VolViewer

All open release software from the BanghamLab

What? How? Where?

The VolViewer main application window.

VolViewer is an open source application for the interactive visualisation and quantification of biological data. The application is written in C++ using OpenGL and Qt.

Features:

• Real-time volume rendering using an optimized 3D texture slicing algorithm.
• Interactive transfer functions to independently adjust opacity and intensity for up to three data channels.
• Real-time per channel thresholding, brightness and contrast operators.
• On-the-fly gradient computation for local illumination.
• Iso-surface computation with surface smoothing.
• Section viewing in any orientation / position.
• Real-time volume clipping.
• 3D measurements, filters & segmentation.
• Key frame interpolation for easy movie creation.
• Stereo rendering using either quad buffer or anaglyph mode.

Requirements: An OpenGL 2.1 / GLSL 1.20 compatible GPU with a recomended 512MB of memory.

User Documentation

• Tutorial on dealing with proprietory file formats (BioformatsConverter)
  
• Tutorial on loading and saving data
  
• Tutorial on user interface
  
• Tutorial on exploring data
  
• Tutorial on high quality projections and movies
  
• Tutorial on filters, quantification, segmentation and scripting
  
• Scripting in more detail - e.g. Matlab functions
  

Quick Guide Video Tutorials

Sample Data

Antirinhium Meristem	Arabidopsis Seedling	Arabidopsis Leaf (GL2:GUS expression in red)	Arabidopsis Leaf (Ath8:::GUS expression in red)
Download	Download	Download	Download

* all data courtesy of Karen Lee [1]

Download

Although we try to keep up to date builds these sometimes lag behind the SVN trunk. So if you want the latest version / features, it is best to build the application from the trunk of the SVN. The build system is based on qmake for easy cross platform compilation.

Windows (32bit)

Windows (64bit)

Linux

MacOS X (i386/x86_64/10.5+)

Note that for the windows versions you will need to install the corresponding Microsoft Visual C++ 2010 SP1 Redistributable Package which can be found here: 32bit and 64bit.

Source Code

Public SVN: https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/

Building from source

• Building VolViewer from source

Media/Press

VolViewer has appeared in the following:

Front cover: Handbook of Plant Science | Front cover: The Plant Cell | Royal Microscopical Society: Infocus Magazine | Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer | The Guardian newspaper: 3D Fruit fly | Qt Ambassador program | Triffid Nurseries website

Author

• Dr Jerome Avondo