VolViewer: Difference between revisions
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[[Software#VolViewer| Back to BanghamLab software]]<br> | [[Software#VolViewer| Back to BanghamLab software]]<br> | ||
=What? How? Where?= | =<span style="color: Navy">What? How? Where?</span>= | ||
[[Image:VolViewer.png|256px|thumb|The VolViewer main application window.]] | [[Image:VolViewer.png|256px|thumb|The VolViewer main application window.]] | ||
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Requirements: An OpenGL 2.1 / GLSL 1.20 compatible GPU with a recomended 512MB of memory. | Requirements: An OpenGL 2.1 / GLSL 1.20 compatible GPU with a recomended 512MB of memory. | ||
==User Documentation== | ==<span style="color: Navy">User Documentation</span>== | ||
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes1 Tutorial on dealing with proprietory file formats (BioformatsConverter)]<br> | * [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes1 Tutorial on dealing with proprietory file formats (BioformatsConverter)]<br> | ||
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* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes6 Tutorial on high quality projections and movies]<br> | * [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes6 Tutorial on high quality projections and movies]<br> | ||
* [http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerNotes4 Tutorial on filters, quantification, segmentation and scripting]<br> | * [http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerNotes4 Tutorial on filters, quantification, segmentation and scripting]<br> | ||
* [[VolViewer Scripting in more detail|Scripting in more detail | * [[VolViewer Scripting in more detail|'''Matlab''' interface and Scripting in more detail]]<br> | ||
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=Sample Data= | =<span style="color: Navy">Sample Data</span>= | ||
{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;" | {| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;" | ||
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<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk] | <nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk] | ||
=Download= | =<span style="color: Navy">Download</span>= | ||
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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation. | 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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation. | ||
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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: [http://www.microsoft.com/download/en/details.aspx?id=8328 32bit] and [http://www.microsoft.com/download/en/details.aspx?id=13523 64bit]. | 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: [http://www.microsoft.com/download/en/details.aspx?id=8328 32bit] and [http://www.microsoft.com/download/en/details.aspx?id=13523 64bit]. | ||
=Source Code= | =<span style="color: Navy">Source Code</span>= | ||
Public SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/ https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/] | Public SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/ https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/] | ||
Revision as of 20:21, 1 March 2012
What? How? Where?
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
- Matlab interface and Scripting in more detail
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
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