BanghamLab - User contributions [en]

VolViewer

2013-08-14T14:03:15Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

VolViewer has appeared in the following:

[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=

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

VolViewer

2013-08-14T14:02:40Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

VolViewer has appeared in the following:

[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=

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

Software

2012-12-17T17:42:04Z

JeromeAvondo:

__TOC__

'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.
===Notes on documenting our software===
[[Documenting our software|Transferring Matlab files and zipping toolboxes and dependencies]]
=Computational biology toolboxes=
==Quantitative understanding of growing shapes: '''GFtbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|width="40%"|
For modelling the growth of shapes. 
[[GFtbox|'''What? How? Where?''']] 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). The GPT-framework was used to capture an understanding of (to model) the growing leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract Kuchen et al 2012]) and Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.] The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011])
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>AAMToolbox_logo.jpg|120px|AAMToolbox</imgicon>
|width="40%"|For analysing populations of shapes and colours within the shapes using principal component analysis. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}
=Open source systems to which we contribute=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Algorithms=
==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|A simple reaction-diffusion system develops a pattern of spots.
 
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0004.flv|GPT_rd_rk_tentacles_20120417-0004_First.png</wikiflv>
|- valign="top"
|width="700pt"|Two simple growth rules translate the pattern into directed growth. The changing geometry that arises through growth causes the reaction-diffusion patterning to continue to change.
 
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0001.flv|GPT_rd_rk_tentacles_20120417-0004.png</wikiflv>
|}

==Non-linear signal processing==
==Art==

VolViewer

2012-12-17T17:40:48Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

==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://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

VolViewer has appeared in the following:

[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=

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

VolViewer

2012-10-15T14:28:51Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

==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://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

VolViewer has appeared in the following:

[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.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=

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

VolViewer

2012-10-15T14:27:30Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

==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://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

VolViewer has appeared in the following:

[http://www.cell.com/cell_picture_show-plantbio Cell] | [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.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=

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

VolViewerOMERO

2012-07-27T16:43:56Z

JeromeAvondo:

=Overview=

It is possible to build VolViewer with support for reading/saving images directly from an OMERO server.

The viewer can read/write XYZC image stacks from OMERO with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.

For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.

=Requirements=

To build VolViewer with OMERO 4.3.x support you will require the following:

* An SVN client, to check out the VolViewer source code, such as [http://tortoisesvn.tigris.org/ TortoiseSVN] for windows or svn for linux/[http://www.open.collab.net/downloads/community/ mac].
* The latest [http://qt.nokia.com/downloads Qt SDK].
* The [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries].

=How To=

*Start by checking out the latest VolViewer source code from the SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer VolViewer SVN]
*Next build the OMERO cpp libraries following this guide: [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries]
** To build the OMERO cpp you will require the [http://www.zeroc.com/download_3_3_1.html ICE libraries]. Note that these exist in binary form for certain platforms. ''NB'' You should only use version 3.3.1 of ICE with OMERO.
*Now that you have the OMERO cpp library built you are ready to build VolViewer with OMERO support. VolViewer is built using qmake so it is relatively straight forward.
* Start by enabling the OMERO support in the source code by editing the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/MyDefines.h MyDefines.h] file and un-commenting the line:

''//#define OMERO_SUPPORT'' '''=>''' ''#define OMERO_SUPPORT''

* Next we turn on OMERO support in the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/src.pro scr.pro] project file by adding ''omero'' in the CONFIG variable:

''CONFIG += qt thread x86_64'' '''=>''' ''CONFIG += qt thread x86_64 omero''

* Lastly we are now ready to run the qmake command. You will need to set your own paths for the environment variables ''ICE_HOME'' and ''OMERO_HOME''.
** Example build scripts can be found for:
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_win.bat Windows]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_mac.sh Mac OS X]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_linux.sh Linux]
*** Note that there is also a support for a Visual Studio 2010 project for windows found [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/ here].

=Example Server side scripts=
* [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/pythonscrits/ OMERO/VolViewer Scripts]

=Screenshot=

[[Image:VolViewerOMERO.png|thumb|256px|left|OMERO / VolViewer integration.]]

VolViewer

2012-05-29T11:11:46Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

==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://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/BioptonicsViewerV2/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-05-25T15:02:25Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

==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/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewerOMERO

2012-04-02T15:41:56Z

JeromeAvondo:

=Overview=

It is possible to build VolViewer with support for reading images directly from an OMERO server.

