3-D imaging

Information

• Matti Haveri's FAQ on medical volume visualization and imaging (latest version dated 2000 Jan, as of 2006 Jun 2) [version at www.faqs.org is from 1999 Dec 26]
• See Ralf Dreesen's Open source software for medical images (2005 May 27)
• 3D Reconstruction page at Stanford, incl. information about available software (as of 2006 Jun 2, only 1 programme has been added since 2002 Jan, but it was added some time after 2005 Mar according to the Wayback Machine)

Software

• ImageJ - image display, editing, processing and analysis, including stacks; written in Java, for Mac, Windows, Unix; open-source, free; as of 2011 Dec 7, latest version is 1.46b dated 2011 Nov 29. Fiji is a repackaging of ImageJ, designed to make it easy to install and use ImageJ and its plugins (especially Benjamin Schmid's Java3D-based Volume Viewer) under Linux. ImageJDev (aka ImageJ2) is a backward-compatible rewrite of ImageJ. To import and explore a set of images as a 3-D stack: do File ▶ Import ▶ Image sequence, browse to the directory containing the set of images, select one of the images and click on Open. Set up the various parameters in the Sequence options dialogue box and click on OK. Then to Plugins ▶ 3D ▶ Volume Viewer. Click and drag in the main window to rotate; use the Dist slider to move the cross-section back and forth. This worked nicely on a set of smallish MRM images On my laptop, for a set of 600 1024&1024 µCT images I had to check the Use Virtual Stack box to avoid a fatal error during the import, and then it ran out of memory trying to run the volume viewer. Even after scaling in x and y by 50% using Image ▶, the volume viewer ran out of memory.
• Slicer is an 'open source software package for visualization and image analysis' for *n*x, Mac Os X and Windows. As of 2017 Jun 8, the latest version is 4.6.2, released 2016 Nov 8. See my notes.
• Seg3D: ‘a free volume segmentation and processing tool’. As of 2021 Apr 9, the latest release is 2.5.0 dated 2020 Aug 6, and the latest commit is dated 2021 Feb 2. I downloaded it to Windows 10 and installed it, but it fails to start.
• NLM Insight Segmentation and Registration Toolkit (ITK): open-source, to support the Visible Human Project; cross-platform, implemented in C++; does not address visualisation or GUI, provides minimal tools for file interface (use with VTK, VisPack, 3DViewnix, MetaImage, etc.) Latest version is 3.16 released 2009 Sep 15, as of 2009 Nov 1. SimpleITK is ‘a simplified layer built on top of ITK’. VTK ‘is often used in conjunction with ITK’. ‘Applications that use VTK include Molekel, ParaView, VisIt, VisTrails, MOOSE, 3D Slicer, MayaVi, and OsiriX’ (ref).
• ITK-SNAP: ‘a user friendly application developed on top of ITK’. GPL, cross-platform. As of 2013 Jun 7, latest version is 2.4 dated 2012 Nov 27. They request that users cite Yushkevich et al. (2006) in publications. Convert3D is a companion command-line tool.
• Elastix is ‘a toolbox for rigid and nonrigid registration of images’ based on ITK. It's accompanied by SimpleElastix, and SlicerElastix makes it available in Slicer.
• MIPAV is from the NIH Center for Information Technology. Free/libre. Java. As of 2018 Mar 10, latest version is 8.0.2 dated 2018 Feb 13. Segmentation methods include RubberbandLivewire (‘Intelligent Scissors’).
• InVesalius, GPL, for GNU Linux and MS Windows. 3-D reconstruction, handles DICOM. As of 2018 Mar 10, latest release is version 3.1.1 (apparently dated 2017 Aug 10 according to changlog on github, with latest commit dated 2018 Mar 9).
• ImageVis3D from SCI at the University of Utah. I was able to start visualizing a smallish MRM dataset by opening the multi-image TIFF file, but it crashed when I asked it to crop and thereafter it wasn't able to open the file. The latest version is dated 2014 Apr 8 as of 2018 Mar 10.
• VisIt, LLNL's open-source 'interactive parallel visualization and graphical analysis tool for viewing scientific data'; for *n*x, MacOS X, MS Windows; as of 2010 Jun 24, latest version is 2.0.0, released 2010 May. I tried it on my 6-year-old laptop with 512 MB of memory; working with 299 CT images of 512×512 pixels, I had some crashes and didn't manage any volume visualization. To treat a set of JPEG images as a volume, I just had to create a text file called name.imgvol that lists the files.
• ParaView is an 'open-source, multi-platform data analysis and visualization application' from Kitware, Sandia National Laboratories and Los Alamos National Laboratory. It is a ‘a scalable front-end for visualization with VTk’. For *n*x, MacOS X, MS Windows; as of 2010 Jun 24, the latest version is 3.8.0, released 2010 Apr 5. I downloaded it but it couldn't import JPEG images so I gave up.
