VolViewer

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What? How? Where?

The VolViewer main application window.

What? VolViewer is used for viewing volume images from, for example, confocal microscopy or optical projection tomography (OPT).

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 movie export.
• Stereo rendering using either quad buffer or anaglyph mode.
• Scripting interface to other systems, e.g. Matlab, OMERO, etc.

How? It is open source and written in C++ using OpenGL, OpenCL and Qt.
Where? Binaries are available for the Windows, Mac OS X and Linux, see below.

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

User Documentation

• Tutorials
• Quick Guide
• Video Tutorials

Image Gallery

<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> 1272_wh_rgb.png Am0front.png Anthers.PNG Anti_flower_OPT.png Antirrhinum_flower_small.png Ara_seedling_colour.png Cells.png Cs0prxz0.png GL2_GUS.png Leaf_trichomes.png Leaf5.png LFY_GUS_Arabidopsis_inflorescence_512.png OleosinSeed.png OPT_Leaf_copy.png Seedling_copy.png Senecio_floret_copy.png Snapdragon_Peloric_mutant.png Tissue.png|128px]][[Image:Z9r3j2yx.png Zeds48ci.png </sgallery> <sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> 1272_wh_rgb.png Am0front.png Anthers.PNG Anti_flower_OPT.png Antirrhinum_flower_small.png Ara_seedling_colour.png Cells.png Cs0prxz0.png GL2_GUS.png Leaf_trichomes.png Leaf5.png LFY_GUS_Arabidopsis_inflorescence_512.png OleosinSeed.png OPT_Leaf_copy.png Seedling_copy.png Senecio_floret_copy.png Snapdragon_Peloric_mutant.png Tissue.png|128px]][[Image:Z9r3j2yx.png Zeds48ci.png </sgallery> <sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> Cells.png Anti_flower_OPT.png Cs0prxz0.png GL2_GUS.png Antirrhinum_flower_small.png Ara_seedling_colour.png OleosinSeed.png Anthers.PNG Senecio_floret_copy.png Leaf_trichomes.png Leaf5.png LFY_GUS_Arabidopsis_inflorescence_512.png Snapdragon_Peloric_mutant.png Tissue.png|128px]][[Image:Z9r3j2yx.png OPT_Leaf_copy.png Seedling_copy.png 1272_wh_rgb.png Am0front.png Zeds48ci.png </sgallery>

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 Supported by the BBSRC through UEA Computing School and JIC.