DArT_Toolshed - User contributions [en]

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-12T11:40:28Z

Admin:

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

===WLZ to PNG Converter===

This software is useful to convert WLZ files to stacks of PNGs. Put your WLZ in the IN directory, then run the program and the stacks will appear in the OUT directory as subdirectories for each WLZ filename.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolProcess_rev1396.zip QtVolProcess_rev1396.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-12T09:55:10Z

Admin: /* WLZ to PNG Converter */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

===WLZ to PNG Converter===

This software is useful to convert WLZ files to stacks of PNGs. Put your WLZ in the IN directory, then run the program and the stacks will appear in the OUT directory as subdirectories for each WLZ filename.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolProcess_rev232.zip QtVolProcess_rev232.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-12T09:54:14Z

Admin: /* WLZ to PNG Converter */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

===WLZ to PNG Converter===

This software is useful to convert WLZ files to stacks of PNGs. Put your WLZ in the IN directory, then run the program and the stack will appear in the OUT directory.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolProcess_rev232.zip QtVolProcess_rev232.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-12T09:53:59Z

Admin: /* Software */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

===WLZ to PNG Converter===

This software is useful to convert WLZ files to stacks of PNGs. Put your WLZ in the IN directory, then run the program and the stack will appear in the OUT directory.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolProcess_rev232.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-12T09:52:11Z

Admin: /* Software */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

===WLZ to PNG Converter===

This software is useful to convert WLZ files to stacks of PNGs. Put your WLZ in the IN directory, then run the program and the stack will appear in the OUT directory.

[]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-09T16:19:21Z

Admin: /* MovieMake */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images. See the PDF included in the zip for instructions.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1_1.zip MovieMakev1_1.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2009-06-09T16:12:57Z

Admin: /* Software */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

===MovieMake===

This software is useful to make movies out of stack of images.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/MovieMakev1.zip MovieMakev1.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-25T12:45:02Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Below you can find the actual PNG stacks for the datasets presented in the paper. To download a specific dataset click on the DOWNLOAD link below the animated GIF preview of the dataset.

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:40:03Z

Admin:

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:39:06Z

Admin: /* QtVolViewerLITE v1 */

[[Image:Plant cell.png|right|thumb|512px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:38:20Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|512px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip Download] || 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/Arabidopsis_Slique(372).zip Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:37:24Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|512px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower294.zip| Download] || 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/Arabidopsis_Slique(372).zip| Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_LeafGL2_GUS(624).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisLeafAth8_GUS(460).zip| Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/ArabidopsisSeedlingAth8_GUS(463).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_MeristemLFY_GUS(423).zip| Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:30:16Z

Admin:

[[Image:Plant cell.png|right|thumb|512px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower%20294.zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem%20(r512g110usmall).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling%20(174).zip| Download]|| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Slique%20(372).zip| Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Leaf%20GL2_GUS%20(624).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Leaf%20Ath8_GUS%20(460).zip| Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Seedling%20Ath8_GUS%20(463).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Meristem%20LFY_GUS%20(423).zip| Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:29:27Z

Admin: /* Software */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

The software used to produce all the figures in the paper can be found below.

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower%20294.zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem%20(r512g110usmall).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling%20(174).zip| Download]|| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Slique%20(372).zip| Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Leaf%20GL2_GUS%20(624).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Leaf%20Ath8_GUS%20(460).zip| Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Seedling%20Ath8_GUS%20(463).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Meristem%20LFY_GUS%20(423).zip| Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:28:46Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

===Single channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower%20294.zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem%20(r512g110usmall).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling%20(174).zip| Download]|| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Slique%20(372).zip| Download]

|}

===Multi channel data sets:===

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Leaf%20GL2_GUS%20(624).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Leaf%20Ath8_GUS%20(460).zip| Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Seedling%20Ath8_GUS%20(463).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Meristem%20LFY_GUS%20(423).zip| Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:28:19Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Anti_Flower%20294.zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Antiriniuhm_Meristem%20(r512g110usmall).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Seedling%20(174).zip| Download]|| align="center"|[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Slique%20(372).zip| Download]

|}

Multi channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|-
| align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arab_Leaf%20GL2_GUS%20(624).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Leaf%20Ath8_GUS%20(460).zip| Download] || align="center" | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis%20Seedling%20Ath8_GUS%20(463).zip| Download] || align="center"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/PlantCellOPT/Arabidopsis_Meristem%20LFY_GUS%20(423).zip| Download]
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T16:15:42Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|}

Multi channel data sets:

{| border="0" cellspacing="20" cellpadding="10"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|}

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T15:21:43Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|}

Multi channel data sets:

{| border="0" cellspacing="20" cellpadding="10"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure8.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Ath8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (Ath8:::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|}

Optical Projection Tomograpy dataset, for figures 1 and 2. [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/Fig1a_2a_rgb.zip]

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

File:Figure8.gif

2008-07-24T15:20:22Z

Admin:

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T14:57:25Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|}

Multi channel data sets:

{| border="0" cellspacing="20" cellpadding="10"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure7.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Leaf''' (Anth8::GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|}

Optical Projection Tomograpy dataset, for figures 1 and 2. [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/Fig1a_2a_rgb.zip]

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

File:Figure7.gif

2008-07-24T14:55:59Z

Admin:

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T14:34:35Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

{| border="0" cellspacing="10" cellpadding="5"
|-
| align="center"| [[Image:Figure1.gif]] || [[Image:Figure2.gif]] || [[Image:Figure3.gif]] || [[Image:Figure4.gif]]
|-
| align="center"| '''Antirinhium Flower''' || align="center"| '''Antirinhium Meristem''' || align="center"| '''Arabidopsis Seedling''' || align="center"| '''Arabidopsis Slique'''
|}

