VolViewer: Difference between revisions

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<span style="color: Navy">Features:</span>
<span style="color: Navy">Features:</span>


* '''Real-time''' volume rendering using an optimized 3D texture slicing algorithm.
* Real-time volume rendering using an optimized 3D texture slicing algorithm.
* Provides a''' 3D viewer service''' to other systems, e.g. Matlab, 'C', Python, etc.
* Interactive transfer functions to independently adjust opacity and intensity for up to three data channels.
* Interactive transfer functions to independently adjust opacity and intensity for up to three data channels.
* Real-time per channel thresholding, brightness and contrast operators.
* Real-time per channel thresholding, brightness and contrast operators.
* On-the-fly gradient computation for local illumination.
* On-the-fly gradient computation for local illumination.
* Iso-surface computation with surface smoothing.
* Iso-surface computation with surface smoothing.
* '''Section viewing''' in any orientation / position.
* Section viewing in any orientation / position.
*''' Real-time volume clipping'''.
* Real-time volume clipping.
* '''3D measurements, filters & segmentation.'''
* 3D measurements, filters & segmentation.
* '''Cool movies''' interpolation between zooms, pans, brightness/contrast.
* Key frame interpolation for movie export.
* '''Stereo rendering''' using either quad buffer or anaglyph mode. (Requires nvidea quadro board or equivalent and 3D display.)<br>
* Stereo rendering using either quad buffer or anaglyph mode.
* Scripting interface to other systems, e.g. Matlab, OMERO, etc.
<br>


<span style="color: Navy">'''How'''?</span> It is open source and written in C++ using OpenGL and Qt.<br>
<span style="color: Navy">'''How'''?</span> It is open source and written in C++ using OpenGL and Qt.<br>
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==<span style="color: Navy">User Documentation</span>==
==<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/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|'''Matlab''' interface and Scripting in more detail]]<br>


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[[VolViewerCourse|Tutorials]]
[[VolViewerUserManual|Quick Guide]]  
[[VolViewerUserManual|Quick Guide]]  
[[VolViewerTutorials|Video Tutorials]]
[[VolViewerTutorials|Video Tutorials]]

Revision as of 13:34, 5 March 2012

Back to BanghamLab software

What? How? Where?

VolViewer fast 3D image volume viewer, also on stereo monitor. Stand-alone or a slave viewport for Matlab and other systems or server-side for OMERO.

What? VolViewer is used for viewing volume images from, for example, confocal microscopy or optical projection tomography (OPT). VolViewer provides tools for making measurements in three dimensions. It also makes 'cool' movies such as fly-throughs.
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 and Qt.
Where? Binaries are available for the PC, Mac 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

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

Author

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