The viewer can read/write XYZC image stacks from OMERO with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.

For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.

=Requirements=

To build VolViewer with OMERO support you will require the following:

* An SVN client, to check out the VolViewer source code, such as [http://tortoisesvn.tigris.org/ TortoiseSVN] for windows or svn for linux/[http://www.open.collab.net/downloads/community/ mac].
* The latest [http://qt.nokia.com/downloads Qt SDK].
* The [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries].

=How To=

*Start by checking out the latest VolViewer source code from the SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer VolViewer SVN]
*Next build the OMERO cpp libraries following this guide: [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries]
** To build the OMERO cpp you will require the [http://www.zeroc.com/download_3_3_1.html ICE libraries]. Note that these exist in binary form for certain platforms. ''NB'' You should only use version 3.3.1 of ICE with OMERO.
*Now that you have the OMERO cpp library built you are ready to build VolViewer with OMERO support. VolViewer is built using qmake so it is relatively straight forward.
* Start by enabling the OMERO support in the source code by editing the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/MyDefines.h MyDefines.h] file and un-commenting the line:

''//#define OMERO_SUPPORT'' '''=>''' ''#define OMERO_SUPPORT''

* Next we turn on OMERO support in the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/src.pro scr.pro] project file by adding ''omero'' in the CONFIG variable:

''CONFIG += qt thread x86_64'' '''=>''' ''CONFIG += qt thread x86_64 omero''

* Lastly we are now ready to run the qmake command. You will need to set your own paths for the environment variables ''ICE_HOME'' and ''OMERO_HOME''.
** Example build scripts can be found for:
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_win.bat Windows]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_mac.sh Mac OS X]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_linux.sh Linux]
*** Note that there is also a support for a Visual Studio 2010 project for windows found [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/ here].

=Example Server side scripts=
* [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/pythonscrits/ OMERO/VolViewer Scripts]

=Screenshot=

[[Image:VolViewerOMERO.png|thumb|256px|left|OMERO / VolViewer integration.]]

VolViewerOMERO

2012-04-02T15:41:44Z

JeromeAvondo:

=Overview=

It is possible to build VolViewer with support for reading images directly from an OMERO server.

The viewer can read/write XYZC image stacks with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.

For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.

=Requirements=

To build VolViewer with OMERO support you will require the following:

* An SVN client, to check out the VolViewer source code, such as [http://tortoisesvn.tigris.org/ TortoiseSVN] for windows or svn for linux/[http://www.open.collab.net/downloads/community/ mac].
* The latest [http://qt.nokia.com/downloads Qt SDK].
* The [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries].

=How To=

*Start by checking out the latest VolViewer source code from the SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer VolViewer SVN]
*Next build the OMERO cpp libraries following this guide: [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries]
** To build the OMERO cpp you will require the [http://www.zeroc.com/download_3_3_1.html ICE libraries]. Note that these exist in binary form for certain platforms. ''NB'' You should only use version 3.3.1 of ICE with OMERO.
*Now that you have the OMERO cpp library built you are ready to build VolViewer with OMERO support. VolViewer is built using qmake so it is relatively straight forward.
* Start by enabling the OMERO support in the source code by editing the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/MyDefines.h MyDefines.h] file and un-commenting the line:

''//#define OMERO_SUPPORT'' '''=>''' ''#define OMERO_SUPPORT''

* Next we turn on OMERO support in the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/src.pro scr.pro] project file by adding ''omero'' in the CONFIG variable:

''CONFIG += qt thread x86_64'' '''=>''' ''CONFIG += qt thread x86_64 omero''

* Lastly we are now ready to run the qmake command. You will need to set your own paths for the environment variables ''ICE_HOME'' and ''OMERO_HOME''.
** Example build scripts can be found for:
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_win.bat Windows]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_mac.sh Mac OS X]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_linux.sh Linux]
*** Note that there is also a support for a Visual Studio 2010 project for windows found [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/ here].

=Example Server side scripts=
* [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/pythonscrits/ OMERO/VolViewer Scripts]

=Screenshot=

[[Image:VolViewerOMERO.png|thumb|256px|left|OMERO / VolViewer integration.]]

VolViewerOMERO

2012-04-02T15:41:09Z

JeromeAvondo:

=Overview=

It is possible to build VolViewer with support for reading images directly from an OMERO server.

