2012 Progress Report HIGHLIGHTS - Revision history

Will at 16:53, 23 April 2012

2012-04-23T16:53:40Z

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2012-04-23T16:53:28Z

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2.3 NA-MIC Kit

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	= 2 Highlights =		= 2 Highlights =
	The scope of NA-MIC activities includes advanced medical image analysis research combined with leading edge software processes and computational platforms. To reflect these activities, the NA-MIC Computer Science Core efforts are organized around two teams: Algorithms and Engineering. Their joint output is the NA-MIC Kit which embodies a comprehensive set of analysis techniques in a well architected, documented, and widely used platform as described in the following paragraphs.		The scope of NA-MIC activities includes advanced medical image analysis research combined with leading edge software processes and computational platforms. To reflect these activities, the NA-MIC Computer Science Core efforts are organized around two teams: Algorithms and Engineering. Their joint output is the NA-MIC Kit which embodies a comprehensive set of analysis techniques in a well architected, documented, and widely used platform as described in the following paragraphs.

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 ** Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype tools, enabling local and distributed scripted execution of processing pipelines. Such methods for distributed computing are essential to tackling the Big Data and complex algorithms that current research is producing.
 ** Finally a whole host of application improvements including an improved flexible view layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster hardware accelerated volume rendering; improved markups and annotations; improved atlas and model hierarchy support; a streamlined and revised diffusion MRI implementation.
-* Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to transition new technologies to the wider community, to enable community members to contribute back to Slicer and the NA-MIC Kit, and to ensure high-quality systems.
+* Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to transition new technologies to the wider community, to enable community members to contribute back to Slicer and the NA-MIC Kit, and to ensure high-quality systems. Beyond some of the support activities mentioned previously, the following are other accomplishments.
-**
+** We have begun integrating the SimpleITK module of ITKv4 into Slicer to ensure simple integration capabilities with emerging algorithms.
 == 2.3 NA-MIC Kit ==

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 ** Slicer Execution Model modules (also known as Command Line Modules) are now available as Nipype tools, enabling local and distributed scripted execution of processing pipelines. Such methods for distributed computing are essential to tackling the Big Data and complex algorithms that current research is producing.
 ** Finally a whole host of application improvements including an improved flexible view layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster hardware accelerated volume rendering; improved markups and annotations; improved atlas and model hierarchy support; a streamlined and revised diffusion MRI implementation.
-* Finally the Slicer4 computational model was extended to include:
+* Community support for NA-MIC and the various NA-MIC Kit tools continues. The goals of this effort are to transition new technologies to the wider community, to enable community members to contribute back to Slicer and the NA-MIC Kit, and to ensure high-quality systems.
-** Multivolume analysis
+**
 == 2.3 NA-MIC Kit ==

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 ** Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard clinical image management environments and workflows.
 ** Compatibility with ITK version 4 was developed and continuously maintained over the past year as ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 ** Finally a whole host of application improvements including an improved flexible view layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster hardware accelerated volume rendering; improved markups and annotations; improved atlas and model hierarchy support; a streamlined and revised diffusion MRI implementation.
 * Finally the Slicer4 computational model was extended to include:

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 * The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much current work, and it is an enabling technology for the wider biomedical computing community. This past year saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000 times, at a rate of over 100 downloads per day, from users and research groups located around the world. Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated the previous KWWidgets GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more responsive behavior.
 * Beyond the core Slicer4 platform, several important features were also added to the application. These include:
-** The Slicer Extension Manager is now the "Slicer Catalog" and will enable the community to create compact modules which extend the core functionality.
+** The Slicer Extension Manager is now the "Slicer Catalog" (an App Store) and will enable the community to create compact modules which extend the core functionality.
 ** Python has been adopted as the preferred scripting language, a preferred programming language in the scientific computing community. Hence a variety of computational packages are now available to extend Slicer capabilities at run-time.
 ** Slicer4 includes a DICOM listener and DICOM Query/Retrieve capabilities for integration with standard clinical image management environments and workflows.
 ** Compatibility with ITK version 4 was developed and continuously maintained over the past year as ITKv4 matured. Slicer will officially switch to ITKv4 in the coming months.
 ** Finally a whole host of application improvements including an improved flexible view layout system; a revised implementation of the Expectation Maximization (EM) Segmenter; faster hardware accelerated volume rendering; improved markups and annotations; improved atlas and model hierarchy support; a streamlined and revised diffusion MRI implementation.
-* New Features
+* Finally the Slicer4 computational model was extended to include:
 ** Multivolume analysis
 ** Interactive methods

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 == 2.2 Engineering ==
 The Engineering Team build bridges between the various NAMIC cores and ultimately to the wider biomedical computing community. Working with the Algorithms Team, it deploys leading edge biomedical computing tools back to the DBPs, which are then used to perform impactful health research. In addition, the tools developed by the Engineering Team are used to train and disseminate technologies across research community. The Team places particular focus on developing sustainable communities through the creation of open platforms, quality-inducing software processes, and integration to a broad variety of computational tools and databases. The following describes some of the highlights of the past year's work.
-* The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much current work, and it is an enabling technology for the wider biomedical computing community. This past year saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000 times, at a rate of over 100 downloads per day, from users and research groups located around the world.
+* The flagship product from the Engineering Team is the 3D Slicer application. It is the delivery platform for much current work, and it is an enabling technology for the wider biomedical computing community. This past year saw the release of Slicer version 4.0 (Slicer4) which represents a significant advance in capabilities and underlying technologies. Since its release at RSNA in November, Slicer4 has been downloaded over 45,000 times, at a rate of over 100 downloads per day, from users and research groups located around the world. Slicer4 is now a modern, stable platform built with the Qt GUI system (eliminated previous KWWidgets GUI), and rewritten for simplicity, enabling simpler approaches to debugging, faster startup, and more responsive behavior.
 * Extending Slicer
 ** Python has been adopted as the preferred scripting language,

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 * Recent developments are in process of being integrated into the NA-MIC Kit and the Slicer application platform.
 ** The Slicer Catalog allows users to install, unstall, search, browse, and rank Slicer extensions. This user experience is available from within Slicer and over the web - much like the Android and Apple App Stores. Developers can contribute, update, document, and post screenshots on their modules and receive community feedback.
-**
+** The analysis infrastructure for Diffusion Weighted MRI (DWI) IO and visualization has been generalized to be used for other time varying acquisitions like multivolume analysis, dynamic contrast enhanced MRI (DCE), and gated cardiac CT.