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European Research Council Kapteyn Astronomical Institute

Introduction and Acknowledgements

Davide Punzo (Kapteyn Astronomical Institute, University of Groningen)
Thijs van der Hulst (Kapteyn Astronomical Institute, University of Groningen)
Jos Roerdink (Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen)

Jean-Christophe Fillion-Robin (Kitware)
Steve Pieper (Isomics)
Andras Lasso (PerkLab, Queen's)

This work was supported by the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement nr. 291-531.


  • Davide Punzo, <email></email>; <email></email>
  • Thijs van der Hulst, <email></email>
  • Jos Roerdink <email></email>

Source: [1]
License: Slicer license
Download/install: install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerAstro extension[2].

Extension Description


Upcoming HI (neutral Hydrogen) surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize HI objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain.

Objective: general description

  • 1) proper visualization of astronomical data cubes: using data astronomical data formats, such as FITS, and astronomical world coordinates system (WCS);
  • 2) generation of Histogram, flux density profiles, moment maps and position-velocity diagrams linked with the 3-D view;
  • 3) enabling interactive smoothing in all three dimensions;
  • 4) interactive HI data modeling coupled to visualization;
  • 5) introduction of the SAMP protocol to enable interoperability with Topcat, and other VO tools and catalogs.

for more info see [3] and [4], [5].


Use Cases

Visualization of HI dataset: exploiting 3-D visualization for data inspection. 3-D gives an immediate overview of the coherence along the spatial and velocity dimensions such as tidal tail, gas stripping and filaments. Example:

Slicer Astro Screenshot


How to cite

Please cite the following paper when referring to SlicerAstro in your publication:

   author = {{Punzo}, D. and {van der Hulst}, T. and {Roerdink}, J. and {Fillion-Robin}, J.-C.
    title = "{SlicerAstro: Astronomy (HI) extension for 3D Slicer}",
 keywords = {Software },
howpublished = {Astrophysics Source Code Library},
     year = 2016,
    month = nov,
archivePrefix = "ascl",
   eprint = {1611.021},
   author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and 
	{Fillion-Robin}, J.~C. and {Yu}, L.},
    title = "{SlicerAstro: A 3-D interactive visual analytics tool for HI data}",
  journal = {Astronomy and Computing},
archivePrefix = "arXiv",
   eprint = {1703.06651},
 primaryClass = "astro-ph.IM",
 keywords = {Radio lines: galaxies, Scientific visualization, Visual analytics, Agile software development, Object oriented development, Empirical software validation},
     year = 2017,
    month = apr,
   volume = 19,
    pages = {45-59},
      doi = {10.1016/j.ascom.2017.03.004},
   author = {{Punzo}, D. and {van der Hulst}, J.~M. and {Roerdink}, J.~B.~T.~M. and {Oosterloo}, T.~A. and {Ramatsoku}, M. and {Verheijen}, M.~A.~W.},
    title = "{The role of 3-D interactive visualization in blind surveys of H I in galaxies}",
  journal = {Astronomy and Computing},
archivePrefix = "arXiv",
   eprint = {1505.06976},
 primaryClass = "astro-ph.IM",
 keywords = {Radio lines: galaxies, Galaxies: kinematics and dynamics, Surveys, Scientific visualization, Visual analytics},
     year = 2015,
    month = sep,
   volume = 12,
    pages = {86-99},
      doi = {10.1016/j.ascom.2015.05.004},