The viewer can read XYZC image stacks with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.

For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.

=Requirements=

To build VolViewer with OMERO support you will require the following:

* An SVN client, to check out the VolViewer source code, such as [http://tortoisesvn.tigris.org/ TortoiseSVN] for windows or svn for linux/[http://www.open.collab.net/downloads/community/ mac].
* The latest [http://qt.nokia.com/downloads Qt SDK].
* The [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries].

=How To=

*Start by checking out the latest VolViewer source code from the SVN: [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer VolViewer SVN]
*Next build the OMERO cpp libraries following this guide: [http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCpp OMERO cpp libraries]
** To build the OMERO cpp you will require the [http://www.zeroc.com/download_3_3_1.html ICE libraries]. Note that these exist in binary form for certain platforms. ''NB'' You should only use version 3.3.1 of ICE with OMERO.
*Now that you have the OMERO cpp library built you are ready to build VolViewer with OMERO support. VolViewer is built using qmake so it is relatively straight forward.
* Start by enabling the OMERO support in the source code by editing the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/MyDefines.h MyDefines.h] file and un-commenting the line:

''//#define OMERO_SUPPORT'' '''=>''' ''#define OMERO_SUPPORT''

* Next we turn on OMERO support in the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/src.pro scr.pro] project file by adding ''omero'' in the CONFIG variable:

''CONFIG += qt thread x86_64'' '''=>''' ''CONFIG += qt thread x86_64 omero''

* Lastly we are now ready to run the qmake command. You will need to set your own paths for the environment variables ''ICE_HOME'' and ''OMERO_HOME''.
** Example build scripts can be found for:
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_win.bat Windows]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_mac.sh Mac OS X]
*** [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/build_linux.sh Linux]
*** Note that there is also a support for a Visual Studio 2010 project for windows found [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/ here].

=Example Server side scripts=
* [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/pythonscrits/ OMERO/VolViewer Scripts]

=Screenshot=

[[Image:VolViewerOMERO.png|thumb|256px|left|OMERO / VolViewer integration.]]

VolViewer

2012-03-27T11:53:43Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| 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=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

==Windows Specific Notes==

*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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewerCourse

2012-03-27T11:50:51Z

JeromeAvondo:

=VolViewer Tutorials=

* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes1 Dealing with proprietory file formats (BioformatsConverter)] 
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes5 Loading and saving data] 
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes2 User interface overview] 
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes3 Exploring data] 
* [http://DMBI.nbi.bbsrc.ac.uk/index.php/VolViewerNotes6 High quality projections and movies] 
* [http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerNotes4 Filters, quantification, segmentation and scripting] 

=Misc=

* [[VolViewer Scripting in more detail|'''Matlab''' interface and Scripting in more detail]]

VolViewer

2012-03-27T11:44:23Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

==Windows Specific Notes==

*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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-27T11:43:15Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

==Windows Specific Notes==
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.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-27T11:42:46Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

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

==Windows Specific Notes==
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].

Also note WindowsXP users will need to change the '''view_gldrawbuffer = "GL_FRONT_AND_BACK"''' to '''view_gldrawbuffer = "GL_BACK"''' in the settings.ini file.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-27T11:39:41Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [http://www.microsoft.com/download/en/details.aspx?id=8328 32bit] and [http://www.microsoft.com/download/en/details.aspx?id=13523 64bit].

Also note WindowsXP users will need to change the '''view_gldrawbuffer = "GL_FRONT_AND_BACK"''' to '''view_gldrawbuffer = "GL_BACK"''' in the settings.ini file.

=Source Code=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-27T10:26:20Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerCourse|TUTORIALS]]
| align="center"|[[VolViewerTutorials|Video Demos]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewerUserManual

2012-03-27T10:25:24Z

JeromeAvondo:

=Quick Guide=

=Loading Volume Data=

The viewer supports two types of file formats for loading volume data. It also supports four different ways to actually load data into the viewer. See the subsections for more information about the file formats and data loading mechanisms.

==Supported File Formats==

===Image Stacks===

The viewer supports image stacks in the following file formats: PNG, BMP, TIFF, JPG. For data that does not have equal spacing in the X,Y,Z dimensions, ie: confocal data, you may also create a text file called voxelspacing.txt to specify the voxel spacing independently for each axis. This file needs to be in the same folder as where your image stack files are. This text file takes the following format:

x 0.488281
y 0.488281
z 1.506024

Note that an image stack is a series of 2D images for each z-series of your stack. The images can be 8bit grey scale or 8bit RGB.

