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Release Notes for SCIRun/BioPSE Version 3.0.2

SCIRun Version 3.0.2
Release date: March 8, 2007
Includes: SCIRun (Core), Packages (BioPSE, Teem, MatlabInterface, Insight)


This was mainly a bug fix release based on Version 3.0.0

  • We have created a WIndows binary distribution
  • We revived and updated the Component Wizard
  • We added hot-keys to Viewer (press 'I' to see all of the options)
  • We added more ./ installation options (e.g. --no-ctest, --cmake- args, --seg3d-only, etc)

Bug Fixes

  • fixed image saving under OSX (byte ordering problem)
  • added streamline auto-determination of step size and tolerance
  • fixed PowerApps under Windows
  • fixed names of: FieldToNrrd, NrrdToField, CreateFieldFromNrrdData, and ConvertNrrdsFromField
  • changed lock/unlock from color-changes to icons
  • fixed OSX mouse bindings for Seg3D
  • fixed GDCM support (for reading DICOM files)
  • fixed texture size determination (for volume rendering) on Apple
  • fixed volume rendering with low-res colormaps
  • added many fixes and enhancements to Seg3D

For the complete list of 3.0.2 source code commit message, see:

Release Notes for SCIRun/BioPSE Version 3.0.0

SCIRun Version 3.0.0
Release date: December 22, 2006
Includes: SCIRun (Core), Packages (BioPSE, Teem, MatlabInterface, Insight)



Seg3D is a standalone executable for the segmentation of volumetric (3D) medical imaging data. Seg3D can handle data types ranging from eight-bit to double precision floating point formats and features three-dimensional navigation and editing of scalar, vector, and RGBA data. Users can simultaneously view multiple orthogonal, two-dimensional slices of the data and create segmentation masks (labeled images) using manual drawing tools and automated segmentation algorithms. Any number of volumes can be displayed relative to each other with correct origin, orientations, and data spacing. Visualization tools include standard and custom color lookup tables, infinite zooming, paning, and surface and volume rendering. Multiple modalities acquired at different resolutions can be displayed using separate color maps with transparency for manual registration. Data may be cropped, resampled, and thresholded. This tool integrates powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit such as anisotropic blurring, edge-detection, image statistics, flood filling, morphological operations, and level-set segmentation algorithms.

Windows Port

We now have a Windows port of the SCIRun / BioPSE! Our Windows port is fully featured, including the SCIRun dataflow prolem solving environment, and all of our PowerApps. In our next release we will add support for a binary download, but for this 3.0 release, users will have to compile SCIRun from source. In our SCIRun Installation Guide, we provide details instructions on how to perform this installation. Enjoy!

CMAKE Build System

We are now using CMAKE instead of configure to build SCIRun. This change allows us greater portability across platforms, and allows us to make use of the CTEST system for regression testing. We have put together a CIBC Dart Dashboard to track the stability of SCIRun, and over the coming months we will add more tests and more machines to our regression testing suite.


  • We have created a Wiki-based Installation Guide to facilitate SCIRun installation.
  • We have transformed our build system from using configure to using CMAKE.
  • SCIRun's ThirdParty installation now includes the following new packages: LibPNG, LibXML, FreeType, and Glew.
  • The following packages have been removed from ThirdParty: Xerces, ImageMagick.
  • ThirdParty is now built using a single script for Linux and Mac OSX.
  • The SCIRun and ThirdParty source trees have been migrated to svn, and can be browsed online from here or here.

Supported systems

  • Added support for Windows XP (exception for interactive Matlab modules)
  • Added support for Intel based Macintosh machines.
  • Discontinued support for OS X 10.3 or lower (SCIRun now requires the execution of static constructors upon loading a library).


  • The volume renderer now supports a label map (segmentation) to select a specific 2D colormap
  • The volume renderer has been rewritten to support larger volumes and automatic bricking if not enough memory is available
  • The viewer now supports the visualization of degenerate meshes
  • Added support for visualization of nonlinear mesh types
  • Added ShowField support for computing default sizes for node-spheres and edge-cylinders


  • Finite element support has been completely rewritten and now both anisotropic as well as isotropic models are supported for each mesh class available in SCIRun (including hexahedral elements).
  • Generalized basis functions have been added into all SCIRun fields, to support higher-order element shapes and data interpolation.
  • More bridges to mesh generation, manipulation, and analysis tools (TetGen, Verdict, and Mesquite)

Network Editor

  • The network editor now blocks all editing while a network is executing.
  • The network editor is now able to save relative filenames for increased portablity between systems.
  • The network fileformat has been ported to XML. The new network files are now called .srn instead of the old .net files.
  • User can control which Ports get cached.
  • All modules have been given a new name.


  • The new Seg3D PowerApp provides an intuitive and powerful interface for segmenting volumetric data.


  • Documentation has been merged over into a Wiki, so users can see the very latest documentation and can help update and document the software system.

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