Difference between revisions of "VolViewer"

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* [[VolViewerUserManual|Quick Guide]]  
 
* [[VolViewerUserManual|Quick Guide]]  
 
* [[VolViewerTutorials|Video Tutorials]]
 
* [[VolViewerTutorials|Video Tutorials]]
 
=<span style="color: Navy">Image Gallery</span>=
 
 
{| border="0"  width="100%" cellspacing="5" cellpadding="5" style="background-color:#000000;  text-align:center;"
 
|-
 
||
 
<center>
 
<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>
 
|}
 
 
=<span style="color: Navy">Sample Data</span>=
 
=<span style="color: Navy">Sample Data</span>=
  
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[http://www.amazon.co.uk/Handbook-Plant-Science-Keith-Roberts/dp/0470057238/ref=sr_1_19?s=books&ie=UTF8&qid=1289321357&sr=1-19 Front cover: Handbook of Plant Science] | [http://www.plantcell.org/content/18/9.toc Front cover: The Plant Cell] | [http://www.rms.org.uk/Resources/Royal%20Microscopical%20Society/infocus/Edgar%20article.pdf  Royal Microscopical Society: Infocus Magazine] | [http://www.bioptonics.com/Home.htm Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer] | [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 The Guardian newspaper: 3D Fruit fly] | [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program] | [http://www.triffidnurseries.co.uk/special3.php Triffid Nurseries website]
 
[http://www.amazon.co.uk/Handbook-Plant-Science-Keith-Roberts/dp/0470057238/ref=sr_1_19?s=books&ie=UTF8&qid=1289321357&sr=1-19 Front cover: Handbook of Plant Science] | [http://www.plantcell.org/content/18/9.toc Front cover: The Plant Cell] | [http://www.rms.org.uk/Resources/Royal%20Microscopical%20Society/infocus/Edgar%20article.pdf  Royal Microscopical Society: Infocus Magazine] | [http://www.bioptonics.com/Home.htm Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer] | [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 The Guardian newspaper: 3D Fruit fly] | [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program] | [http://www.triffidnurseries.co.uk/special3.php Triffid Nurseries website]
 +
 +
 +
=<span style="color: Navy">Image Gallery</span>=
 +
 +
{| border="0"  width="100%" cellspacing="5" cellpadding="5" style="background-color:#000000;  text-align:center;"
 +
|-
 +
||
 +
<center>
 +
<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>
 +
|}
  
 
=<span style="color: Navy">Author</span>=
 
=<span style="color: Navy">Author</span>=
  
 
* [[Jerome Avondo| Dr Jerome Avondo]] Supported by the BBSRC through UEA Computing School and JIC.
 
* [[Jerome Avondo| Dr Jerome Avondo]] Supported by the BBSRC through UEA Computing School and JIC.

Revision as of 15:40, 5 March 2012

Back to BanghamLab software

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

Sample Data

VolViewer Figure2.gif VolViewer Figure3.gif VolViewer Figure5.gif VolViewer Figure7.gif
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

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


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>

Author