===Raw Volume===

Raw volumes are supported, these volumes are made up of two files, a .raw and a .dat file. The .raw file is the volume values. These values are stored in binary format, and the voxel values are ordered as R/G/B triplets and in X,Y,Z traversal order. The .dat file with the same filename as the .raw file contains the metadata of the volume. This metadata is the extra information you need to be able to load the volume. This data is X,Y,Z dimensions and the data type.

==Loading Data==

To load data into the viewer, this can be achieved by one of three mechanisms:

* Using the '''FILE''' dropdown menu.
* Using the '''Drag&Drop''' event.
* Using the '''scripting interface'''

===The File Dropdown Menu===

The easiest method to load data is to do this via the '''FILE''' dropdown menu.

Once you select either a stack or a raw volume you will be presented with a file dialogue which you can point to the file you want to load. Note that when loading an image stack you can point the viewer to any file in your stack, it does not have to be the first image of the stack.

Note there are keyboard short-cuts to facilitate the loading of volume data:

* '''CTRL + R''': load a raw volume
* '''CTRL + S''': load an image stack

===The Drag&Drop Event===

With the Drag&Drop event you can load data into the viewer by simply dragging one of the supported files to the main rendering window. See the figure below.

The Drag&Drop accepts drops of either; a single image file in you stack, a .dat file or a .raw file.

===Scripting Interface===

See [http://dmbi.nbi.bbsrc.ac.uk/index.php/VolViewerScriptsAPI this] site for more information.

'''*Exercise 1:'''
Try loading a volume by downloading the sample volume [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip here] and using the drag and drop method.

=Saving Volume Data=

The viewer allows you to save your volume data either as a .RAW binary file or a stack of PNG images. This is achieved by using the '''FILE''' dropdown menu and choosing the '''SAVE''' option. Note that when saving a PNG image stack you will be asked to point the viewer to a directory that it store the volume stack.

=Interacting with the Volume=

Once a volume is loaded you can interact with the volume by rotating it, moving it (translating), or zooming in and out. This is achieved via the mouse.

==Arcball Rotation==

To rotate a volume you use the left mouse button. Click on the centre (more or less) of the view screen and without releasing the left mouse button drag the volume in your desired direction you wish to rotate it. See the figure below for more details.

==Zooming In/Out==

Zooming in and out is achieved using the right mouse button. You can zoom in by clicking and not releasing the right mouse button and moving the mouse down. Or to zoom out you click the right mouse button and without releasing move the mouse up.

==Translation==

To move or translate a volume you use the middle mouse button. Translation is achieved by clicking and keeping pressed the middle mouse button, then by either moving left, right, up or down you are able to move the volume. To stop translation simply release the middle mouse button.

(NB) Currently the centre of rotation is not affected by the translation, and the volume will still rotate about it's centre even after translation. The ability to change this behaviour will be introduced in a future release.

'''*Exercise 2:'''
Try rotating and zooming the volume.

=Toolbars=

==Viewing==

[[Image:VolViewerMenuTools.PNG]]

This toolbar allows you to control various viewing options.

* '''I''': Toggles the volume greyscale channel
* '''R''': Toggles the volume red channel
* '''G''': Toggles the volume green channel
* '''B''': Toggles the volume blue channel
* '''S''': Toggles the iso-surface (if computed)
* '''mip''': Toggles the Maximum Intensity Projection mode
* '''BG''': Allows you to specify the background colour
* '''3D''': Allows you to enable stereo rendering (requires a 3D screen)
* '''camera icon''': Takes a screen grab of the current view and prompts you with a save file dialogue.
* '''qual''': Various viewing quality presets.
* '''view''': Various view direction presets.
* '''on/off''': Various viewing toggles.

'''*Exercise 3:'''
Enable/Disable the red channel
Toggle the MIP rendering mode
Use the view menu to view your data from the LEFT orientation.
Use the on/off menu to toggle the axis

==Tools==

[[Image:VolViewerTools.png]]

* '''graph icon''': Brings up the transfer function widget.
* '''crop icon''': Brings up the crop widget.
* '''clipping plane icon''': Brings up the clipping widget.
* '''measure icon''': Brings up the measure widget.
* '''surface icon''': Brings up the iso-surface widget.
* '''filter icon''': Brings up the filter widget.

