Latest revision as of 18:17, 13 December 2019

NOTICE
This page is being migrated to Read The Docs! For the up to date version please see this page!

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

Frequently Asked Questions (FAQ)

API

Nightly generated Doxygen.
Release 1.0 Doxygen.
Release 0.10 Doxygen.
Release 0.9 Doxygen.
Release 0.8 Doxygen.
Release 0.7 Doxygen.
Release 0.6.1 Doxygen.

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

SPIE Medical Imaging 2018, Houston TX, USA: SimpleITK Jupyter Notebooks: Biomedical Image Analysis in Python.

Past

The International Symposium on Biomedical Imaging (ISBI) 2016, Prague, Czech republic: SimpleITK: An Interactive, Python-Based Introduction to SimpleITK with the Insight Segmentation and Registration Toolkit (ITK)
SPIE Medical Imaging 2016, San Diego, USA: ITK in Biomedical Research and Commercial Applications

Tutorial material: git repository additional presentations .

Medical Image Computing and Computer Assisted Intervention (MICCAI) 2015, Munich, Germany: a Python based tutorial on the use of the ITKv4 registration framework via SimpleITK.

Tutorial material: git repository.

ImageJ User & Developer Conference 2015, Madison, WI, USA: an introductory tutorial in Python.

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).

General introduction of SimpleITK on the International Society for Computer Aided Surgery blog, 1 March 2017.
SimpleITK and R, 22 May 2015.
Medical Image Analysis Course, 20 December 2014.
Image Segmentation with Python and SimpleITK, October/November 2014.

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:

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.

@@ Line 1: / Line 1: @@
+{{SimpleITKMigrationHeader}}
 [[Image: SimpleITK-SquareTransparentLogo.png|center]]
@@ Line 12: / Line 14: @@
 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.
+= 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
+* 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])
 = Getting Started =
@@ Line 26: / Line 38: @@
 SimpleITK currently provides binary distribution for Python, CSharp and Java language bindings.
-You can download the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.10.0/ 0.10.0 release from SourceForge].
+You can download the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/ 1.0.0 release from SourceForge].
 = Documentation =
@@ Line 53: / Line 65: @@
 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 ==
@@ Line 66: / Line 70: @@
 === Upcoming ===
-* none
+* 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 ===
@@ Line 90: / Line 95: @@
 =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.
+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 ==
 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 Jira Issue Tracker ] hosted by the University of Iowa.
+[https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK Legacy Jira Issue Tracker ] hosted by the University of Iowa.
 == Releases ==
-* [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/SimpleITKDoxygen010/html/index.html Doxygen]
+* [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]
+* [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]
 * [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]
 * [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]
@@ Line 113: / Line 119: @@
 = 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.
-* [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:
+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.cmake.org/Wiki/CMake/Git/Develop CMake Development Process ]
@@ Line 128: / Line 129: @@
 == 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 ].
+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/Topic
-Additional information on how SimpleITK uses git can be found here: https://itk.org/SimpleITKDoxygen/html/GitPage.html.
+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: Difference between revisions

Latest revision as of 18:17, 13 December 2019

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