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'''Simple ITK'''
{{SimpleITKMigrationHeader}}


= Goals =
[[Image: SimpleITK-SquareTransparentLogo.png|center]]


* Provide an easy-access layer to ITK for non-C++ expert developers
=Overview=


= Sandbox =
Welcome to the National Library of Medicine Insight Segmentation and Registration Toolkit (ITK). [http://www.itk.org/ 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:


* http://github.com/dblezek/SimpleITK
* 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


= Scope =
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.


== Suggested Areas to Cover ==
= How to Cite =


* IO
If you find SimpleITK useful in your research, please cite the relevant publications:
* Basic Filters
* Registration
** Basic Framework
** Deformable registration
*** BSplines
*** Demons
* Segmentation
** Region Growing
** Level Sets
** Classifiers


== Types ==
* 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


* Image pixel types supported
* 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])
** int8_t
** int16_t
** int32_t
** float
* Image dimensions supported
** 3D
** Is 2D managed as a 3D image of 1 slice ?
*** Performance penalty for neighborhood filters... ?
*** Could be "2D" versions of 3D filters, i.e. RecursiveGaussianFilter2D. This would work on a slice-by-slice basis.


== Languages ==
Wrapped languages will be any that SWIG supports, if someone is willing to write tests / any needed glue code.
* C++ Layer
* Python
* Lua
* Java
* ?


= Implementation Details =


* Coding Style
= Getting Started =
** Copyright Headers & License
* Const correctness (can we avoid using const's completely?)
* Testing
** C++ testing (Google Test?)
** Python tests (PyUnit?)
** Lua tests (?!?)
** Java tests (JUnit)
** ? other languages ?
* Managing basic types
** Arrays
** Regions
** Transforms
* Not so basic types (could these be enums passed as ivars?)
** Interpolators
** Optimizers
** Metrics


= Plan =
* [[SimpleITK/GettingStarted|Getting Started For Users]]
** [[SimpleITK/GettingStarted#Binaries|downloading the binaries]]
** [[SimpleITK/GettingStarted#Build_It_Yourself|build the code yourself]]
** [[SimpleITK/GettingStarted#Recommended_Software|additional software]] which is useful with SimpleITK
* [[SimpleITK/GettingStarted/Visual_guide_to_building_on_Linux|A Visual Guide to Building SimpleITK on Linux]]
* [[SimpleITK/GettingStarted/A_visual_guide_to_SimpleITK_in_Java|A Visual Guide to SimpleITK with Java and Eclipse]]
* [[SimpleITK/GettingStarted/A_visual_guide_to_SimpleITK_with_CSharp|A Visual Guide to SimpleITK with CSharp on Microsoft Visual Studio]]


* Image classes
== Download ==
* IO


= TCons =
SimpleITK currently provides binary distribution for Python, CSharp and Java language bindings.
== Tcon topics 7/15/2010 ==
You can download the [https://sourceforge.net/projects/simpleitk/files/SimpleITK/1.0.0/ 1.0.0 release from SourceForge].
Toll-Free #:      1-800-704-9804
International #:  1-404-920-6604
Participant Code: 61466276
Thursday, July 15th, 3:30-5:00pm EDT
(2:30-4:00pm Central).


* General architecture
= Documentation =
* Wrapping efficiency
* Should SimpleITK be mixable with normal ITK ?
** At C++ level ?
** At WrapITK (Python, Tcl ) level ?
** Provide access to the underlying ITK image ?
* SimpleImage class
** Include casting to other image types.
** Introduce in ITK an itk::ImageBase class that is not templated over Dimension.
* Use Pointer semantics ?
** image->getDepth() vs image.getDepth()


* What kind of flexibility to provide for Users to add functionalities to SimpleITK
* [[SimpleITK/FAQ|Frequently Asked Questions (FAQ)]]
** It should be easy to write (even if the class is conceptually complex).
** User says : "I need this data type X..."
*** Then, how hard is for the developer of SimpleITK classes to satisfy the user's request.