'''*Exercise 4:'''
Open the transfer function widget and adjust the opacity and threshold the volume.
Open the clipping widget to clip the volume
Open the filter widget to apply some Gaussian smoothing to your volume.

==Settings==

[[Image:VolViewerSettings.png]]

* '''visual bookmarks icon''': Allows you to save an orientation, clip state and transfer function state of your volume as a bookmark
* '''movie icon''': Allows you to save movie frames for your volume.
* '''lighting icon''': Allows you to apply lighting to your volume data.
* '''settings icon''': Allows you to control various performance and quality setting

'''*Exercise 5:'''
Use the visual bookmarks to save two different views of you volume, and toggle between them by double clicking the thumbnails.
Use the movie icon to save the frames for a movie

Main Page

2012-03-08T17:32:14Z

JeromeAvondo:

__NOTOC__
=Bangham Lab - Home=

'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.
=Computational biology toolboxes=
==GFtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|width="40%"|
For modelling the growth of shapes. 
[[GFtbox|'''What? How? Where?''']] 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). The GPT-framework was used to capture an understanding of (to model) the growing leaf (Kuchen et al 2012) and Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.] The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011])
|}

==VolViewer==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring biological images. 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 
[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]
 
|width="50%"| VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|}

{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:Cs0prxz0.png|32x32px]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:Cs0prxz0.png|32x32px]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:OPT_Leaf_copy.png|32x32px]]
[[Image:Seedling_copy.png|32x32px]]
[[Image:Senecio_floret_copy.png|32x32px]]
[[Image:Snapdragon_Peloric_mutant.png|32x32px]]
[[Image:Tissue.png|32x32px]]
[[Image:Z9r3j2yx.png|32x32px]]
[[Image:Zeds48ci.png|32x32px]]
[[Image:1896_wh_txr_light.png|32x32px]]
[[Image:Ara_flower.png|32x32px]]
[[Image:Arableaf_ath8_OPT.png|32x32px]]
[[Image:Arableaf_young_ath8_OPT.png|32x32px]]
[[Image:Enhby820.png|32x32px]]
|}
==AAMToolbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>AAMToolbox_logo.jpg|120px|AAMToolbox</imgicon>
|width="40%"|For analysing populations of shapes and colours within the shapes using principal component analysis. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/ShapeModelToolbox.zip '''''Download''''' ] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. The analysis can be applied to art, for example, finding systematic differences between portraits by, for example, Rembrandt and Modigliani.
|}

Main Page

2012-03-08T17:31:03Z

JeromeAvondo:

__NOTOC__
=Bangham Lab - Home=

'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.
=Computational biology toolboxes=
==GFtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|width="40%"|
For modelling the growth of shapes. 
[[GFtbox|'''What? How? Where?''']] 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). The GPT-framework was used to capture an understanding of (to model) the growing leaf (Kuchen et al 2012) and Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.] The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011])
|}

==VolViewer==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring biological images. 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 
[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]
 
|width="50%"| VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|}

{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:Cs0prxz0.png|32x32px]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:Cs0prxz0.png|32x32px]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:OPT_Leaf_copy.png|32x32px]]
[[Image:Seedling_copy.png|32x32px]]
[[Image:Senecio_floret_copy.png|32x32px]]
[[Image:Snapdragon_Peloric_mutant.png|32x32px]]
[[Image:Tissue.png|32x32px]]
[[Image:Z9r3j2yx.png|32x32px]]
[[Image:Zeds48ci.png|32x32px]]
[[Image:1896_wh_txr_light.png|32x32px]]
[[Image:Ara_flower.png|32x32px]]
[[Image:Arableaf_ath8_OPT.png|32x32px]]
|}
==AAMToolbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>AAMToolbox_logo.jpg|120px|AAMToolbox</imgicon>
|width="40%"|For analysing populations of shapes and colours within the shapes using principal component analysis. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/ShapeModelToolbox.zip '''''Download''''' ] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. The analysis can be applied to art, for example, finding systematic differences between portraits by, for example, Rembrandt and Modigliani.
|}

Main Page

2012-03-08T17:26:18Z

JeromeAvondo:

