Available Software
To get an up-to-date list of the installed image processing and visualization tools, log on to UVA HPC 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 |
|---|---|---|
| assimp | vis | Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. |
| at-spi2-atk | vis | AT-SPI 2 toolkit bridge |
| at-spi2-core | vis | Assistive Technology Service Provider Interface. |
| 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 |
| 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. |
| fiji | vis | Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1 |
| 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. |
| fontconfig | vis | Fontconfig is a library designed to provide system-wide font configuration, customization and application access. |
| freetype | vis | FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. |
| gdk-pixbuf | vis | The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. |
| gl2ps | vis | GL2PS: an OpenGL to PostScript printing library |
| glib | vis | GLib is one of the base libraries of the GTK+ project |
| gnuplot | vis | Portable interactive, function plotting utility |
| grace | vis | Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. |
| gst-plugins-base | vis | GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. |
| gstreamer | vis | GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. |
| gtk3 | vis | GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. |
| harfbuzz | vis | HarfBuzz is an OpenType text shaping engine. |
| 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. |
| jbigkit | vis | JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. |
| leptonica | vis | Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. |
| libglu | vis | The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. |
| mayavi | vis | A tool for easy and interactive visualization of data. |
| mesa | vis | Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. |
| 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 | vis | OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). |
| openslide-python | vis | Python bindings for the OpenSlide libary |
| optix | vis | OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. |
| pango | vis | Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. |
| paraview | vis | ParaView is a scientific parallel visualizer. |
| pixman | vis | Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. |
| pymol | vis | PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger. |
| 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 |
| togl | vis | Togl is a Tk widget for OpenGL rendering |
| 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 |
| vesta | vis | VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies. |
| 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. |
| wayland | vis | Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. |
| wxpython | vis | Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code. |
| wxwidgets | vis | wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. |
| x11 | vis | The X Window System (X11) is a windowing system for bitmap displays |
| x264 | vis | x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. |
| x265 | vis | x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. |
| 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 the HPC system, 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 UVA HPC 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.