2008 Winter Project Week:Astronomical Medicine

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Mockup of a future version of Slicer with features desired by the Astronomical Medicine project.

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 implement a mechanism that will allow world coordinate system information to travel through the ITK pipeline via an ITK image's metadata dictionary. If we accomplish this, and there is time left over, then we hope to implement bidirectional procedural transforms to map between voxel coordinates and world coordinates.

Progress

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 this 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.