__NOTOC__
=Bangham Lab - Home=

'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.
=Computational biology toolboxes=
==GFtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|width="40%"|
For modelling the growth of shapes. 
[[GFtbox|'''What? How? Where?''']] 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). The GPT-framework was used to capture an understanding of (to model) the growing leaf (Kuchen et al 2012) and Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.] The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011])
|}

==VolViewer==
{| border="0" style="background-color:#000000;"
|-
|align="center"|
[[Image:Cs0prxz0.png|64x64px]]
[[Image:GL2_GUS.png|64x64px]]
[[Image:Leaf_trichomes.png|64x64px]]
[[Image:Leaf5.png|64x64px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|64x64px]]
[[Image:OleosinSeed.png|64x64px]]
|}
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring biological images. 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 
[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]
 
|width="50%"| VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|}

==AAMToolbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>AAMToolbox_logo.jpg|120px|AAMToolbox</imgicon>
|width="40%"|For analysing populations of shapes and colours within the shapes using principal component analysis. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/ShapeModelToolbox.zip '''''Download''''' ] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. The analysis can be applied to art, for example, finding systematic differences between portraits by, for example, Rembrandt and Modigliani.
|}

VolViewer

2012-03-05T15:33:38Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[[VolViewerCourse|Tutorials]]
| align="center"|[[VolViewerUserManual|Quick Guide]]
| align="center"|[[VolViewerTutorials|Video Tutorials]]
|}

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-05T15:12:49Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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=

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-05T15:10:21Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-05T15:08:59Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Image Gallery=

{| 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]]
|}
=Media/Press=

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]

=Author=

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

VolViewer

2012-03-05T15:08:28Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

=Image Gallery=

{| 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]]
|}

VolViewer

2012-03-05T15:06:18Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

=Image Gallery=

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#000000;"
|-
||
[[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]]
|}

VolViewer

2012-03-05T15:00:40Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

=Image Gallery=

<gallery widths=100px heights=100px perrow=7 caption="">
File:1272_wh_rgb.png
File:Am0front.png
File:Anthers.PNG
File:Anti_flower_OPT.png
File:Antirrhinum_flower_small.png
File:Ara_seedling_colour.png
File:Cells.png
File:Cs0prxz0.png
File:GL2_GUS.png
File:Leaf_trichomes.png
File:Leaf5.png
File:LFY_GUS_Arabidopsis_inflorescence_512.png
File:OleosinSeed.png
File:OPT_Leaf_copy.png
File:Seedling_copy.png
File:Senecio_floret_copy.png
File:Snapdragon_Peloric_mutant.png
File:Tissue.png
File:Z9r3j2yx.png
File:Zeds48ci.png
File:1896_wh_txr_light.png
File:Ara_flower.png
File:Arableaf_ath8_OPT.png
File:Arableaf_young_ath8_OPT.png
File:Enhby820.png
File:Nilleafdev.png
File:Seedling_OPT.png
File:Senecioclip.png
</gallery>

VolViewer

2012-03-05T14:59:40Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

=Image Gallery=

<gallery widths=100px heights=100px perrow=7 caption="">
File:1272_wh_rgb.png
File:Am0front.png
File:Anthers.PNG
File:Anti_flower_OPT.png
File:Antirrhinum_flower_small.png
File:Ara_seedling_colour.png
File:Cells.png
File:Cs0prxz0.png
File:GL2_GUS.png
File:Leaf_trichomes.png
File:Leaf5.png
File:LFY_GUS_Arabidopsis_inflorescence_512.png
File:OleosinSeed.png
File:OPT_Leaf_copy.png
File:Seedling_copy.png
File:Senecio_floret_copy.png
File:Snapdragon_Peloric_mutant.png
File:Tissue.png
File:Z9r3j2yx.png
File:Zeds48ci.png
File:1896_wh_txr_light.png
File:Ara_flower.png
File:Arableaf_ath8_OPT.png
File:Arableaf_young_ath8_OPT.png
File:Enhby820.png
File:Nilleafdev.png
File:Seedling_OPT.png
File:Senecioclip.png
File:Silique.PNG
</gallery>

File:Silique.PNG

2012-03-05T14:59:35Z

JeromeAvondo:

File:Senecioclip.png

2012-03-05T14:59:25Z

JeromeAvondo:

File:Seedling OPT.png

2012-03-05T14:59:16Z

JeromeAvondo:

File:Nilleafdev.png

2012-03-05T14:59:05Z

JeromeAvondo:

