2009 Winter Project Week LungImagingPlatform
- James Ross
- Raul San Jose
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.
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.
- LungImagingPlatform Module has been created. The code is currently available through the LMI repository (password = bwhspl):
- 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.
Other projects that share some common goals are:
- | User Interface Flexible Layouts
- | Vessel Segmentation in Slicer using VMTK
- | Tubular volumetric segmentation framework