CAVASS: A Computer-Assisted Visualization and Analysis Software System George Grevera,1,2Jayaram Udupa,2 Dewey Odhner,2 Ying Zhuge,2 Andre Souza,2 Tad Iwanaga,2 and Shipra Mishra2 The Medical Image Processing Group at the University of and display device dependency, this package was Pennsylvania has been developing (and distributing with distributed to over 150 sites with source code source code) medical image analysis and visualization “ ” software systems for a long period of time. Our most worldwide long before the term open source was recent system, 3DVIEWNIX, was first released in 1993. coined. This package was also incorporated into the Since that time, a number of significant advancements General Electric (GE) computed tomography (CT)/T have taken place with regard to computer platforms and 8800 scanner.3 We subsequently developed a more operating systems, networking capability, the rise of advanced package4 for the GE 9800 CT scanner. parallel processing standards, and the development of open-source toolkits. The development of CAVASS by GE distributed widely these on-the-scanner pack- our group is the next generation of 3DVIEWNIX. ages. Earlier, we implemented DISPLAY and CAVASS will be freely available and open source, and DISPLAY82 at the Mayo Clinic, whose inves- it is integrated with toolkits such as Insight Toolkit and tigators used these packages until they started Visualization Toolkit. CAVASS runs on Windows, Unix, developing the Analyze system5 around 1984–1985. Linux, and Mac but shares a single code base. Rather than requiring expensive multiprocessor systems, it Around 1987, we started the development of a seamlessly provides for parallel processing via inexpen- Unix-work-station-based software system named sive clusters of work stations for more time-consuming 3DVIEWNIX,6 which was based on standard C algorithms. Most importantly, CAVASS is directed at the programming language and a graphical user visualization, processing, and analysis of 3-dimensional interface library developed by us based on X and higher-dimensional medical imagery, so support for digital imaging and communication in medicine data and Windows. It also incorporated a multidimensional the efficient implementation of algorithms is given paramount importance. KEY WORDS: Visualization, 3-dimensional imaging, software systems, image analysis 1From the Department of Mathematics and Computer Science, Saint Joseph’s University, 5600 City Avenue, Philadelphia, PA INTRODUCTION 19131, USA. 2From the Medical Image Processing Group (MIPG), Department of Radiology, University of Pennsylvania, 423 oftware development for 3-dimensional com- Guardian Drive, 4th Floor Blockley Hall, Philadelphia, PA S puter-aided visualization and analysis (CAVA) 19104-6021, USA. in our group started in the 1970s. In 1980, we Correspondence to: George Grevera, Department of Math- brought out the first ever such package for medical ematics and Computer Science, Saint Joseph’s University, 5600 3-dimensional CAVA.1 This software worked on a City Avenue, Philadelphia, PA 19131, USA; tel: +1-610- Data General minicomputer, which drove a Comtal 6601535; fax: +1-610-6603082; e-mail: [email protected] Copyright * 2007 by Society for Imaging Informatics in image display frame buffer. In 1982, we brought Medicine out a significantly expanded version of this Online publication 6 September 2007 2 software package. In spite of its high machine doi: 10.1007/s10278-007-9060-5 Journal of Digital Imaging, Vol 20, Suppl 1, 2007: pp 101Y118 101 102 GREVERA ET AL. generalization7 of the 2-dimensional digital im- Current Software Systems agingandcommunicationinmedicine(DICOM) and their Limitations image representation standards. This issue of the need to handle a multidimensional vectorial image During the past 10 years, the software devel- as a single entity and also to handle nonimage opment activity for CAVA has increased consid- structure information such as surfaces is only now erably, making several open-source systems being looked into by the standards committees available. In the rest of this section, we shall related to DICOM. These issues were addressed review the currently available software systems and in 3DVIEWNIX in the early stage of its design examine their limitations that were considered in during 1987–1990. 