File:Enhby820.png

2012-03-05T14:58:56Z

JeromeAvondo:

File:Arableaf young ath8 OPT.png

2012-03-05T14:58:44Z

JeromeAvondo:

File:Arableaf ath8 OPT.png

2012-03-05T14:58:32Z

JeromeAvondo:

File:Ara flower.png

2012-03-05T14:58:21Z

JeromeAvondo:

File:1896 wh txr light.png

2012-03-05T14:58:03Z

JeromeAvondo:

VolViewer

2012-03-05T14:47:31Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

=Image Gallery=

<gallery widths=100px heights=100px perrow=7 caption="">
File:1272_wh_rgb.png
File:Am0front.png
File:Anthers.PNG
File:Anti_flower_OPT.png
File:Antirrhinum_flower_small.png
File:Ara_seedling_colour.png
File:Cells.png
File:Cs0prxz0.png
File:GL2_GUS.png
File:Leaf_trichomes.png
File:Leaf5.png
File:LFY_GUS_Arabidopsis_inflorescence_512.png
File:OleosinSeed.png
File:OPT_Leaf_copy.png
File:Seedling_copy.png
File:Senecio_floret_copy.png
File:Snapdragon_Peloric_mutant.png
File:Tissue.png
File:Z9r3j2yx.png
File:Zeds48ci.png
</gallery>

VolViewer

2012-03-05T14:47:03Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Image Gallery=

<gallery widths=100px heights=100px perrow=7 caption="">
File:1272_wh_rgb.png
File:Am0front.png
File:Anthers.PNG
File:Anti_flower_OPT.png
File:Antirrhinum_flower_small.png
File:Ara_seedling_colour.png
File:Cells.png
File:Cs0prxz0.png
File:GL2_GUS.png
File:Leaf_trichomes.png
File:Leaf5.png
File:LFY_GUS_Arabidopsis_inflorescence_512.png
File:OleosinSeed.png
File:OPT_Leaf_copy.png
File:Seedling_copy.png
File:Senecio_floret_copy.png
File:Snapdragon_Peloric_mutant.png
File:Tissue.png
File:Z9r3j2yx.png
File:Zeds48ci.png
</gallery>

=Author=

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

VolViewer

2012-03-05T14:40:14Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

* [[VolViewerCourse|Tutorials]]
* [[VolViewerUserManual|Quick Guide]]
* [[VolViewerTutorials|Video Tutorials]]
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Image Gallery=

{| border="0" width="100%" cellspacing="5" cellpadding="5" style="background-color:#000000; text-align:center;"
|-
||
<center>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
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|128px]][[Image:Z9r3j2yx.png
Zeds48ci.png
</sgallery>
|}

=Author=

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

VolViewer

2012-03-05T14:22:19Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

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

=Image Gallery=

{| border="0" width="100%" cellspacing="5" cellpadding="5" style="background-color:#000000; text-align:center;"
|-
||
<center>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
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|128px]][[Image:Z9r3j2yx.png
Zeds48ci.png
</sgallery>
|}
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

VolViewer

2012-03-05T14:21:25Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

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

=Image Gallery=

{| border="0" width="100%" cellspacing="5" cellpadding="5" style="background-color:#000000; text-align:center;"
|-
||
<center>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
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|128px]][[Image:Z9r3j2yx.png
Zeds48ci.png
</sgallery>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
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|128px]][[Image:Z9r3j2yx.png
Zeds48ci.png
</sgallery>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
Cells.png
Anti_flower_OPT.png
Cs0prxz0.png
GL2_GUS.png
Antirrhinum_flower_small.png
Ara_seedling_colour.png
OleosinSeed.png
Anthers.PNG
Senecio_floret_copy.png
Leaf_trichomes.png
Leaf5.png
LFY_GUS_Arabidopsis_inflorescence_512.png
Snapdragon_Peloric_mutant.png
Tissue.png|128px]][[Image:Z9r3j2yx.png
OPT_Leaf_copy.png
Seedling_copy.png
1272_wh_rgb.png
Am0front.png
Zeds48ci.png
</sgallery>
</center>
|}
=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#000000; text-align:center;"
|-
||
[[Image:1272_wh_rgb.png|128px]][[Image:Am0front.png|128px]][[Image:Anthers.PNG|128px]][[Image:Anti_flower_OPT.png|128px]][[Image:Antirrhinum_flower_small.png|128px]][[Image:Ara_seedling_colour.png|128px]][[Image:Cells.png|128px]][[Image:Cs0prxz0.png|128px]][[Image:GL2_GUS.png|128px]][[Image:Leaf_trichomes.png|128px]][[Image:Leaf5.png|164px]][[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|128px]][[Image:OleosinSeed.png|128px]][[Image:OPT_Leaf_copy.png|128px]][[Image:Seedling_copy.png|128px]][[Image:Senecio_floret_copy.png|32px]][[Image:Snapdragon_Peloric_mutant.png|128px]][[Image:Tissue.png|128px]][[Image:Z9r3j2yx.png|128px]][[Image:Zeds48ci.png|128px]]
|}

