net/10380/3542 additional presentations] .
 
: Tutorial material: [https://github.com/InsightSoftwareConsortium/SimpleITKTutorialSPIE2016 git repository] [https://hdl.handle.net/10380/3542 additional presentations] .
 
* Medical Image Computing and Computer Assisted Intervention (MICCAI) 2015, Munich, Germany: a Python based tutorial on the use of the [[SimpleITK/Tutorials/MICCAI2015 | ITKv4 registration framework via SimpleITK]].
 
* Medical Image Computing and Computer Assisted Intervention (MICCAI) 2015, Munich, Germany: a Python based tutorial on the use of the [[SimpleITK/Tutorials/MICCAI2015 | ITKv4 registration framework via SimpleITK]].
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== Community Blogs ==
 
== Community Blogs ==
  
These are blog entries written by people who are not directly involved with SimpleITK. If you want us to link to your SimpleITK blog entry just let us know on the mailing list (community@itk.org).  
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These are blog entries written by people who are not necessarily directly involved with SimpleITK. If you want us to link to your SimpleITK blog entry just let us know on the mailing list (community@itk.org).  
  
 +
* General introduction of SimpleITK on the [http://news.iscas.co/simpleitk-a-simplified-multi-language-interface-to-the-insight-segmentation-and-registration-toolkit/  International Society for Computer Aided Surgery blog], 1 March 2017.
 
* [http://zarquon42b.github.io/2015/05/22/SimpleITKandR/  SimpleITK and R], 22 May 2015.
 
* [http://zarquon42b.github.io/2015/05/22/SimpleITKandR/  SimpleITK and R], 22 May 2015.
 
* [http://kevin-keraudren.blogspot.com/2014/12/medical-image-analysis-ipython-tutorials.html Medical Image Analysis Course], 20 December 2014.
 
* [http://kevin-keraudren.blogspot.com/2014/12/medical-image-analysis-ipython-tutorials.html Medical Image Analysis Course], 20 December 2014.
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=Support=
 
=Support=
  
SimpleITK is supported through the ITK community and the active developers. In addition to the resources listed above in the documentation section, the [http://www.itk.org/ITK/help/mailing.html ITK mailing lists] can be used to asked questions and obtain additional help.
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SimpleITK is supported through the ITK community and the active developers. In addition to the resources listed above in the documentation section, the [https://discourse.itk.org discourse forum]  can be used to ask questions and obtain additional help from the ITK community. The legacy [http://www.itk.org/ITK/help/mailing.html ITK mailing lists] is no longer prefered.
  
 
== Issue Tracking And Feature Requests ==
 
== Issue Tracking And Feature Requests ==
  
We are currently using the [https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK Jira Issue Tracker ] hosted by the University of Iowa.
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We are currently using the [https://github.com/SimpleITK/SimpleITK/issues github issue tracker]. Before switching to github issue tracking we used an instance of the
 +
[https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK Legacy Jira Issue Tracker ] hosted by the University of Iowa.
  
