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

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=== Brief intro to COPD ===
 
=== Brief intro to COPD ===
[http://www.na-mic.org/Wiki/images/2/26/BreakoutSession-CIP-COPDIntro.pptx slides]
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[https://na-mic.org/w/images/2/26/BreakoutSession-CIP-COPDIntro.pptx slides]
  
 
=== Team ===
 
=== Team ===
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[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 [http://www.na-mic.org/Wiki/images/0/0b/CipTools.pptx slides]
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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
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=== Command Line Tools ===
 
=== Command Line Tools ===
[http://www.na-mic.org/Wiki/images/0/06/BreakoutSession-CIP-CommandLineTools.pptx slides]
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== Testing Infrastructure ==
 
== Testing Infrastructure ==
  
* [http://www.na-mic.org/Wiki/images/3/33/BreakoutSession-CIP-InfrastructureAndTesting.pptx  Slides]
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=== Slicer Module Examples ===
 
=== Slicer Module Examples ===
[http://www.na-mic.org/Wiki/images/5/5c/BreakoutSession-CIP-SlicerModules.pptx slides]
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== New Developments: Organ Detection ==
 
== New Developments: Organ Detection ==
[http://www.na-mic.org/Wiki/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]
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[https://na-mic.org/w/images/5/50/BreakoutSession-CIP-NextDevelopment.pptx slides]

Latest revision as of 14:27, 10 July 2017

Home < 2015 Winter Project Week COPD Breakout

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

slides

Team

  • Raul San Jose
  • James Ross
  • Rola Harmouche
  • Jorge Onieva
  • German Gonzalez
  • Alex Yarmakovich

Collaborators

  • George Washko
  • Alejandro Diaz

Architecture

CIPArchitecture.png

Chest Imaging Platform (CIP)

Git Repository

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]


Command Line Tools

slides

Testing Infrastructure

Slicer CIP

Git Repository

MRML Types

Slicer Module Examples

slides

New Developments: Organ Detection

slides