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=Description=
[[Software#VolViewer| Back to BanghamLab software]]<br>
=<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.]]


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.
<span style="color: Navy">'''What'''?</span> VolViewer is used for''' viewing volume images''' from, for example, '''confocal''' microscopy or optical projection tomography ('''OPT''').


Features:
<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.
Line 15: Line 16:
* Real-time volume clipping.
* Real-time volume clipping.
* 3D measurements, filters & segmentation.
* 3D measurements, filters & segmentation.
* Key frame interpolation for easy movie creation.
* Key frame interpolation for movie export.
* Stereo rendering using either quad buffer or anaglyph mode.
* Stereo rendering using either quad buffer or anaglyph mode.
* Scripting interface to other systems, e.g. Matlab, OMERO, etc.
<span style="color: Navy">'''How'''?</span> It is open source and written in C++ using OpenGL, OpenCL and Qt.<br>
<span style="color: Navy">'''Where'''? </span>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.
Requirements: An OpenGL 2.1 / GLSL 1.20 compatible GPU with a recomended 512MB of memory.


==User Manual==
=<span style="color: Navy">User Documentation</span>=


[[VolViewerUserManual|Quick Guide]] | [[VolViewerTutorials|Video Tutorials]]
{| border="1"  cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]  
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
| align="center|[http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI SCRIPTING]
|}


=Sample Data=
=<span style="color: Navy">Sample Data</span>=


  {| border="0"  cellspacing="5" cellpadding="5" style="background-color:#ffffff;"
  {| border="0"  cellspacing="5" cellpadding="5" style="background-color:#ffffff;  text-align:center;"
  |-
  |-
  | align="center"|[[Image:VolViewer_Figure2.gif|150px]]||[[Image:VolViewer_Figure3.gif|256px]]||[[Image:VolViewer_Figure5.gif|128px]]||[[Image:VolViewer_Figure7.gif|128px]]  
  | align="center"|[[Image:VolViewer_Figure2.gif|75px]]||[[Image:VolViewer_Figure3.gif|128px]]||[[Image:VolViewer_Figure5.gif|64px]]||[[Image:VolViewer_Figure7.gif|64px]]  
  |-
  |-
  | align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Leaf''' <small>(GL2:GUS expression in red)</small> || align="center"| '''Arabidopsis Leaf''' <small>(Ath8:::GUS expression in red)</small>
  | align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Leaf''' <small>(GL2:GUS expression in red)</small> || align="center"| '''Arabidopsis Leaf''' <small>(Ath8:::GUS expression in red)</small>
  |-
  |-
  | align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem(r512g110usmall).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling(174).zip Download]|| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download]
  | align="center"| [http://cmpdartsvr3.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem(r512g110usmall).zip Download] || align="center"| [http://cmpdartsvr3.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling(174).zip Download]|| align="center"| [http://cmpdartsvr3.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"|[http://cmpdartsvr3.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download]
  |}
  |}


<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.


{| border="1"  cellspacing="5" cellpadding="5" style="background-color:#ffffff;"
==OpenGL + Qt + OpenCL + LibTIFF + OMERO==
{| border="1"  cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
  |-
  |-
  | align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x86.exe Windows (32bit)]
  | align="center"|[http://cmpdartsvr3.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x86.exe Windows (32bit)]
  | align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe |Windows (64bit)]
  | align="center"|[http://cmpdartsvr3.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe Windows (64bit)]
  | align="center"|[[VolViewerLinux|Linux]]
  | align="center"|[[VolViewerLinux|Linux]]
  | align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewer_MACOSX.zip MacOS X (i386/x86_64/10.5+)]
  | align="center"|[http://cmpdartsvr3.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg MacOS X (i386/x86_64/10.5+)]
|}
|}


=Source Code=
==OpenGL + Qt + LibTIFF==


Public SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/ https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/]
*Coming soon.


