Using 3D Slicer in Astronomy
The 3D Slicer software package is AM's core tool for astronomical 3D data visualization. Originally designed for medical image analysis, 3D Slicer has many capabilities that are uncommon in astronomy software. This page provides everything you need to try out Slicer on astronomy data.
Table of Contents:
To simplify this process as much as possible, 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 documentation of the most important Slicer features.
Caveats
We are currently at the early stages of adapting 3D Slicer for astronomy. There's much work in progress, including integrated FITS support, WCS handling, and more quantitative tools. These features aren't available in the current release, and the process of visualizing astronomy data with Slicer is still somewhat manual, inconvenient, and unintuitive to the astronomer.
However, we made the decision that many "early-adopter" astronomers could benefit from a preview release of the software tools we have successfully used for qualitative visualization of astronomy data.
Please help us improve Slicer and other visualization software tools for astromony through your experimentation, evaluation, and feedback.
3D Slicer Installation & System Requirements
The 3D Slicer project was initiated as a collaboration between the MIT Artificial Intelligence Lab and the Surgical Planning Lab at Brigham & Women's Hospital, a teaching affiliate of Harvard Medical School. The software is documented and distributed at www.slicer.org.
Iso-intensity surfaces for L1448.
Slicer binaries have been precompiled for several platforms. To install the software, simply uncompress the distributed files into a directory of your choice. You can run the Slicer binaries without further configuration.
Macintosh OS X: available as PowerPC binaries and Intel Mac binaries. (Note that X11 must be installed and running before you can run Slicer. X11 comes on the OS X installation disks, but is not installed during the default OS installation process. Consequently, you must install it manually if it is not already installed on your machine. If you cannot locate your installation disks, you can download X11 for OS X from here.)
Linux: available for 32 bit binaries and 64 bit binaries. You must have csh installed on your machine.
Microsoft Windows: available as 32 bit binaries. Use user "anonymous" and password "bwhspl" to access CVS during the installation process. Otherwise, skip unpacking the protected files.
Solaris: available as SPARC binaries.
If you'd prefer to build Slicer from source code, the source code can be obtained here.
Although the aforementioned web pages are likely to be sufficient for your needs, more detailed installation instructions can be found here. There is also a tutorial called Slicer 101 that introduces the use of Slicer for medical imaging purposes.
For smooth operation of 3D Slicer we recommend a minimum of 1 GB of RAM, a processor speed of 1.5 GHz or greater, and a graphics card with hardware 3D support.
"Guided Tours" Using Example Data
L1448 decomposed by CLUMPFIND.
Explore our example data sets to get a first sense of Slicer's capabilities. We provide a set of example scenes preconverted from original FITS format and 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 receding 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 version 2, releases 2.6 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 AM'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: WCS information isn't maintained. However, future versions of 3D Slicer will have a built-in FITS reader that will also preserve coordinate information.
See our FITS reader documentation for details and download.
3D Slicer Tutorial
The following tutorial illustrates a typical astronomy data exploration session. For this purpose, please download the example FITS data (24 MB) for the tutorial. You can also download pre-created NRRD files (24 MB), in case you prefer to skip the FITS-to-NRRD conversion. This data is kindly provided by the COMPLETE survey of star forming regions.
The tutorial focuses 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.
Slicer interfaces: basic window and menu structure, terminology
reading data: how to read data into Slicer
data navigation: controls for 3D and slice views
colorscale adjustment: how to adjust color scales and contrast settings
surface creation: creating surfaces for 3D display
scene adjustment: how to optimize scene projections and to save scenes
Please do not hesitate to contact us at iic-astromed-info@harvard.edu in case of questions.
Contact
Please refer to our contact page.