Difference between revisions of "VolViewer"

From BanghamLab
Jump to navigation Jump to search
Line 1: Line 1:
 
[[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.]]
Line 21: Line 21:
 
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>
Line 29: Line 29:
 
* [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 - e.g. Matlab functions]]<br>
+
* [[VolViewer Scripting in more detail|'''Matlab''' interface and Scripting in more detail]]<br>
  
  
Line 39: Line 39:
 
|}
 
|}
  
=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;"
Line 52: Line 52:
 
<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.
Line 67: Line 67:
 
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

Back to BanghamLab software

What? How? Where?

The VolViewer main application window.

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


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