• SIM Voleon is a volume-rendering technology for use together with Coin3D; available with GPL licence for non-commercial use; for MS Windows, Linux, etc. Comes with example source code. The latest version of the Coin library itself is 3.1.2 dated 2009 Oct 28, as of 2009 Nov 1. The latest version of the Voleon add-on is 2.0.1 dated 2004 Dec 30, as of 2009 Nov 1. The following notes about trying it are from 2006 Jun 3-4. (* examples which use fake data generate it with generate8bitVoxelSet, which causes an unresolved-symbol error):
  • changingdataset: displays a cloud of random data points changing with time (after a number of iterations it stopped generating new data with what looked like an out-of-range data error, but the examiner continued to work)
  • examine (uses fake data*)
  • orthoslicer (can't compile because it requires Qt .h files)
  • raypick (uses fake data*)
  • readvol (can't build because it requires Qt .h files)
  • rgbload: loads a set of RGB files, applies a filter and shows the volume with a clip-plane dragger (can't compile because it refers to 'RGBA' which is not a member of 'SoVolumeData'; successfully compiled by removing SoVolumeData::RGBA from call to setVolumeData, thus accepting default which is apparently monochrome, UNSIGNED_BYTE, the only other type defined in SoVolumeData.h being UNSIGNED_SHORT; programme successfully displays a small corner of a large monochrome jpg file)
  • simple8bit (uses fake data*)
• MeVisLab is ‘a powerful, modular framework for image processing research and development with a special focus on medical imaging … developed by MeVis Medical Solutions AG in close cooperation with the research institute Fraunhofer MEVIS’. There are several commercial and non-commercial licences, including a restricted free one. For Linux, Windows and Mac OS X. As of 2018 Mar 10, the latest version is 3.0.2 dated 2018 Jan 31.
• Volocity: Volocity LE, the ‘core’ of the commercial version, is available free; for Windows and Mac. Latest version was 5.2.1 (or 5.2.2 beta) dated 2009 Sep 17, as of 2009 Nov 1; as of 2018 Mar 10, the URL leads to a commercial page with no mention of Volocity.
• sliceOmatic from TomoVision, commercial, with a limited evaluation version.
• MRIcron by Chris Rorden, for *n*x, MacOS X, MS Windows. As of 2018 Mar 10, latest version is dated 2016 Oct 12.
  Replaces older MRIcro, last version was 1.40 build 1 dated 2006 Jul 19.
• Huygens Software for fluorescence-microscopy image processing, a commercial package which is partially usable as freeware. Includes image restoration, interactive analysis and volume visualization. For Linux, MacOS X and Windows.
• Ensight is a commercial product line. They have a free limited version of their CFD product.
• Materialise - Mimics is an image-processing package for creating 3-D models (for CAD or for rapid prototyping) from 3-D CT or MRI data. 3-D segmentation by thresholding. Price for universities is $6000. 30-day Demo available. (information as of 1999 Mar 12)
• Stefan Roettger's V^3 (Versatile Volume Viewer): GPL; latest stable version 2.2 dated 2005 Apr 28, latest version 2.3 dated 2007 Mar 16 (as of 2009 Nov 1), 'runs on Linux and Windows (VC++ and cygwin)', 'requires at minimum a NVIDIA GeForce4, better a GeForce FX graphics accelerator (ATI is not supported)'. Windows executable available for download (I tried running it with a glut32.dll dated 2004 Aug 13 and 2008 Aug 7, from 3Dconnexion and Instant Player, respectively, but it gave a fatal error).
• OpenDX, open-source version of IBM's Visualization Data Explorer; for Linux, Mac, MS Windows (with Cygwin or an X server); as of 2009 Feb 21, latest version is 4.4.4 released 2006 Aug 30.
• Julius Model Viewer, part of Julius framework project. As of 2006 Jun 2, latest version was MV1 Alpha 3 released 2006 May 22; as of 2006 Nov 10 there was a version 1.0.0; as of 2009 Nov 1 the URL doesn't respond and I can't find anything more recent elsewhere. For Linux and MS Windows.
• OpenQVis (last version dated 2003 Mar 19, as of 2009 Nov 1)
• 3DVIEWNIX: latest version 1.5 dated ~2004. For *n*x. Binary was available free via FTP, but doesn't respond as of 2009 Nov 1; source code was available for $1000 with a confidentiality agreement.
• NIH Image for Mac (last version 1.63 released 2002 Nov 19) was the predecessor of ImageJ. The related Scion Image is an ‘extended’ version of NIH Image for Win 95/NT (free; beta version as of 1999 Mar 12; as of 2009 Nov 1 it is available for download from Scion's Web site but to get further information I'd need to register).
• Osiris - free imaging software from Geneva; for Windows and Mac (supported Unix until version 2, ca. 1997); includes 3-D segmentation by threshold-based region growing. As of 2006 Jun 2, version 4.19 dated 2003 Nov 4 for MS Windows, 4.07 for Mac OS 9; OsiriX 2.4 released 2006 May 15 for Mac OS X.
• SLED slice editor. As of 2009 Nov 1, last (and first) release was 2003 Jan 7. Was being developed under Linux; GPL; based on OpenVL, whose last activity was also in 2003. This was the only result of a search in sourceforge.net for "volume visualization" in the category of Multimedia ▶ Graphics.
• VolPack: source code available. Last version was 1.0 beta 3 dated 1994 Dec 31, as of 2009 Nov 1.