Let’s have a quick look at some of the software projects that have recently released new versions.
Mango is a do-it-all program from the Research Imaging Institute at the University of Texas. It’s easy to use for beginners, but offers great powers to advanced users, particularly those in the brain sciences. It’s written in Java so it runs on any OS, and comes with platform-specific installers. It has developer tools available, and a range of useful plugin modules. And let’s not forget the variant that displays DICOM images on a browser (webMango) and the iPad app, iMango (though it’s not free software).
For introductory users, it can quickly let you view images in DICOM or a half-dozen other formats. But there’s a lot more functionality built in to the program, and with its plugin architecture, it can be expanded to perform a very wide range of tasks. While suitable for general purpose image viewing and analysis, there’s an emphasis on neuro imaging including support for file formats specific for that field: AFNI, NIFTI (use the Search page of this site and you’ll find 9 programs that support the former and 20 for the latter), also FSL and BrainVisa (which we’ve not yet got around to categorizing, ahem).
Advanced users will find useful features including a comprehensive package of ROI operations, image co-registration and overlays, statistical analysis, and image processing. Plugins providing advanced neuro analysis tools and support for additional file formats are installed as needed from a library modules offered from the Mango site: adding and running these is straight-forward. For programmers, there’s good support. A package of developer tools can be downloaded and the API for developing plugins is well-documented.
Mango is a thriving project with much to offer everyone from the casual user to neuroscientist.
Nanodicom is one for the programmers. It’s a PHP toolkit for reading and manipulating DICOM files (no flashy screen caps here sorry). It’s one of very few (n=1) DICOM projects written entirely in PHP and is optimised for speed and a small memory footprint. There’s a core class providing functions to read and modify the file header, as well as operations upon the pixel data. Several ready-made sample applications are useful in their own right as well as providing reference implementations: there are programs provided for dumping, modifying or anonymizing the file header.
The package is well-supported, with extensive documentation, example programs, sample data, and a comprehensive test suite provided. Since it’s hosted on GitHub, it’s available for developers to download, modify, and contribute to.
While Nanodicom does not handle DICOM networking, there is an existing class (not yet added to I Do Imaging) called DICOM PHP Class, which does just that. It differs from NanoDicom in that it does its heavy DICOM work with the DCMTK toolkit.
Nanodicom is developed by Nano Documet, and the current release is version 1.3.
On the subject of DICOM libraries for interpreted languages, Ruby Dicom is well worth a look. It supports reading, editing and writing file headers as well as network operations: querying, retrieving and sending files. In conjunction with other Ruby packages, image data operations are also possible.
It’s written by Christoffer Lervåg who’s put out a steady stream of updates since the project’s inception in 2008. The package is distributed in source form and as a Ruby gem through RubyForge, allowing one-line installation. The program is of course backed by a comprehensive site including tutorials, one of which walks you through creating a DICOM viewer with GUI controls in a few pages of code, using the Qt cross-platform toolkit. Another tutorial uses the Rails framework to quickly build a web app to display DICOM header information on a browser. Ruby Dicom is a cool application of a popular language with a devoted following.
Amide has been a major force in imaging software for a long time. Developed and actively maintained by Andreas Loening, it is by its own description a “Medical Imaging Data Examiner”. As such, it’s strong on technical features and low-level operations on a broad range of file formats. It’s written using the GTK+ cross-platform GUI toolkit which, together with good software design and a lot of hard work, means it will run on Windows and Windows computers as well as Linux. There are too many features to go into here, but they include co-registering and fusing multiple data sets, volumetric rendering, 3-D ROIs, persistent storage of studies, and more.
Amide’s a good example of the collaborative nature of the open source imaging community. The author uses (and contributes to) a variety of software packages, some specific to medical imaging (Medcon for conversions, DCMTK for DICOM support) and some more general (VolPack, FFMPEG, GSL).
Amide is notable in its support of the nuclear medicine formats ECAT and Interfile – strangers to those outside the field (just about everyone) but critical to those of us whose day jobs make possible the (admittedly spotty) maintenance of I Do Imaging. Check it out, especially if you’re of a technical nature.
Medcon, together with its X Windows GUI xmedcon, is a medical image powerhouse for power users. A product of Erik Nolf at Ghent University, it’s a format conversion program that supports a very wide range of file formats, with particular strengths in nuclear medicine but supporting all the widely-used formats. It can work down to the voxel level to reslice image volumes along any axis and resample at varying resolutions. Medcon can convert individual image slices to and from an image volume, convert the image value encoding, change colour maps, normalise values, and perform a number of other low-level operations.
Medcon has been in steady development for over 10 years, issuing dozens of releases, all well-documented and with careful attribution of fixes and feature requests. It is particularly powerful when used from the command line or called from scripts, allowing full automation of complex repetitive actions. There are distributions available for numerous Linux variants as well as the Macintosh and Windows platforms, and full source code (together with cross-platform make files) is provided under the (L)GPL license. There’s not much he’s left out here! (X)Medcon is a nice example of a defined problem (conversion of nuclear medicine file formats) being executed really well.