NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-27T14:31:24Z

Fritzoid: /* Project Status */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

===Project Status===

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Adjusted our image data containers to more efficiently store our data set. ( short int's over int's )
* Begun revision of our color mapping function for the 3D model to prefer the built-in classes over a more exhaustive approach.
* Setup Dashboard for the project and can successfully submit test results.
* Adjusted Pipeline to release unneeded data in earlier portions of the pipeline.
* Dabbled in CPack.
* Successfully created many empty packages.
* Decided the ''install'' target via CMake needs work ( ...or to work ).
</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-27T14:31:01Z

Fritzoid: /* Project Status */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

===Project Status===

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Adjusted our image data containers to more efficiently store our data set. ( short int's over int's )
* Begun revision of our color mapping function for the 3D model to prefer the built-in classes over a more exhaustive approach.
* Setup Dashboard for the project and can successfully submit test results.
* Adjusted Pipeline to release unneeded data in earlier portions of the pipeline.
* Dabbled in CPack.
* Successfully created create empty packages.
* Decided the ''install'' target via CMake needs work ( ...or to work ).
</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-27T12:55:53Z

Fritzoid: /* Project Status */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

===Project Status===

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Adjusted our image data containers to more efficiently store our data set.
* Begun revision of our color mapping function for the 3D model to prefer the built-in classes over a more exhaustive approach.
* Setup Dashboard for the project and can successfully submit test results.
* Dabbled in CPack.
* Successfully created create empty packages.
* Decided the ''install'' target via CMake needs work ( ...or to work ).
</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-27T11:48:49Z

Fritzoid: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

===Project Status===

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Adjusted our image data containers to more efficiently store our data set.
* Setup Dashboard for the project and can successfully submit test results.
* Dabbled in CPack.
* Successfully created create empty packages.
* Decided to setup the ''install'' target via CMake.
</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-24T20:09:51Z

Fritzoid: /* Key Investigators */

{|
|[[Image:ProjectWeek-2008.png|thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page]] ]]
|[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
|}

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Nathan Fritze, Iowa
* Nathan Burnette, Iowa
*Bill Hoffman
*Sebastien Barre, Kitware
*Katie Hayes, BWH
*Jim Miller
*Luis Ibanez, Kitware (image registration regression testing, Cpack, and ITK)
*Will Schroeder, Kitware (license issues)

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

Develop a software tool for visualizing and querying an electronic lung airway atlas. We are developing atlases of the human lung R01 HL64368, the rat lung R01HL073598, and the mouse lung R01 HL080285. We want to make a common software tool that can be customized for specific atlases. The image data and semantic information will be stored in a database and will be indexed through a graphical user interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our plan for the project week is to
*Reduce bottlenecks for the atlas application
*Setup CMake, CPack, and Dashboard for project.
*Select a license for software
*Look at atlases developed in Slicer3.
*Compare and contrast the performance of Kwwidgets and wxWidgets
*Discuss ideas for a data manager object that is used to read, organize, and manage memory issues for the atlas.
*Learn the best ways to visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software
*Refine user interface for displaying atlas statistics, images, labels, coloring.
*Discuss registration methods for matching airway trees.

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...
* Setup Dashboard for the project and can successfully submit test results.

</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:37:18Z

Fritzoid:

__NOTOC__
[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]

===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Jake Nickel, UIowa ( Atlas Project Software Design )
* Nathan Fritze, UIowa ( Atlas Project Software Design )
* Nick Kiguta, UIowa ( Atlas Project Database Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:35:11Z

Fritzoid:

__NOTOC__
[[Image:AtlasProject Rat Statistics.png | thumb | left | 300px | Atlas Rat Statistics ]]
[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]
[[Image:AtlasProject Rat Query2 Both.png | thumb | right | 300px | Atlas Rat Database Results ]]

===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Jake Nickel, UIowa ( Atlas Project Software Design )
* Nathan Fritze, UIowa ( Atlas Project Software Design )
* Nick Kiguta, UIowa ( Atlas Project Database Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

File:AtlasProject Rat Query2 Both.png

2008-06-11T16:32:44Z

Fritzoid: Query results from the Rat Atlas Project database

Query results from the Rat Atlas Project database

File:AtlasProject Rat Statistics.png

2008-06-11T16:32:04Z

Fritzoid: Summary statistics for the Rat Atlas Project

Summary statistics for the Rat Atlas Project

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:29:53Z

Fritzoid:

__NOTOC__
[[Image:AtlasProject Splash.png | thumb | center | 300px | Atlas Project Splash Image ]]


===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Jake Nickel, UIowa ( Atlas Project Software Design )
* Nathan Fritze, UIowa ( Atlas Project Software Design )
* Nick Kiguta, UIowa ( Atlas Project Database Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:25:36Z

Fritzoid:

__NOTOC__
[[Image:AtlasProject Splash.png]]


===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Jake Nickel, UIowa ( Atlas Project Software Design )
* Nathan Fritze, UIowa ( Atlas Project Software Design )
* Nick Kiguta, UIowa ( Atlas Project Database Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

File:AtlasProject Splash.png

2008-06-11T16:24:45Z

Fritzoid: The Atlas Project main splash screen

The Atlas Project main splash screen

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:23:57Z

Fritzoid: /* References */

__NOTOC__

===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Jake Nickel, UIowa ( Atlas Project Software Design )
* Nathan Fritze, UIowa ( Atlas Project Software Design )
* Nick Kiguta, UIowa ( Atlas Project Database Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:23:49Z

Fritzoid:

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:23:30Z

Fritzoid: /* References */

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:23:09Z

Fritzoid:

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-11T16:22:39Z

Fritzoid: /* Key Investigators */

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-10T16:47:47Z

Fritzoid:

__NOTOC__

===Key Investigators===
* Gary Christensen, UIowa ( Atlas Project Principle Investigator )
* Nathan Fritze, UIowa ( Atlas Project Software Design )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>

We are...

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>

Our approach...

Our plan...

</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>

We have...

</div>

<br style="clear: both;" />

</div>

===References===

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-10T16:37:35Z

Fritzoid:

===Key Investigators===
# Gary Christensen, Iowa ( Atlas principal investigator )
# Nathan Fritze ( Atlas software developer )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
Our current objective is to create a stream-lined, easy to use and maintain lung atlas interface.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
Our current approach involves...
</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
Currently, we're...
</div>

<br style="clear: both;" />
</div>

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-10T16:34:08Z

Fritzoid:

===Key Investigators===
# Gary Christensen, Iowa ( Atlas principal investigator )
# Nathan Fritze ( Atlas software developer )

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
</div>

<br style="clear: both;" />
</div>

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-10T15:12:03Z

Fritzoid:

===Key Investigators===
* UIowa: Nathan Fritze

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Objective</h1>
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h1>Approach, Plan</h1>
</div>

<div style="width: 40%; float: left;">
<h1>Progress</h1>
</div>

<br style="clear: both;" />
</div>

NA-MIC/Projects/Collaboration/Lung Atlas

2008-06-10T15:10:55Z

Fritzoid: New page: ===Key Investigators=== * UIowa: Nathan Fritze <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h1>Objective</h1> </div> <div style="width: 27%; f...

===Key Investigators===
* UIowa: Nathan Fritze

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Objective</h1>
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h1>Approach, Plan</h1>
</div>

<div style="width: 40%; float: left;">

<h1>Progress</h1>
</div>

<br style="clear: both;" />

</div