 
== Releases ==
 
== Releases ==
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=ec033f0be4f67b2e21483ed9bc3698f07dba9d06 v0.9.1] [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.1_Release|Release Notes]] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1 Downloads]  
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=refs/tags/v1.0.1 v1.0.1] [https://github.com/SimpleITK/SimpleITK/releases/tag/v1.0.1 Release Notes]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=7f06e9fc7f3cda9c47e8b7d6d37885b1f425ea3b v0.9.0] [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.9.0_Release|Release Notes]] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.0 Downloads] [http://www.itk.org/SimpleITKDoxygen09/html/index.html Doxygen]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=refs/tags/v1.0.0 v1.0.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v1.0.0 Release Notes] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0 Downloads] [https://www.itk.org/SimpleITKDoxygen100/html/index.html Doxygen]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=d0a90983877b46631e69a398bd8341889912c8c2 v0.8.1] [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.1_Release|Release Notes]]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/ Downloads]  [http://www.itk.org/SimpleITKDoxygen08/html/index.html Doxygen]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=4a3376df08f27162b4d2a90e4a0452a839ab3124 v0.10.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.10.0 Release Notes] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0 Downloads] [https://www.itk.org/SimpleITKDoxygen010/html/index.html Doxygen]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=11bff587f8a930bbca02813595aa3d08388af979 v0.8.0] [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.8.0_Release|Release Notes]]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.0/ Downloads]  
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=ec033f0be4f67b2e21483ed9bc3698f07dba9d06 v0.9.1] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.9.1 Release Notes] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.1 Downloads]  
* [http://itk.org/gitweb?p=SimpleITK.git;a=commit;h=a2b29110771a1eb0b09d18ff8e98a784dc6e6451 v0.7.1]  [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.7.1_Release|Release Notes]]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.1/ Downloads]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=7f06e9fc7f3cda9c47e8b7d6d37885b1f425ea3b v0.9.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.9.0 Release Notes] [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.9.0 Downloads] [https://www.itk.org/SimpleITKDoxygen09/html/index.html Doxygen]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=6fecf5ae5859295082b9016c97bf4bd68a961a62 v0.7.0] [[SimpleITK/ReleaseNotes#SimpleITK_-_Version_0.7.0_Release|Release Notes]]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.0/ Downloads]  [http://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=d0a90983877b46631e69a398bd8341889912c8c2 v0.8.1] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.8.1 Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.1/ Downloads]  [https://www.itk.org/SimpleITKDoxygen08/html/index.html Doxygen]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=fc17df598cac97d344c875fed117f03ae7d1aacd v0.6.1]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.1/ Downloads] [http://www.itk.org/SimpleITKDoxygen06/html/index.html Doxygen]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=11bff587f8a930bbca02813595aa3d08388af979 v0.8.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.8.Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.0/ Downloads]  
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=c055ef4e4cd2802c56e169084d9dd1bc655b4e93 v0.6.0]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.0/ Downloads]  
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* [https://itk.org/gitweb?p=SimpleITK.git;a=commit;h=a2b29110771a1eb0b09d18ff8e98a784dc6e6451 v0.7.1]  [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.7.Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.1/ Downloads]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=41fbb6d69f88fa1c8ab3b9d710b7ae57bb975721 v0.5.1]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.5.1/ Downloads]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=6fecf5ae5859295082b9016c97bf4bd68a961a62 v0.7.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.7.Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.0/ Downloads]  [https://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen]
* [http://itk.org/gitweb?p=SimpleITK.git;a=tag;h=35ccfd2b99b4b5675d4d0894bb870574396408b6 v0.5.0]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.5.0/ Downloads]
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* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=fc17df598cac97d344c875fed117f03ae7d1aacd v0.6.1]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.1/ Downloads] [http://www.itk.org/SimpleITKDoxygen06/html/index.html Doxygen]
 +
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=c055ef4e4cd2802c56e169084d9dd1bc655b4e93 v0.6.0]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.6.0/ Downloads]  
 +
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=41fbb6d69f88fa1c8ab3b9d710b7ae57bb975721 v0.5.1]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.5.1/ Downloads]
 +
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=35ccfd2b99b4b5675d4d0894bb870574396408b6 v0.5.0]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.5.0/ Downloads]
  
 
= Development =
 
= Development =
  
SimpleITK follows many of the conventions established by  ITK. For user contributions the gerrit based work flow from ITK can be followed:
+
SimpleITK has moved to a [https://github.com/SimpleITK/SimpleITK Github] based work flow for issues tracking and contribution.
  
* [http://www.itk.org/Wiki/ITK/Git/Develop ITK Development Process].
 
  
We certainly welcome contributions from the users and the community. Currently the development team is small, so may of our practices are not fully document, but this will be improving in the future.
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SimpleITK utilizes an additional "next" branch to merge and test changes before merging into the master branch. This makes our "master" branch more stable and reliable. This follows the CMake development process:
 
 
* [http://www.itk.org/SimpleITKDoxygen/html/DeveloperPage.html Additional Developer Information ]
 
 
 
A main difference between the SimpleITK and ITK development is that we have an additional "next" branch which is used for topics underdevelopment, so that they can be tested on the dashboard without being merged into the "master" branch. This will make the "master" branch more stable and reliable. This follows the CMake development process more:
 
  
 
* [http://www.cmake.org/Wiki/CMake/Git/Develop CMake Development Process ]
 
* [http://www.cmake.org/Wiki/CMake/Git/Develop CMake Development Process ]
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== Source Code Repository ==
 
== Source Code Repository ==
  
SimpleITK uses git as the revision control system.  The main repository is hosted along side ITK as http://itk.org/SimpleITK.git  [http://public.kitware.com/gitweb?p=SimpleITK.git]. It is also mirrored on  [https://github.com/SimpleITK/SimpleITK Github ].
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SimpleITK uses git as the revision control system.  The official repository is hosted along side ITK as http://itk.org/SimpleITK.git  [http://public.kitware.com/gitweb?p=SimpleITK.git]. It is also mirrored on  [https://github.com/SimpleITK/SimpleITK Github ].
  