VolViewer

2012-03-05T14:19:00Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

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

=Image Gallery=

<center>
<sgallery width="256" height="256" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
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|128px]][[Image:Z9r3j2yx.png
Zeds48ci.png
</sgallery>
</center>

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#000000; text-align:center;"
|-
||
[[Image:1272_wh_rgb.png|128px]][[Image:Am0front.png|128px]][[Image:Anthers.PNG|128px]][[Image:Anti_flower_OPT.png|128px]][[Image:Antirrhinum_flower_small.png|128px]][[Image:Ara_seedling_colour.png|128px]][[Image:Cells.png|128px]][[Image:Cs0prxz0.png|128px]][[Image:GL2_GUS.png|128px]][[Image:Leaf_trichomes.png|128px]][[Image:Leaf5.png|164px]][[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|128px]][[Image:OleosinSeed.png|128px]][[Image:OPT_Leaf_copy.png|128px]][[Image:Seedling_copy.png|128px]][[Image:Senecio_floret_copy.png|32px]][[Image:Snapdragon_Peloric_mutant.png|128px]][[Image:Tissue.png|128px]][[Image:Z9r3j2yx.png|128px]][[Image:Zeds48ci.png|128px]]
|}

VolViewer

2012-03-05T14:12:19Z

JeromeAvondo:

[[Software#VolViewer| Back to BanghamLab software]] 
=What? How? Where?=

[[Image:VolViewer.png|256px|thumb|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==

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

=Image Gallery=

[[Image:1272_wh_rgb.png|128px]][[Image:EarlyLeavesVolviewer.jpg|128px]][[Image:Am0front.png|128px]][[Image:Anthers.PNG|128px]][[Image:Anti_flower_OPT.png|128px]][[Image:Antirrhinum_flower_small.png|128px]][[Image:Ara_seedling_colour.png|128px]][[Image:Cells.png|128px]][[Image:Cs0prxz0.png|128px]][[Image:GL2_GUS.png|128px]][[Image:Leaf_trichomes.png|128px]][[Image:Leaf5.png|128px]][[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|128px]][[Image:OleosinSeed.png|128px]][[Image:OPT_Leaf_copy.png|128px]][[Image:Seedling_copy.png|128px]][[Image:Senecio_floret_copy.png|128px]][[Image:Snapdragon_Peloric_mutant.png|128px]][[Image:Tissue.png|128px]][[Image:Z9r3j2yx.png|128px]][[Image:Zeds48ci.png|128px]]

=Sample Data=

{| border="0" cellspacing="5" cellpadding="5" style="background-color:#ffffff; text-align:center;"
|-
| 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''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8:::GUS expression in red)
|-
| 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]
|}

<nowiki>*</nowiki> all data courtesy of Karen Lee [mailto:kareen.lee@bbsrc.ac.uk]

=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 [http://doc.qt.nokia.com/latest/qmake-manual.html qmake] for easy cross platform compilation.

{| border="1" cellspacing="5" cellpadding="5" style="background-color:#cccccc;"
|-
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x86.exe Windows (32bit)]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewerInstaller_x64.exe Windows (64bit)]
| align="center"|[[VolViewerLinux|Linux]]
| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/VolViewerOpenSource/VolViewer.dmg 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: [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=

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

==Building from source==

* [[VolViewerBuildingFromSource|Building VolViewer from source]]

=Media/Press=

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]

=Author=

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

File:Zeds48ci.png

2012-03-05T14:12:10Z

JeromeAvondo:

File:Z9r3j2yx.png

2012-03-05T14:11:50Z

JeromeAvondo:

File:Tissue.png

2012-03-05T14:11:37Z

JeromeAvondo: