Difference between revisions of "2015 Winter Project Week COPD Breakout"

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== Introduction==
 
== Introduction==
 +
Chest Imaging Platform 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.
  
−
=== Project Goals and Funding ===
+
* 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): First consolidate of our development for high-throughput image analysis in [www.copdgene.org COPDGene] with dependencies to Slicer3.
 +
* 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 0.1 of the Chest Imaging Platform
  
 
=== Brief intro to COPD ===
 
=== Brief intro to COPD ===
  
 
=== Team ===
 
=== Team ===
 +
* James Ross
 +
* Rola Harmouche
 +
* Jorge Onieva
 +
* German Gonzalez
 +
* Alex Yarmakovich
  
 
== Architecture ==
 
== Architecture ==

Revision as of 10:38, 6 January 2015

Home < 2015 Winter Project Week COPD Breakout

Introduction

Chest Imaging Platform 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): First consolidate of our development for high-throughput image analysis in [www.copdgene.org COPDGene] with dependencies to Slicer3.
  • 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 0.1 of the Chest Imaging Platform

Brief intro to COPD

Team

  • James Ross
  • Rola Harmouche
  • Jorge Onieva
  • German Gonzalez
  • Alex Yarmakovich

Architecture

Chest Imaging Platform (CIP)

Git Repository

Code Structure

CIP has four main components

  • 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]


Command Line Tools

slides

Testing Infrastructure

Slicer CIP

Git Repository

MRML Types

Modules Categories

Slicer Module Examples

slides

New Developments: Organ Detection

slides

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