Difference between revisions of "2008 Winter Project Week:Astronomical Medicine"
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<h1>Approach, Plan</h1> | <h1>Approach, Plan</h1> | ||
| − | Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach | + | Our approach is summarized on the [http://astromed.iic.harvard.edu Astronomical Medicine web site]. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems. |
| − | Our plan for the project week is to | + | Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers. |
</div> | </div> | ||
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<h1>Progress</h1> | <h1>Progress</h1> | ||
| + | ====January 2008 Project Week==== | ||
| + | |||
| + | * Created vtkCoordinateSpaceManager, a container that manages multiple named coordinate spaces and the transforms between them. A reader can populate a coordinate space manager with all the coordinate spaces it knows about. Registration tools can link otherwise unrelated coordinate spaces, and the manager can hand back a (possibly composite) transform between any two related spaces. This module hasn't been incorporated into Slicer3 yet. | ||
| + | * With Wendy Plesniak's help, we now have the ability to recenter on data not located at the origin in Slicer. She's incorporating similar changes into the "look from" Slicer control. We'll need to look at autozooming as well for very small volumes. | ||
| + | * Slicer3 volume rendering works reasonably well with astronomical data, but the world size of model seems to influence rendering appearance. Solved some performance issues on the Mac. | ||
| + | * Experimental linearized celestial coordinate system implementation being tested now. | ||
| + | * Prototyped Slicer3 plugin module adapter for fits2itk. | ||
| + | ** Debugged performance issues with the Slicer3 implementation of plugin modules for OS X and submitted bug report. | ||
| + | * Prototyped ITK-based NaN masking filter. | ||
| + | ** Still need standard way to deal with NaNs in ITK/VTK/Slicer3. | ||
| + | |||
====June 2007 Project Week==== | ====June 2007 Project Week==== | ||
| − | Worked with Jim Miller to implement preservation of the ITK metadata | + | Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters. |
| − | dictionary through the Slicer pipeline, worked with Luis Ibanez to | ||
| − | help implement ITK streaming file I/O, set up more robust dependency | ||
| − | rules in our CMake config, and debugged a problem with our use of ITK | ||
| − | filters. | ||
====Jan 2007 Project Half Week==== | ====Jan 2007 Project Half Week==== | ||
| − | Solved problem of itk::ImageIOBase being incompatible with CFITSIO's | + | Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary. |
| − | "extended filename syntax", identified compatibility issues present in | ||
| − | the most recent version of Slicer 3, and devised a plan for passing | ||
| − | FITS WCS transforms around in Slicer by encapsulating them in | ||
| − | itk::Transform objects held in an image's metadata dictionary. | ||
====June 2006 Project Week==== | ====June 2006 Project Week==== | ||
| − | Implemented a prototype FITS reader for ITK. We later released | + | Implemented a prototype FITS reader for ITK. We later released a subsequent version as an open-source FITS-to-NRRD file converter, which is available [http://astromed.iic.harvard.edu/FITS-reader here]. |
| − | as an open-source FITS-to-NRRD file converter, which is available | ||
| − | [http://astromed.iic.harvard.edu/FITS-reader here]. | ||
</div><br style="clear: both;" /></div> | </div><br style="clear: both;" /></div> | ||
| − | <h1> | + | <h1></h1><br> |
| + | ====References==== | ||
| + | * The [http://am.iic.harvard.edu Astronomical Medicine web site] | ||
| + | * [http://am.iic.harvard.edu/FITS-reader Open-source release] of our ITK-based FITS file reader/converter. | ||
* Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF]. | * Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, [http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=2006AAS...209.5706B&db_key=AST&data_type=HTML&format=&high=438a74bfef26079 "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data"], 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.ppt PPT] [http://www.cfa.harvard.edu/COMPLETE/astromed/aas209/057.06_borkin.pdf PDF]. | ||
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* Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604. | * Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, [http://lanl.arxiv.org/abs/astro-ph/0506604 "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348"], 5/2005, astro-ph/0506604. | ||
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Latest revision as of 21:34, 5 June 2008
Home < 2008 Winter Project Week:Astronomical Medicine Return to 2008_Winter_Project_Week |
Key Investigators
- Havard IIC: Douglas Alan
- BWH/Harvard IIC: Mike Halle
- Isomics: Steve Pieper
Objective
We are developing tools and enhancements to ITK and Slicer in order to adapt Slicer to be a tool that is useful for the visualization of astronomical data, specifically spectral line data cubes for now.