* Design a Simple calling convention
== API ==
** Procedural-like notation...


== Tcon topics 7/22/2010 ==
* Nightly generated [https://www.itk.org/SimpleITKDoxygen/html/ Doxygen].
* 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].
* Release 0.8 [https://www.itk.org/SimpleITKDoxygen08/html/index.html Doxygen].
* Release 0.7 [https://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen].
* Release 0.6.1 [https://www.itk.org/SimpleITKDoxygen06/html/ Doxygen].


* Should SimpleITK be mixable with VTK?
== Short Examples ==
** SimpleImage class include casting to vtkImage?
 
** Concept: interactive programming languages are really cool if they include data visualization.  We need to have a way to visualize images as we process them.
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 ==
 
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 [http://jupyter.org/ 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 [https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks github].
 
Additional repositories containing tutorial specific notebooks are listed in the [http://www.itk.org/Wiki/SimpleITK#SimpleITK_Tutorials Tutorials section] below.
 
== SimpleITK Tutorials ==
 
=== Upcoming ===
 
* 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 ===
* 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: ITK in Biomedical Research and Commercial Applications
: 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]].
: Tutorial material: [https://github.com/InsightSoftwareConsortium/SimpleITKTutorialMICCAI2015.git git repository].
* ImageJ User & Developer Conference 2015, Madison, WI, USA: [http://imagej.net/Conference_2015_Program#Matt_McCormick_-_SimpleITK an introductory tutorial] in Python.
: Tutorial material: [https://github.com/InsightSoftwareConsortium/SimpleITKWorkshopImageJ2015 git repository]. 
* Medical Image Computing and Computer Assisted Intervention (MICCAI) 2011, Toronto, Canada: a general [[ITK_Release_4/Outreach/Conferences/MICCAI 2011/SimpleITK|tutorial on SimpleITK]].
: Tutorial material: [https://github.com/SimpleITK/SimpleITK-MICCAI-2011-Tutorial/blob/master/Presentation/SimpleITK-MICCAI-2011.pdf?raw=true PDF of presentation], [http://midas.kitware.com/collection/view/175 virtual machine], and [https://github.com/SimpleITK/SimpleITK-MICCAI-2011-Tutorial  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 [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://kevin-keraudren.blogspot.com/2014/12/medical-image-analysis-ipython-tutorials.html Medical Image Analysis Course], 20 December 2014.
* [https://pyscience.wordpress.com/tag/simpleitk 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  [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 Legacy Jira Issue Tracker ] hosted by the University of Iowa.
 
== Releases ==
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=refs/tags/v1.0.1 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]
* [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]
* [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]
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=11bff587f8a930bbca02813595aa3d08388af979 v0.8.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.8.0  Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.8.0/ Downloads]
* [https://itk.org/gitweb?p=SimpleITK.git;a=commit;h=a2b29110771a1eb0b09d18ff8e98a784dc6e6451 v0.7.1]  [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.7.1  Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.1/ Downloads]
* [https://itk.org/gitweb?p=SimpleITK.git;a=tag;h=6fecf5ae5859295082b9016c97bf4bd68a961a62 v0.7.0] [https://github.com/SimpleITK/SimpleITK/releases/tag/v0.7.0  Release Notes]  [https://sourceforge.net/projects/simpleitk/files/SimpleITK/0.7.0/ Downloads]  [https://www.itk.org/SimpleITKDoxygen07/html/index.html Doxygen]
* [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 =
 
SimpleITK has moved to a [https://github.com/SimpleITK/SimpleITK 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:
 
* [http://www.cmake.org/Wiki/CMake/Git/Develop 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  [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 repository. This workflow is described here:
*http://public.kitware.com/Wiki/Git/Workflow/Stage
*http://public.kitware.com/Wiki/Git/Workflow/Topic
 
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]] ==

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!

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

Retrieved from "https://public.kitware.com/Wiki/index.php?title=SimpleITK&oldid=63990"