NAMIC Wiki - User contributions [en]

NA-MIC/Projects/Collaboration/Non-rigid image registration

2008-06-27T13:10:09Z

Jsong: /* Key Investigators */

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

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Paul Song, Iowa
* Cheng Zhang, Iowa
* Ying Wei, Iowa
* Kate Raising, Iowa
*Bill Hoffman
*Will Schroeder, Kitware (license issues)
*Jim Miller
*Luis Ibanez, Kitware

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

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

<h1>Objective</h1>
To develop applications for image registration that can be distributed easily to other sites.

</div>

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

<h1>Approach, Plan</h1>
Our plan for the project week is to
*Convert the SICLE image registration algorithm to use ITK.
*Use CPack to package the sicle.exe program.
*Setup and use a DART Dashboard at Iowa.
*Select a license for software.
*Compare and contrast the execution speed and memory requirements of the ITK sicle.exe with original lereg2.exe.
*Investigate integration of wxWidgets with ITK and VTK.
*Compare and contrast the performance of Kwwidgets and wxWidgets
</div>

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

<h1>Progress</h1>
*Started taking apart our existing SICLE implementation and reorganizing classes. The code base is in need of renovation.
*CDash has been set up.
*Discussed licensing issues - need final decision.
*Discussed performance issues involving porting our code to use ITK - particularly memory issues involved with strided images (complex conjugate symmetry).
*Learned more about CMake and CPack.

</div>

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

</div>

===References===

NA-MIC/Projects/Collaboration/Non-rigid image registration

2008-06-27T13:09:28Z

Jsong: /* Key Investigators */

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

__NOTOC__

===Key Investigators===
* Gary Christensen, Iowa
* Paul Song, Iowa
* Cheng Zhang, Iowa
* Ying Wei, Iowa
* Kate Raising, Iowa
*Bill Hoffman
*Will Schroeder, Kitware (license issues)
*Jim Miller
*Luis Ibanez, Kitware

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

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

<h1>Objective</h1>
To develop applications for image registration that can be distributed easily to other sites.

</div>

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

<h1>Approach, Plan</h1>
Our plan for the project week is to
*Convert the SICLE image registration algorithm to use ITK.
*Use CPack to package the sicle.exe program.
*Setup and use a DART Dashboard at Iowa.
*Select a license for software.
*Compare and contrast the execution speed and memory requirements of the ITK sicle.exe with original lereg2.exe.
*Investigate integration of wxWidgets with ITK and VTK.
*Compare and contrast the performance of Kwwidgets and wxWidgets
</div>

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

<h1>Progress</h1>
*Started taking apart our existing SICLE implementation and reorganizing classes. The code base is in need of renovation.
*CDash has been set up.
*Discussed licensing issues - need final decision.
*Discussed performance issues involving porting our code to use ITK - particularly memory issues involved with strided images (complex conjugate symmetry).

</div>

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

</div>

===References===

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-29T14:39:23Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|}

{|
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas polyDataPicker.jpg|thumb|320px|3D surface rendering of a human airway tree with the annotated picker displaying the 3D coordinate on the selected surface.]]
|}

{|
|[[Image:UIowaAtlas GUI Snapshot.jpg|thumb|500px|Snapshot of the UIowaAtlas GUI]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH
*Curtis Lisle, Isomics
*Will Schroeder, Kitware

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Learned about the functionalities of CMake.
*Learned about the features of Subversion revision control system.
*Learned about Dart and the nightly builds.
*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Rendered Analyze image volumes with 3D volume renderer in VTK.
*Converted Analyze-format images to VTK image volumes and surfaces.
*Rendered VTK image volumes with 3D surface renderer in VTK.
*Picked points on the 3D rendered surface and got the corresponding 3D coordinates.
*Developing a GUI for the Atlas that features the 3 orthogonal views of the image volume and 3D renderings.
{|
|[[Image:Never-finish.jpg|thumb|320px|Geek Philosophy [Source: http://www.thinkgeek.com]]]
|}

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

File:UIowaAtlas GUI Snapshot.jpg

2007-06-29T14:35:41Z

Jsong: Snapshot of the UIowaAtlas GUI

Snapshot of the UIowaAtlas GUI

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-29T14:09:45Z

Jsong: /* References */

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|}

{|
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas polyDataPicker.jpg|thumb|320px|3D surface rendering of a human airway tree with the annotated picker displaying the 3D coordinate on the selected surface.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Learned about the functionalities of CMake.
*Learned about the features of Subversion revision control system.
*Learned about Dart and the nightly builds.
*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Rendered Analyze image volumes with 3D volume renderer in VTK.
*Converted Analyze-format images to VTK image volumes and surfaces.
*Rendered VTK image volumes with 3D surface renderer in VTK.
*Picked points on the 3D rendered surface and got the corresponding 3D coordinates.
*Developing a GUI for the Atlas that features the 3 orthogonal views of the image volume and 3D renderings.
[[Image:Never-finish.jpg|thumb|320px|Geek Philosophy [Source: http://www.thinkgeek.com]]]

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-29T13:11:08Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|}

{|
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas polyDataPicker.jpg|thumb|320px|3D surface rendering of a human airway tree with the annotated picker displaying the 3D coordinate on the selected surface.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Learned about the functionalities of CMake.
*Learned about the features of Subversion revision control system.
*Learned about Dart and the nightly builds.
*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Able to render the Analyze image volumes with 3D volume rendering.
*Able to convert Analyze-format images to VTK image volumes (.vti/.vtp).
*Able to render the VTK image volumes with 3D surface rendering (much faster than the volume renderer).
*Able to pick a point on the 3D rendered surface and get the corresponding 3D coordinate.
*In the process of developing a GUI for the Atlas that features the 3 orthogonal views of the image volume and the 3D rendered image.
*Planning to implement the database interface to pull up the relevant Atlas information.
[[Image:Never-finish.jpg|thumb|320px|Geek Philosophy [Source: http://www.thinkgeek.com]]]