Approach, Plan
Our approach is summarized on the Astronomical Medicine web site. The main challenge to this approach at the moment, is the impedance mismatch between celestial coordinates and medical imaging coordinates, and a lack of infrastructure within ITK and Slicer to allow for alternative coordinate systems.
Our plan for the project week is to make further progress in integrating our ITK FITS reader into Slicer as a plug-in, and to begin work on Slicer GUI enhancements to support our FITS plug-in and to allow the display of astronomical coordinates in slice viewers.
Progress
January 2008 Project Week
- Created vtkCoordinateSpaceManager, a container that manages multiple named coordinate spaces and the transforms between them. A reader can populate a coordinate space manager with all the coordinate spaces it knows about. Registration tools can link otherwise unrelated coordinate spaces, and the manager can hand back a (possibly composite) transform between any two related spaces. This module hasn't been incorporated into Slicer3 yet.
- With Wendy Plesniak's help, we now have the ability to recenter on data not located at the origin in Slicer. She's incorporating similar changes into the "look from" Slicer control. We'll need to look at autozooming as well for very small volumes.
- Slicer3 volume rendering works reasonably well with astronomical data, but the world size of model seems to influence rendering appearance. Solved some performance issues on the Mac.
- Experimental linearized celestial coordinate system implementation being tested now.
- Prototyped Slicer3 plugin module adapter for fits2itk.
- Debugged performance issues with the Slicer3 implementation of plugin modules for OS X and submitted bug report.
- Prototyped ITK-based NaN masking filter.
- Still need standard way to deal with NaNs in ITK/VTK/Slicer3.
June 2007 Project Week
Worked with Jim Miller to implement preservation of the ITK metadata dictionary through the Slicer pipeline, worked with Luis Ibanez to help implement ITK streaming file I/O, set up more robust dependency rules in our CMake config, and debugged a problem with our use of ITK filters.
Jan 2007 Project Half Week
Solved problem of itk::ImageIOBase being incompatible with CFITSIO's "extended filename syntax", identified compatibility issues present in the most recent version of Slicer 3, and devised a plan for passing FITS WCS transforms around in Slicer by encapsulating them in itk::Transform objects held in an image's metadata dictionary.
June 2006 Project Week
Implemented a prototype FITS reader for ITK. We later released a subsequent version as an open-source FITS-to-NRRD file converter, which is available here.
References
- The Astronomical Medicine web site
- Open-source release of our ITK-based FITS file reader/converter.
- Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, Jens Kauffmann, "Application of Medical Imaging Software to the 3D Visualization of Astronomical Data", 1/2007, 2007 AAS/AAPT Joint Meeting, American Astronomical Society Meeting 209, #57.06. Presentation: PPT PDF.
- Michelle Borkin, Alyssa Goodman, Michael Halle, Douglas Alan, "Application of Medical Imaging Software to 3D Visualization of Astronomical Data", 10/2006, ADASS XVI Conference. Presentation: PPT PDF (linked movies).
- Michelle A. Borkin, "A COMPLETE Survey of Velocity Features in Perseus", 5/2006, Harvard University Undergraduate Senior Thesis.
- Michelle A. Borkin, Naomi A. Ridge, Alyssa A. Goodman, Michael Halle, "Demonstration of the Applicability of "3D Slicer" to Astronomical Data using 13CO and C18O Observations of IC348", 5/2005, astro-ph/0506604.