==Building from source==
==Windows Specific Notes==


To build from source your only pre-requisit is to have the [http://qt.nokia.com/downloads Qt SDK] installed. It is then possible to build VolViewer from source using qmake by running to following command:
*You may need to install the corresponding Microsoft Visual C++ 2008 Redistributable Package which can be found here: [http://www.microsoft.com/download/en/details.aspx?id=29 32bit] and [http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=15336 64bit].
*WindowsXP users will need to change the '''view_gldrawbuffer = "GL_FRONT_AND_BACK"''' to '''view_gldrawbuffer = "GL_BACK"''' in the settings.ini file.
*The binaries are built with OMERO 4.3.4 support.


qmake src.pro
=<span style="color: Navy">Source Code</span>=


from within the ''[https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/ VolViewer/src/]'' folder.
Public SVN: [https://cmpdartsvr3.cmp.uea.ac.uk/banghamlabSVN/VolViewer/ https://cmpdartsvr3.cmp.uea.ac.uk/banghamlabSVN/VolViewer/]


==Building with OMERO support==
==<span style="color: Navy">Building from source</span>==


It is also possible to build VolViewer with support for the [http://www.openmicroscopy.org/site Open Microscopy Environment], please see the guide below:
* [[VolViewerBuildingFromSource|Building VolViewer from source]]


*[[VolViewerOMERO|Buiding with OMERO support]]
=<span style="color: Navy">Image Gallery</span>=


=Media/Press=
{| border="0"  style="background-color:#000000;"
|-
|align="center"|
[[Image:1272_wh_rgb.png|128x128px]]
[[Image:Am0front.png|128x128px]]
[[Image:Anthers.PNG|128x128px]]
[[Image:Anti_flower_OPT.png|128x128px]]
[[Image:Antirrhinum_flower_small.png|128x128px]]
[[Image:Ara_seedling_colour.png|128x128px]]
[[Image:Cells.png|128x128px]]
[[Image:Cs0prxz0.png|128x128px]]
[[Image:GL2_GUS.png|128x128px]]
[[Image:Leaf_trichomes.png|128x128px]]
[[Image:Leaf5.png|128x128px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|128x128px]]
[[Image:OleosinSeed.png|128x128px]]
[[Image:OPT_Leaf_copy.png|128x128px]]
[[Image:Seedling_copy.png|128x128px]]
[[Image:Senecio_floret_copy.png|128x128px]]
[[Image:Snapdragon_Peloric_mutant.png|128x128px]]
[[Image:Tissue.png|128x128px]]
[[Image:Z9r3j2yx.png|128x128px]]
[[Image:Zeds48ci.png|128x128px]]
[[Image:1896_wh_txr_light.png|128x128px]]
[[Image:Ara_flower.png|128x128px]]
[[Image:Arableaf_ath8_OPT.png|128x128px]]
[[Image:Arableaf_young_ath8_OPT.png|128x128px]]
[[Image:Enhby820.png|128x128px]]
[[Image:Nilleafdev.png|128x128px]]
[[Image:Seedling_OPT.png|128x128px]]
[[Image:Senecioclip.png|128x128px]]
[[Image:Silique.PNG|128x128px]]
|}
=<span style="color: Navy">Media/Press</span>=


VolViewer has appeared in the following:
VolViewer has appeared in the following:


[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.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]


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


* [[Jerome Avondo| Dr Jerome Avondo]]
* [[Jerome Avondo| Dr Jerome Avondo]] Supported by the BBSRC through UEA Computing School and JIC.

Latest revision as of 14:03, 14 August 2013

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

Quick Guide TUTORIALS Video Demos SCRIPTING

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.

OpenGL + Qt + OpenCL + LibTIFF + OMERO

Windows (32bit) Windows (64bit) Linux MacOS X (i386/x86_64/10.5+)

OpenGL + Qt + LibTIFF

  • Coming soon.

Windows Specific Notes

  • You may need to install the corresponding Microsoft Visual C++ 2008 Redistributable Package which can be found here: 32bit and 64bit.
  • WindowsXP users will need to change the view_gldrawbuffer = "GL_FRONT_AND_BACK" to view_gldrawbuffer = "GL_BACK" in the settings.ini file.
  • The binaries are built with OMERO 4.3.4 support.

Source Code

Public SVN: https://cmpdartsvr3.cmp.uea.ac.uk/banghamlabSVN/VolViewer/

Building from source

Image Gallery

Media/Press

VolViewer has appeared in the following:

Cell: Online Gallery | Front cover: Handbook of Plant Science | Front cover: The Plant Cell | American Scientist | Royal Microscopical Society: Infocus Magazine | Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer | The Daily Mail | The Guardian newspaper: 3D Fruit fly | Qt Ambassador program | Triffid Nurseries website

Author

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