Development is currently following the branchy workflow with the Kitware stage. This workflow is described here:
+
Development is currently following the branchy workflow with the Kitware stage repository. This workflow is described here:
 
*http://public.kitware.com/Wiki/Git/Workflow/Stage
 
*http://public.kitware.com/Wiki/Git/Workflow/Stage
 
*http://public.kitware.com/Wiki/Git/Workflow/Topic
 
*http://public.kitware.com/Wiki/Git/Workflow/Topic
  
Additional information on how SimpleITK uses git can be found here: http://www.itk.org/SimpleITKDoxygen/html/Git.html.
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Contributions from github will be pushed to the stage repo and merged into the next branch by a SimpleITK developer.
 
 
  
 
== [[SimpleITK/Design_And_Proposals | Design And Proposals]] ==
 
== [[SimpleITK/Design_And_Proposals | Design And Proposals]] ==

Latest revision as of 13:17, 13 December 2019

NOTICE
This page is being migrated to Read The Docs!

For the up to date version please see this page!

SimpleITK-SquareTransparentLogo.png

Overview

Welcome to the National Library of Medicine Insight Segmentation and Registration Toolkit (ITK). ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages. SimpleITK has the following main characteristics:

  • C++ library with wrappers for Python, Java, CSharp, R, Tcl and Ruby
  • Object-oriented
  • Provides a simplified, easy-to-use, procedural interface without templates
  • Is distributed under an open source Apache 2.0 License
  • Binary distributions for Python, Java and CSharp

SimpleITK captures many of features available in ITK, and is under ongoing development. Earlier in the development process a set of Specific Goals were outlined.

How to Cite

If you find SimpleITK useful in your research, please cite the relevant publications:

  • Lowekamp BC, Chen DT, Ibáñez L and Blezek D (2013) The Design of SimpleITK. Front. Neuroinform. 7:45. doi: 10.3389/fninf.2013.00045
  • Z. Yaniv, B. C. Lowekamp, H. J. Johnson, R. Beare, "SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research", J Digit Imaging., https://doi.org/10.1007/s10278-017-0037-8, 2017. (you can freely read the manuscript here)


Getting Started

Download

SimpleITK currently provides binary distribution for Python, CSharp and Java language bindings. You can download the 1.0.0 release from SourceForge.

Documentation

API

Short Examples

Concise examples illustrating the usage of various SimpleITK features. Examples are written in a variety of languages including Python, R, C++, Java...

SimpleITK Notebooks

The SimpleITK Notebooks are examples and tutorials on how to use SimpleITK utilizing Jupyter Notebooks. This approach allows the user to create, edit and re-run scripts and view the results all within a web interface. The authoritative description of what Jupyter Notebooks are can be found on the Jupyter website. While SimpleITK supports a number of programming languages, the majority of notebooks are written in Python and some in R.

The main notebook repository is available on github.

Additional repositories containing tutorial specific notebooks are listed in the Tutorials section below.

SimpleITK Tutorials

Upcoming


Past

Tutorial material: git repository additional presentations .
Tutorial material: git repository.
Tutorial material: git repository.
  • Medical Image Computing and Computer Assisted Intervention (MICCAI) 2011, Toronto, Canada: a general tutorial on SimpleITK.
Tutorial material: PDF of presentation, virtual machine, and git repository.

Community Blogs

These are blog entries written by people who are not necessarily directly involved with SimpleITK. If you want us to link to your SimpleITK blog entry just let us know on the mailing list (community@itk.org).

Support

SimpleITK is supported through the ITK community and the active developers. In addition to the resources listed above in the documentation section, the discourse forum can be used to ask questions and obtain additional help from the ITK community. The legacy ITK mailing lists is no longer prefered.

Issue Tracking And Feature Requests

We are currently using the github issue tracker. Before switching to github issue tracking we used an instance of the Legacy Jira Issue Tracker hosted by the University of Iowa.

Releases

Development

SimpleITK has moved to a Github based work flow for issues tracking and contribution.


SimpleITK utilizes an additional "next" branch to merge and test changes before merging into the master branch. This makes our "master" branch more stable and reliable. This follows the CMake development process:


Source Code Repository

SimpleITK uses git as the revision control system. The official repository is hosted along side ITK as http://itk.org/SimpleITK.git [1]. It is also mirrored on Github .

Development is currently following the branchy workflow with the Kitware stage repository. This workflow is described here:

Contributions from github will be pushed to the stage repo and merged into the next branch by a SimpleITK developer.

Design And Proposals