Available Software
To get an up-to-date list of the installed image processing and visualization tools, log on to Rivanna and run the following command in a terminal window:
module keyword vis
To get more information about a specific module version, run the module spider command, for example:
module spider blender/2.78c
List of Image Processing and Visualization Software Modules
| Module | Category | Description |
|---|---|---|
| atk | vis | ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. |
| blender | vis | Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. |
| cairo | vis | Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB |
| cc3d | vis | CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D's intuitive interface makes Virtual Tissue modeling accessible to users without extensive software development or programming experience. |
| cloudcompare | vis | CloudCompare is a 3D point cloud (and triangular mesh) processing software. It has been originally designed to perform comparison between two dense 3D points clouds (such as the ones acquired with a laser scanner) or between a point cloud and a triangular mesh. |
| ddd | vis | DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb. |
| ffmpeg | vis | A complete, cross-platform solution to record, convert and stream audio and video. |
| fltk | vis | FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. |
| glade | vis | Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment. |
| gnuplot | vis | Portable interactive, function plotting utility |
| grace | vis | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
| gtk+ | vis | The GTK+ 3 package contains libraries used for creating graphical user interfaces for applications. |
| imagemagick | vis | ImageMagick is a software suite to create, edit, compose, or convert bitmap images |
| jasper | vis | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. |
| jtreeview | vis | TreeView is an open-source Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it (or parts of it) into a figure. |
| leptonica | vis | Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. |
| librsvg | vis | librsvg is a library to render SVG files using cairo. |
| mayavi | vis | A tool for easy and interactive visualization of data. |
| ncview | vis | Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. |
| openslide-python | vis | Python bindings for the OpenSlide libary |
| paraview | vis | ParaView is a scientific parallel visualizer. |
| poppler | vis | Poppler is a PDF rendering library based on the xpdf-3.0 code base. |
| pov-ray | vis | The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. |
| pycairo | vis | Python bindings for the cairo library |
| pygobject | vis | Python Bindings for GLib/GObject/GIO/GTK+ |
| pygtk | vis | PyGTK lets you to easily create programs with a graphical user interface using the Python programming language. |
| pyopengl | vis | PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. |
| sibil-env | vis | This module sets up the environment for the SIBIL application. |
| snap-stanford | vis | Snap.py is a Python interface for SNAP. SNAP is a general purpose, high performance system for analysis and manipulation of large networks. SNAP is written in C++ and optimized for maximum performance and compact graph representation. It easily scales to massive networks with hundreds of millions of nodes, and billions of edges. |
| tesseract | vis | Tesseract is an optical character recognition engine |
| vapor | vis | VAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images |
| vigra | vis | VIGRA stands for "Vision with Generic Algorithms". It's an image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images, because many algorithms (e.g. filters, feature computation, superpixels) are implemented for arbitrary high dimensions. |
| visit | vis | VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. |
| vtk | vis | The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. |
| wxpython | vis | wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. |
| wxwidgets | vis | wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. |
| xcrysden | vis | XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. |
Running Interactive Visualizations
Many of the provided image processing and visualization applications provide a graphical user interface (GUI). In order to use a GUI on Rivanna, users must log in through a client capable of displaying X11 graphics. We recommend FastX Web which provides a GPU to accelerate rendering.
To start an applications GUI in an X11-enabled terminal, first load the software module and then run the GUI application executable, e.g.
module load blender
When connected to Rivanna via FastX Web, rendering of the graphical user interface can be accelerated by executing this command:
module load blender
vglrun -c proxy blender &
The ampersand & returns the terminal to input mode while the application is running.