Difference between revisions of "VolViewer"

From BanghamLab
Jump to navigation Jump to search
 
(115 intermediate revisions by 2 users not shown)
Line 1: Line 1:
__NOTOC__
+
[[Software#VolViewer| Back to BanghamLab software]]<br>
=Description=
+
=<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.
* Interactive transfer functions to independently adjust opacity and luminance 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.
Line 16: 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/export by interpolating transformations, clipping and transfer function states.
+
* 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.
 +
 
 +
 
 +
<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 with exercises.]]
+
{| 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]
 +
|}
  
=Image Gallery / 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;"
 
 
  |-
 
  |-
  | 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"| '''Antirinhium Seedling''' || align="center"| '''Arabidopsis Leaf''' <small>(GL2:GUS expression in red)</small> || align="center"| '''Arabidopsis Meristem''' <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/VolViewer_win32.zip 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/VolViewer_x64.zip Windows (64bit)]
+
  | align="center"|[http://cmpdartsvr3.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe  Windows (64bit)]
  | align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/BioptonicsViewer.tar.gz Linux (64bit)]
+
  | 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.
  
=Video Demos=
+
==Windows Specific Notes==
  
{|border="0" align="center" style="text-align:center;"  cellpadding="15" cellspacing="3"
+
*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].
|<wikiflv width="320" height="240" logo="false">Interaction_Demo3.flv|Interaction_Demo3.png</wikiflv> <br><center>This video shows the interactive visualisation capabilities of VolViewer.</center>
+
*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.
|-
+
 
|<wikiflv width="320" height="240" logo="false">Measure1_Demo.flv|Measure1_Demo.png</wikiflv><br><center>This video illustrates how to capture the shape of cell outlines using the measurement tool.</center>
+
=<span style="color: Navy">Source Code</span>=
|<wikiflv width="320" height="240" logo="false">Measure2_Demo.flv|Measure2_Demo.png</wikiflv><br><center>This video shows the measurement and clipping capabilities of VolViewer to capture a 3D cell.</center>
+
 
|-
+
Public SVN: [https://cmpdartsvr3.cmp.uea.ac.uk/banghamlabSVN/VolViewer/ https://cmpdartsvr3.cmp.uea.ac.uk/banghamlabSVN/VolViewer/]
|}
 
  
=Media/Press=
+
==<span style="color: Navy">Building from source</span>==
  
VolViewer has appeared in the following:
+
* [[VolViewerBuildingFromSource|Building VolViewer from source]]
  
* Front cover: [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 Handbook of Plant Science]
+
=<span style="color: Navy">Image Gallery</span>=
  
* Bundled with the commercial Optical Projection Tomography Bioptonic 3001 scanner: [http://www.bioptonics.com/Home.htm Bioptonics Viewer]
+
{| 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>=
  
* In the Guardian newspaper: [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 3D Fruit fly]
+
VolViewer has appeared in the following:
  
* Showcased in the [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program].
+
[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

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.

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

1272 wh rgb.png Am0front.png Anthers.PNG Anti flower OPT.png Antirrhinum flower small.png Ara seedling colour.png Cells.png Cs0prxz0.png GL2 GUS.png Leaf trichomes.png Leaf5.png LFY GUS Arabidopsis inflorescence 512.png OleosinSeed.png OPT Leaf copy.png Seedling copy.png Senecio floret copy.png Snapdragon Peloric mutant.png Tissue.png Z9r3j2yx.png Zeds48ci.png 1896 wh txr light.png Ara flower.png Arableaf ath8 OPT.png Arableaf young ath8 OPT.png Enhby820.png Nilleafdev.png Seedling OPT.png Senecioclip.png Silique.PNG

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