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

File:Never-finish.jpg

2007-06-29T13:08:04Z

Jsong: Geek Philosophy [Source: http://www.thinkgeek.com]

Geek Philosophy
[Source: http://www.thinkgeek.com]

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-29T03:34:24Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|}

{|
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas polyDataPicker.jpg|thumb|320px|3D surface rendering of a human airway tree with the annotated picker displaying the 3D coordinate on the selected surface.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Learned about the functionalities of CMake.
*Learned about the features of Subversion revision control system.
*Learned about Dart and the nightly builds.
*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Able to render the Analyze image volumes with 3D volume rendering.
*Able to convert Analyze-format images to VTK image volumes (.vti/.vtp).
*Able to render the VTK image volumes with 3D surface rendering (much faster than the volume renderer).
*Able to pick a point on the 3D rendered surface and get the corresponding 3D coordinate.
*In the process of developing a GUI for the Atlas that features the 3 orthogonal views of the image volume and the 3D rendered image.
*Planning to implement the database interface to pull up the relevant Atlas information.

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

File:UIowaAtlas polyDataPicker.jpg

2007-06-29T03:23:50Z

Jsong: 3D surface rendered human airway tree with annotated picker displaying the 3D coordinate on the surface.

3D surface rendered human airway tree with annotated picker displaying the 3D coordinate on the surface.

File:UIowaAtlas volRender.jpg

2007-06-28T18:01:12Z

Jsong:

Snapshot of the 3D volume rendering of the rat airway tree

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-28T18:00:43Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|}

{|
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Able to render the Analyze image volumes with 3D volume rendering.
*Able to convert Analyze-format images to VTK image volumes (.vti/.vtp).
*Able to render the VTK image volumes with 3D surface rendering (much faster than the volume renderer).

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-28T17:57:52Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|[[Image:UIowaAtlas human airway tree.jpg|thumb|320px|3D volume rendering of a human airway tree using the ITK to VTK image converter.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

<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 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
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

</div>

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

<h1>Progress</h1>

*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Able to render the Analyze image volumes with 3D volume rendering.
*Able to convert Analyze-format images to VTK image volumes (.vti/.vtp).
*Able to render the VTK image volumes with 3D surface rendering (much faster than the volume renderer).

</div>

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

</div>

===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

File:UIowaAtlas human airway tree.jpg

2007-06-28T17:56:25Z

Jsong: 3D volume rendering of human airway tree.

3D volume rendering of human airway tree.

Collaboration/UIowa/Developing Electronic Atlas Software using NA-MIC Kit

2007-06-28T16:21:33Z

Jsong:

{|
|[[Image:ProjectWeek-2007.png|thumb|320px|Return to [[2007_Programming/Project_Week_MIT|Project Week Main Page]] ]]
|[[Image:Small66ratLungModel_labelled.jpg|thumb|320px|Labeled 3D rendering of a rat airway tree cast. ]]
|[[Image:Human-airway-tlc.JPG|thumb|320px|3D rendering of a human airway tree at total lung capacity.]]
|[[Image:UIowaAtlas volRender.jpg|thumb|320px|3D volume rendering of a rat airway tree using the ITK to VTK image converter.]]
|}

__NOTOC__
===Key Investigators===
*Gary Christensen, Iowa
*Joo Hyun (Paul) Song, Iowa
*Jake Nickel, Iowa
*Nick Kiguta, Iowa
*Jeff Grethe, UCSD
*Wendy Plesniak, BWH
*Raul San Jose, BWH

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<h1>Objective</h1>
Develop a software tool for visualizing and querying an electronic 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.

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<h1>Approach, Plan</h1>

Our plan for the project week is to
*Learn how to interface NA-MIC tools with database tools such as MySQL
*Learn how to make a GUI for the atlas
*Learn how to render 2D and 3D images using the NA-MIC software
*Learn how to interact with 2D and 3D images by clicking on the images
*Learn how to read, organize, and visualize images, surface models, segmentations and symbolic information referenced by coordinate systems using the NA-MIC software

The database should contain the following information, plus additional information, for every region on the atlas:
*statistics – average length, width, surface area, etc.
*labels – floating labels above the atlas that is visible from all viewing angles.
*associated color – the associated color that marks particular regions on the atlas.
*description – detailed description of the region on the atlas.

Clicking on either the 2D or the 3D image should respond in the following manner:
*Highlight and display the corresponding region for all viewing windows.
*Query the database for the selected point, pull up every relevant information about the location and display.

When dealing with registration images, clicking on the template/target image should highlight and display the corresponding point on a transformed coordinate system.

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<h1>Progress</h1>

*Adopted the itkImageToVTKImageFilter to display Analyze-format images in VTK.
*Able to render the Analyze image volumes with 3D volume rendering.
*Able to convert Analyze-format images to VTK image volumes (.vti/.vtp).
*Able to render the VTK image volumes with 3D surface rendering (much faster than the volume renderer).

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===References===
This work is supported in part by NIH grants HL64368, HL080285, HL073598, and EB004126.

File:UIowaAtlas volRender.jpg

2007-06-28T16:10:46Z

Jsong: Snapshot of the 3D volume rendering of the rat lung airway tree

Snapshot of the 3D volume rendering of the rat lung airway tree