Difference between revisions of "2009 Winter Project Week LungImagingPlatform"

From NAMIC Wiki
Jump to: navigation, search
(New page: {| |thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page ]] |[[]] |[[]] |} __NOTOC__ ===Key Investigators=== * James Ross * Raul San Jose <...)
 
 
(11 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
{|
 
{|
 
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
 
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[]]
+
|[[Image:sagittalLungLobes.jpg]]
|[[]]
+
|[[Image:AirwayInspectorGUI_small.png]]
 
|}
 
|}
  
Line 19: Line 19:
  
 
<h1>Objective</h1>
 
<h1>Objective</h1>
Our goal is to develop a lung imaging platform that can be used for the clinical understanding of multiple lung diseases like, Chronic Obstructive Pulmonary Disease (COPD), Asthma, Interstitial Lung Disease (ILD) among others. Quantitative lung imaging is a key component of on-going genetic and molecular biology studies that are being carried out at BWH and other centers across USA. A significant example of these new efforts is [http://www.copdgene.org/|COPD Genetics Epidemiology] multicenter study.
+
Our goal is to develop a lung imaging platform for the clinical understanding of multiple lung diseases such as Chronic Obstructive Pulmonary Disease (COPD), Asthma, and Interstitial Lung Disease (ILD) among others. Quantitative lung imaging is a key component of on-going genetic and molecular biology studies that are being carried out at BWH and other centers across USA. A significant example of these new efforts is [[http://www.copdgene.org/|COPD Genetics Epidemiology]] multicenter study. The NAMIC Kit and Slicer 3 are ideal candidates for the implementation of such efforts.
  
 
Our goals for this week are threefold:
 
Our goals for this week are threefold:
* User case analysis and design of the main platform components.
+
* Design the main platform components.
 
* Dynamic programming approaches for the extraction of 3D airways.
 
* Dynamic programming approaches for the extraction of 3D airways.
* Porting of our current imaging platform, [[http://www.airwayinspector.org| Airway Inspector]] based on 3D Slicer to Slicer 3.
+
* Porting our current imaging platform, [[http://www.airwayinspector.org| Airway Inspector]] based on 3D Slicer to Slicer 3.
  
 
</div>
 
</div>
Line 31: Line 31:
  
 
<h1>Approach, Plan</h1>
 
<h1>Approach, Plan</h1>
 +
Our approach is to develop a module in Slicer 3 that has the following components:
 +
* A unique library that can be linked against and shared by other Slicer modules or external applications.
 +
* Command Line Modules that encapsulate the individual algorithmic components of the platform without strings attached to a particular solution. The idea is to enable rapid prototyping and deployment of the solutions before they are fully integrated.
 +
* Custom solutions for disease-oriented applications: our plan is to discuss how an application can customize the Slicer 3 layout.
  
 +
We will focus on the following design aspects:
 +
* MRML data structures for tubular-type anatomical structures.
 +
* Support for quantitative imaging: handling data tables in Slicer 3 from MRML to Command Line Modules.
 +
* ITK filter hierarchies for the main image analysis components: extraction of lung lobes, airways and vessels.
 +
* Customizable GUI layout.
  
 
</div>
 
</div>
Line 38: Line 47:
  
 
<h1>Progress</h1>
 
<h1>Progress</h1>
 +
* LungImagingPlatform Module has been created. The code is currently available through the LMI repository (password = bwhspl):
 +
  :pserver:anonymous@cvs.spl.harvard.edu:/projects/cvs/slicer_lmi
 +
* Slicer2 functionality has been ported to the module.
 +
* The plan is to offer the module as an extension using the Extension infrastructure. This is still work in progress
 
* A semiautomatic lobe segmentation has been successfully implemented in Slicer 3 as a Command Line Module.
 
* A semiautomatic lobe segmentation has been successfully implemented in Slicer 3 as a Command Line Module.
* Initial design needs have been discussed.
+
* Design needs have been discussed and integration with vmtk for tubular network representation is going to be adopted.
 
+
* XNAT Desktop has been positively installed and tested as a platform to organize COPDGene datasets at BWH. Dicom rules have been defined to cover the needs of the project.
 +
* Initial discussions with Randy Golub have been carried out to leverage the Harvard XNAT enterprise resources.
 +
* GUI needs have been discussed to enable a module-dependent GUI space with more flexible layouts for reporting visual and quantitative results.
  
 
</div>
 
</div>
Line 48: Line 63:
 
</div>
 
</div>
  
===References===
+
=== Related projects ===
 +
Other projects that share some common goals are:
 +
* [http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]
 +
* [http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK | Vessel Segmentation in Slicer using VMTK ]
 +
* [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week:GT_TubularSurfaceSeg | Tubular volumetric segmentation framework ]
 +
 
 +
=== References ===

Latest revision as of 07:50, 9 January 2009

Home < 2009 Winter Project Week LungImagingPlatform
SagittalLungLobes.jpg AirwayInspectorGUI small.png



Key Investigators

  • James Ross
  • Raul San Jose


Objective

Our goal is to develop a lung imaging platform for the clinical understanding of multiple lung diseases such as Chronic Obstructive Pulmonary Disease (COPD), Asthma, and Interstitial Lung Disease (ILD) among others. Quantitative lung imaging is a key component of on-going genetic and molecular biology studies that are being carried out at BWH and other centers across USA. A significant example of these new efforts is [Genetics Epidemiology] multicenter study. The NAMIC Kit and Slicer 3 are ideal candidates for the implementation of such efforts.

Our goals for this week are threefold:

  • Design the main platform components.
  • Dynamic programming approaches for the extraction of 3D airways.
  • Porting our current imaging platform, [Airway Inspector] based on 3D Slicer to Slicer 3.

Approach, Plan

Our approach is to develop a module in Slicer 3 that has the following components:

  • A unique library that can be linked against and shared by other Slicer modules or external applications.
  • Command Line Modules that encapsulate the individual algorithmic components of the platform without strings attached to a particular solution. The idea is to enable rapid prototyping and deployment of the solutions before they are fully integrated.
  • Custom solutions for disease-oriented applications: our plan is to discuss how an application can customize the Slicer 3 layout.

We will focus on the following design aspects:

  • MRML data structures for tubular-type anatomical structures.
  • Support for quantitative imaging: handling data tables in Slicer 3 from MRML to Command Line Modules.
  • ITK filter hierarchies for the main image analysis components: extraction of lung lobes, airways and vessels.
  • Customizable GUI layout.

Progress

  • LungImagingPlatform Module has been created. The code is currently available through the LMI repository (password = bwhspl):
  :pserver:anonymous@cvs.spl.harvard.edu:/projects/cvs/slicer_lmi
  • Slicer2 functionality has been ported to the module.
  • The plan is to offer the module as an extension using the Extension infrastructure. This is still work in progress
  • A semiautomatic lobe segmentation has been successfully implemented in Slicer 3 as a Command Line Module.
  • Design needs have been discussed and integration with vmtk for tubular network representation is going to be adopted.
  • XNAT Desktop has been positively installed and tested as a platform to organize COPDGene datasets at BWH. Dicom rules have been defined to cover the needs of the project.
  • Initial discussions with Randy Golub have been carried out to leverage the Harvard XNAT enterprise resources.
  • GUI needs have been discussed to enable a module-dependent GUI space with more flexible layouts for reporting visual and quantitative results.


Related projects

Other projects that share some common goals are:

References