VolViewer: Difference between revisions
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==User Documentation== | ==User Documentation== | ||
<br> | |||
* [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/VolViewerNotes5 Tutorial on loading and saving data]<br> | |||
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes2 Tutorial on user interface]<br> | |||
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes3 Tutorial on exploring data]<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> | |||
* [[VolViewer Scripting in more detail|Scripting in more detail - e.g. Matlab functions]]<br> | |||
<br> | |||
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[[VolViewerTutorials|Video Tutorials]] | [[VolViewerTutorials|Video Tutorials]] | ||
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=Sample Data= | =Sample Data= | ||
Revision as of 12:00, 31 January 2012
All open release software from the BanghamLab
Description
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
Sample Data
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| 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