Using 3D Slicer in Astronomy
The 3D Slicer software package is AstroMed's flagship tool for astronomical 3D data visualization. This page provides everything you need for an astronomical Slicer hands-on experience. For this we distribute 3D astronomical data ready to be read into Slicer, tutorials on how to look at these files using Slicer, tools to read in your own FITS data, and a documentation of the most important Slicer features.
Slicer Installation & System Requirements
The 3D Slicer project was initiated at the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham & Women's Hospital, an affiliate of Harvard Medical School. The software is documented at and distributed by www.slicer.org.
Slicer binaries have been compiled for several platforms. To install the software, simply uncompress the distributed files.
Macintosh OS X: available as PowerPC binaries and Intel Mac binaries (as beta release). How to run this.
Linux: available for 32 bit and 64 bit processors. How to run this.
Microsoft Windows: available for 32 bit and 64 bit processors. How to run this.
Solaris: available for 32 bit and 64 bit processors. How to run this.
If desired, the source code can be obained for self-compilation. Though the above information should be sufficient, more detailed installation instructions are available from the Slicer 101 pages.
Computer memory of order 1 GB, a processor speed of about 1.5 GHz, and a graphics card with 3D support are suggested for a smooth operation of 3D Slicer.
"Guided Tours" for Example Data
Explore our example data sets to get a first feeling for Slicers capabilities. For this we provide a set of example scenes ready to be viewed with Slicer. All data comes from observations of the CO molecule using radio telescopes. The third dimension in the provided datasets is not spatial, but encodes velocity information (i.e., whether the gas is approaching to or receeding from earth).
Please see our tour on iso-intensity surfaces in L1448 for details on how to view these scenes in Slicer.
These tours were created and tested for 3D Slicer V2.6 and higher.
Star Formation in Perseus
Explore the distribution of CO gas in the Perseus star formation complex in three dimensions. Take a look at the large-scale structure of the region. Then zoom in towards the smaller L1448 cloud, a region packed with young stars. Based on data kindly provided by the COMPLETE survey of star forming regions.
See the Perseus scenes for details.
Giant Molecular Clouds in Orion-Monoceros
Tour the Orion-Monoceros cloud complex as revealed by emission from CO gas. Intuitively use 3D viewing to explore how structure breaks up in space and velocity. Based on data kindly provided by Thomas Dame (Harvard-Smithsonian Center for Astrophysics).
See the Orion-Monoceros scenes for details.
Reading your own FITS Data
You can read astronomical FITS files using AstroMed's FITS reader. This program bridges the gap between data formats in the astronomical and medical communities. The present version translates FITS files into NRRD data, which then can be read into Slicer. Current Slicer versions cannot handle celestial coordinates yet. Data can only be explored in a qualitative sense. However, future versions of 3D Slicer will have a buld-in FITS reader that will also preserve coordinate information.
See our FITS reader documentation for details and download.
3D Slicer Documentation
AstroMed's 3D Slicer documentation focusses on the features most important to users from astronomy. Please refer to the tutorial and the user's guide at www.slicer.org for a complete documentation.
/SlicerInterfaces: basic window and menu structure, terminology
/ReadingData: how to read data into Slicer
/ReadingScenes: how to read pre-created scenes containing several data sets
/ViewNavigation: how to adjust the 3D view
/ColorscaleAdjustment: how to adjust color scales and contrast settins
/IsosurfaceCreation: how to create iso-intensity surfaces for 3D display
/ClumpSurfaceCreation: how to create surfaces for "clumps" identified in data
Please do not linger to contact us at iic-astromed-info@harvard.edu in case of questions.
Contact
If you would like to receive updates on the project and notifications of new downloads, please send an email with "subscribe" in the subject header to our announcement list, iic-astromed-announce@harvard.edu.
If you have any questions about the project or using 3D Slicer with our sample data sets, please send an email to iic-astromed-info@harvard.edu.
Slicer is engeneered for astronomy by Michael Halle (project management, software design) and Douglas Alan (software engeneering).
Slicer is used for astronomical research by Michelle Borkin (graduate astronomer) and Jens Kauffmann (postdoctoral astronomer). Astronomy-related questions concerning Slicer will be directed to them.