3DVIEWNIX has incorpo- the design and implementation of CAVASS. Our rated numerous advanced 3-dimensional (and survey here considered most of the well-known higher-dimensional) CAVA operations including software systems, including Analyze,5 Digital Data various methods of interpolation, filtering, seg- Viewer (DDV) (http://www.compgeomco.com), mentation, registration, algebraic and morphol- GNU Image Manipulation Program (GIMP) ogical operations, visualization methods for (http://www.gimp.org), Image/J (rsb.info.nih.gov/ surfaces and volumes, interactive structure edit- ij/), Interactive Data Language (IDL) (http://www. ing and manipulation, and scene intensity and rsinc.com), ITK,8 Java ( http://www.javasoft.com), structure-based quantitative analysis. Its binary Khoros ( http://www.khoral.com), Mathematica version is available freely via the Internet and has (http://www.wolfram.com), Matlab (http://www. been used by hundreds of sites, and the source- mathworks.com), Open Data Explorer (OpenDX) code-version has been distributed to more than (http://www.opendx.org), Photoshop (http://www. 180 sites worldwide to date. We continue to adobe.com), Volview (http://www.kitware.com/ maintain, distribute, and develop 3DVIEWNIX products/volview.html), VTK (http://www.vtk.org), by incorporating into it all functions that we find Vision-something-Libraries (VXL) (vxl.sourceforge. useful after rigorously testing them in one or net), and 3DSlicer (http//www.slicer.org). Analyze, more of our ongoing applications. About 60 IDL, Khoros, Mathematica, Matlab, Photoshop, and person years of work has gone into 3DVIEWNIX Volview are excellent commercial software pack- so far. Its design has stood the test of time and of ages. However, none of them are freely available or over 15 applications pursued by us since its available as open source. Academic prices for release. these packages for a single user on a Microsoft Since the time 3DVIEWNIX was first released Windows platform are typically subsidized. Plat- (1993), a number of significant developments forms other than Windows are often more have occurred. Most significantly, PC platforms expensive, as are commercial licenses. These fees (and the Windows OS) have gained in capability, typically include 1 year of updates. After that accompanied by precipitous price reductions. period of time, additional fees are required to They have supplanted traditional Unix-based obtain updated software. Only a few of these work stations as the scientific work stations of vendors offer source code (for an additional fee). choice. Second, network connectivity speed has Additionally, IDL, Khoros, Mathematica, and greatly increased. Third, viable parallel process- MATLAB are not complete medical imaging ing standards have been developed and are now applications but libraries of functions that are freely available for all popular platforms and callable from their own respective proprietary operating systems. Fourth, platform-independent computer programming languages. Note that, in windowing application programming interfaces the case of these proprietary languages, even (APIs), some of which maintain the native look experienced software developers who are typical- and feel, have been defined and implemented. ly already familiar with C++ must learn these Finally, toolkits such as Insight Toolkit (ITK) programming languages. Matlab provides some and Visualization Toolkit (VTK) have been support for libraries that are callable from C/C++ developed and are freely available. Although not and FORTRAN. Analyze is a complete applica- complete applications in themselves, these tool- tion with the Developer Add-On available for the kits provide a breadth of techniques and can be programming of custom applications. Photoshop employed as building blocks of applications. is exclusively oriented towards 2-dimensional CAVASS: A COMPUTER-ASSISTED VISUALIZATION AND ANALYSIS SOFTWARE SYSTEM 103 image processing and manipulation. Photoshop voluminous higher-dimensional and/or multimo- may be extended by user-written plugins. A dality data. Simple, prototype Java-based appli- DICOM plugin is available for Photoshop to cations that we developed required inordinate enable it to read single DICOM image files amounts of memory and executed far more (2-dimensional slices). slowly than their C++ counterparts. We consid- The DDV (free, open source, Windows only) ered using the Java Native Interface (JNI), which software available was not afforded further allows one to combine Java and C++ code but that consideration because it is primarily oriented requires developers to be experts in two program- toward EEG data and not 2-dimensional or ming languages with no benefit over the solution higher-dimensional imagery. Another DDV that we propose below. In fact, a JNI version of software package, available from http://www. 3DVIEWNIX may even be slower because of the compgeomco.com/, is freely available as binary conversion between Java and C++ data structures. executables for a variety of platforms, including In the future, Java compilers [such as Google Code Windows, Linux, Unix, and Mac. Source code is Jam (GCJ)], which compile Java to native machine not available, and even if source