New Releases: October 2012

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.

Five New Programs: October 2012

The majority of this post relates to scientific processing tools that won’t be seen much outside the lab, so we’ll ease into it with something a bit more approachable.

Weasis is a web-based viewer and part of the outstanding DCM4CHE environment.  Weasis is a web-launched viewer in Java that can also be downloaded and run as a stand-alone application.  When run from a web browser, it utilises JNLP, or Java Web Start, to download and start the application.  From that point, it runs independently of the browser.  This makes it ideal for web-based image viewing, since the viewing application is downloaded along with the data.  Weasis has a wide range of viewing tools available and runs at native speed.  A great addition to the ever-increasing line of software from dcm4che.org, developers of professional-grade open source applications and utilities for the healthcare enterprise.

Dicoogle is an innovative PACS system that offers to provide an integrated view of multiple PACS systems.  From the Universidade de Aveiro in Portugal, and in use in several hospitals, it employs a peer-to-peer architecture to implement PACS queries over distributed DICOM repositories.  The project is open source and offers a full set of APIs and an SDK for developers to build upon the platform.  Under development are services for web- and mobile-based clients.

Creatis is a major biomedical imaging research laboratory at Université Lyon 1.  They produce a ton of great software, and Creatools has been added to our database.  This is another major package, providing rapid prototyping of medical imaging applications.  The downloaded package includes ready-to-run applications for end users, as well as the library and API necessary for developers to develop new applications quickly.  Creatools makes it possible for non-programmers to create and run an image processing application from pre-supplied modules that can be connected flexibly.  Creatis have many more tools listed on their software page, once we’ve built and tested them they will be added.

Camino is a heavy-duty toolkit for MRI diffusion imaging.  A specialist group of tools for a specialized field, from the Microstructure Imaging Group at University College, London.  Camino is a large project and backed by a host of academic publications.  The project web site has a vast range of resources, including comprehensive documentation of the many tools provided, tutorials with test data, and resources for software developers (including SVN access to their source code repository).

Lipsia is another heavyweight scientific tool, for functional MRI.  Developed at the Max Planck Institute for Human Cognitive and Brain Sciences, it is a large collection of command line tools to be pipelined for major processing tasks.  Building the application requires quite a few scientific-related tools to be installed: some for the file formats used (Vista, Nifti), some for image analysis, some for processing (scientific libraries, Fourier transforms), some for visualisation (OpenGL).  These can be installed using the usual Linux package managers.  There’s some Fortran in there too – this is for serious work!  Source code in C++ is available for download, as is comprehensive documentation.  A major collection of tools for FMRI.

 

Three new programs for serious science.

Recently added to I Do Imaging are three advanced programs: two image segmentation programs from a very productive collaboration in Vancouver, and a Matlab-based dynamic PET analysis package from Umeå University in Sweden.

TurtleSeg is an advanced 3D image segmentation program developed by a prolific team at Simon Fraser University and the University of British Columbia.  Employing a 3D Livewire algorithm named TurtleMap 3D, also developed by the same team, this program uses minimal interactive guidance to automatically perform and iteratively refine  a full 3D segmentation.  The concept is that the user, with Livewire assistance, generates a small number of nonparallel 2D contours on orthogonal or oblique planes, from which the program generates a dense set of parallel segmentation contours defining a full 3D volume.  As the segmentation progresses, the program can present the user with the plane to contour which would best assist the segmentation.  The results are shown in real time as a 3D rendering.  This is a very well-implemented program, with a thorough website offering documentation, including video guides, and a full manual.  TurtleSeg can read and write a wide range of commonly-used 3D file formats, can store and edit existing contours, and can export the segmentation as an image mask or surface mesh.  The program was developed as part of an MSc project and makes effective use of a wide range of free software, particularly the imaging toolkits ITK for segmentation and VTK for image processing and visualization, and also Qt for the graphical interface.  Using the program for the first time, and with minimal anatomical knowledge, I was able to perform an acceptable aortic segmentation within half an hour.  TurtleSeg is a particularly well-implemented project.

Another, more specialized program from the same collaboration is LiveVessel.  It is designed to perform 2D segmentation of vessels from colour photographs, in particular retinal images.  The development of the segmentation process and its underlying algorithm are described in two publications included in the program’s website.  To perform a segmentation, the user defines the start seed point and traverses the vessel with the mouse, while the application calculates the optimal path and boundaries of the vessel in real time. There’s a video on the site that shows how this process reduces the user input to about as minimal as it can be while still providing guidance. This program is written in a combination of Matlab scripts and MEX-files, which need to be compiled before use.  I was able to compile within Matlab on both Windows and Macintosh systems, however as LiveVessel uses the Signal Processing Toolbox, which I don’t have access to, I was unable to run the application.   LiveVessel looks to be a good implementation of a solution to a specialist need, and is well grounded in original research.

ImLook4D is a Matlab application for the analysis of dynamic PET scans, from Jan Axelsson in Sweden.  This is specialized software for a specialized application, and emphasizes the definition and analysis of volumes of interest over time (hence the 4D).  The program may easily be extended by means of drop-in Matlab scripts, and there are a large number of scripts provided with the program.  It’s also able to import and export its working set to the ImageJ environment for further analysis.  It has native capacity to read and write Dicom and ECAT files, as well as raw binary files.  If you work in the rather esoteric field of PET image analysis, you will be familiar with the features offered by this program.  It’s also quite likely that you are a user or programmer of Matlab, which makes this program doubly useful.