Difference between revisions of "2015 Winter Project Week COPD Breakout"
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== Introduction== | == Introduction== | ||
| + | Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD). | ||
| + | The main development is currently funded through a NHLBI R01 mechanism as part of the [http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html Continued Development and Maintenance of Software PA] | ||
| + | === Project Goals === | ||
| + | * AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms. | ||
| − | + | * AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort. | |
| + | * AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community. | ||
=== History === | === History === | ||
| − | + | * 2006- [http://www.airwayinspector.org Airway Inspector] (2006- ): Slicer2 module for COPD analysis emphysema and airway disease. | |
| + | * Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in [https://www.copdgene.org COPDGene]. | ||
| + | * April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library. | ||
| + | * April 2013 - January 2014: Port to github and further consolidation under a private repository. | ||
| + | * Today: Release 0.0.0 of the [https://github.com/acil-bwh/ChestImagingPlatform Chest Imaging Platform] | ||
=== Brief intro to COPD === | === Brief intro to COPD === | ||
| + | [https://na-mic.org/w/images/2/26/BreakoutSession-CIP-COPDIntro.pptx slides] | ||
=== Team === | === Team === | ||
| + | * Raul San Jose | ||
| + | * James Ross | ||
| + | * Rola Harmouche | ||
| + | * Jorge Onieva | ||
| + | * German Gonzalez | ||
| + | * Alex Yarmakovich | ||
| + | |||
| + | Collaborators | ||
| + | * George Washko | ||
| + | * Alejandro Diaz | ||
== Architecture == | == Architecture == | ||
| − | + | [[File:CIPArchitecture.png]] | |
== Chest Imaging Platform (CIP) == | == Chest Imaging Platform (CIP) == | ||
[https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository] | [https://github.com/acil-bwh/ChestImagingPlatform.git Git Repository] | ||
=== Code Structure === | === Code Structure === | ||
| − | CIP has four main components | + | CIP has four main components [https://na-mic.org/w/images/0/0b/CipTools.pptx slides] |
*Common: base library | *Common: base library | ||
*Utilities: third party libraries | *Utilities: third party libraries | ||
| Line 34: | Line 54: | ||
* Region/Type structure for labelmaps | * Region/Type structure for labelmaps | ||
| − | |||
=== Python and CIP === | === Python and CIP === | ||
| Line 43: | Line 62: | ||
| − | + | === Command Line Tools === | |
| + | [https://na-mic.org/w/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides] | ||
== Testing Infrastructure == | == Testing Infrastructure == | ||
| − | [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard] | + | * [https://na-mic.org/w/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx Slides] |
| + | |||
| + | * [http://cdash.airwayinspector.org/index.php?project=CIP Dashboard] | ||
== Slicer CIP == | == Slicer CIP == | ||
| Line 56: | Line 78: | ||
* [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles] | * [https://github.com/acil-bwh/SlicerCIP/tree/master/Loadable/ParticlesDisplay Particles] | ||
| − | === | + | === Slicer Module Examples === |
| + | [https://na-mic.org/w/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides] | ||
| − | == | + | == New Developments: Organ Detection == |
| + | [https://na-mic.org/w/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides] | ||
Latest revision as of 18:27, 10 July 2017
Home < 2015 Winter Project Week COPD BreakoutContents
Introduction
Chest Imaging Platform (CIP) and SlicerCIP is a multi year development from the Applied Chest Imaging Laboratory (Brigham and Women's Hospital) for quantitative CT in lung disease, in particular Chronic Obstructive Pulmonary Disease (COPD). The main development is currently funded through a NHLBI R01 mechanism as part of the Continued Development and Maintenance of Software PA
Project Goals
- AIM 1: Design and Development of the Chest Imaging Platform (CIP) as a toolkit for lung specific image-based algorithms.
- AIM 2: Integration of CIP components as Slicer 4 plugins for user-driven and workflow-based analysis and validation of emphysema, airway disease and pulmonary vascular disease analysis workflows in our prior study cohorts and the COPDGene cohort.
- AIM 3: Documentation and dissemination of the Chest Imaging Platform within the clinical community.
History
- 2006- Airway Inspector (2006- ): Slicer2 module for COPD analysis emphysema and airway disease.
- Lung Imaging Platform (Jan 2009 - March 2012): Initial consolidation of our developments for high-throughput image analysis in COPDGene.
- April 2012 - March 2013: First consolidation of LIP into CIP as a stand-alone library.
- April 2013 - January 2014: Port to github and further consolidation under a private repository.
- Today: Release 0.0.0 of the Chest Imaging Platform
Brief intro to COPD
Team
- Raul San Jose
- James Ross
- Rola Harmouche
- Jorge Onieva
- German Gonzalez
- Alex Yarmakovich
Collaborators
- George Washko
- Alejandro Diaz
Architecture
Chest Imaging Platform (CIP)
Code Structure
CIP has four main components slides
- Common: base library
- Utilities: third party libraries
- Command Line Tools: Slicer execution model tools
- cip_python: python library
Building CIP
git clone https://github.com/acil-bwh/ChestImagingPlatform.git mkdir ChestImagingPlatform-build cd ChestImagingPlatoform-build ccmake ../ChestImagingPlatform
Components and Data type
- Region/Type structure for labelmaps
Python and CIP
cip_python provides the following functionality:
- Code base for scale-space particles [1]
- Phenotype computation framework [2]
- Nipype interfaces for CLIS [3]