Multi channel data sets:

{| border="0" cellspacing="20" cellpadding="10"
|-
| align="center"| [[Image:Figure5.gif]] || [[Image:Figure6.gif]]
|-
| align="center"| '''Arabidopsis Leaf''' (GL2:GUS expression in red) || align="center"| '''Arabidopsis Meristem''' (LFY::GUS expression in red)
|}

Optical Projection Tomograpy dataset, for figures 1 and 2. [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/Fig1a_2a_rgb.zip]

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T14:10:50Z

Admin:

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

==Datasets used in Figures==

Single channel data sets:

<tab class=wikitable cellpadding=5 cellspacing=5 align=center border=3 sep=comma>
[[Image:Figure1.gif]], [[Image:Figure2.gif]],[[Image:Figure3.gif]], [[Image:Figure4.gif]]
Antirinhium Flower, Antirinhium Meristem, Arabidopsis Seedling, Arabidopsis Slique
</tab>

Multi channel data sets:

<tab class=wikitable cellpadding=5 cellspacing=5 align=center border=3 sep=comma>
[[Image:Figure5.gif]], [[Image:Figure6.gif]]
Arabidopsis Leaf (GL2:GUS expression in red), Arabidopsis Meristem (LFY::GUS expression in red)
</tab>

Optical Projection Tomograpy dataset, for figures 1 and 2. [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/Fig1a_2a_rgb.zip]

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T14:05:31Z

Admin: /* Datasets used in Figures */

[[Image:Plant cell.png|right|thumb|256px|Top row; volume view of mature ATHB8:GUS Arabidopsis leaf with stained veins (m2, 9 dfs) displayed using QtVolView lighting and tone-shader effects. Middle row; combined transmission and fluorescent (GFP1) OPT channels. Visible channel is red, fluorescent channel is green. Bottom row; stained veins extracted using semi-automatic segmentation tools. In the application the leaf can be viewed from any angle, re-coloured, etc.]]

=Abstract=

A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, ﬂowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as b-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantiﬁed and visualized interactively in different ways.

=Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/VisualisingPlantDevelopmentandGeneExpressionin3DusingOpticalProjectionTomography.pdf "Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"], ''K. Lee, J. Avondo, H. Morrison, L. Blot, M. Stark, J. Sharpe, J. A. Bangham, and E. S. Coen''

=Sumplementary Material=

==Datasets used in Figures==

Single channel data sets:

<tab class=wikitable cellpadding=10 cellspacing=10 align=center border=1 sep=comma>
[[Image:Figure1.gif]], [[Image:Figure2.gif]], [[Image:Figure3.gif]], [[Image:Figure4.gif]]
Antirinhium Flower, Antirinhium Meristem, Arabidopsis Seedling, Arabidopsis Slique
</tab>

Multi channel data sets:

<tab class=wikitable cellpadding=10 cellspacing=10 align=center border=1 sep=comma>
[[Image:Figure5.gif]], [[Image:Figure6.gif]]
Arabidopsis Leaf (GL2:GUS expression in red), Arabidopsis Meristem (LFY::GUS expression in red)
</tab>

Optical Projection Tomograpy dataset, for figures 1 and 2. [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/Fig1a_2a_rgb.zip]

==Software==

===QtVolViewerLITE v1===

The QtVolViewLITE program is designed to run on any PC with a 64 Mbyte graphic card. It is suitable for viewing the data shown in Figures 1A and 2A as colour OPT volume and section views of the Antirrhinum flower. Internal floral structures such as anther lobes and the ovary at the base of the carpel are revealed. Three OPT scan channels are visible. Transmission (shown in blue), endogenous fluorescence, Leica TXR filter (shown in red) and GFP fluorescence, GFP1 filter (shown in green).

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1.zip QtVolViewerLITEv1.zip] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1QuickStart.pdf QuickStart.pdf] | [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolViewerLITEv1UserManual.pdf UserManual.pdf]

===QtVolViewer v1.64===

Latest public version of QtVolViewer. Only tested on the following hardware: Nvidia 7900GTX & Nvidia 8800GTX. This version uses advanced features of OpenGL such as the OpenGL Shanding Language (GLSL) and Frame Buffer Objects.

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/QtVolviewerV1.64.zip QtVolviewerV1.64.zip]

=Acknowledgements=

BBSRC for grant support, JIC/UEA/MRC and MRC Technology.

=Software team=

Jerome Avondo with help from Lilian Blot and the Bangham group in the Computational Biology Group, Computing Sciences, University of East Anglia, Norwich,

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T13:58:50Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T13:58:35Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T13:45:05Z

Admin: /* Datasets used in Figures */

File:Figure6.gif

2008-07-24T13:43:52Z

Admin:

File:Figure5.gif

2008-07-24T13:43:32Z

Admin:

File:Figure4.gif

2008-07-24T13:43:12Z

Admin:

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T13:03:03Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:52:57Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:52:43Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:52:34Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:52:01Z

Admin: /* Datasets used in Figures */

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:47:35Z

Admin: /* Datasets used in Figures */

File:Figure1.gif

2008-07-24T12:46:17Z

Admin: uploaded a new version of "Image:Figure1.gif"

File:Figure3.gif

2008-07-24T12:39:41Z

Admin: uploaded a new version of "Image:Figure3.gif"

File:Figure3.gif

2008-07-24T12:38:47Z

Admin: uploaded a new version of "Image:Figure3.gif"

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:36:41Z

Admin: /* Datasets used in Figures */

File:Figure3.gif

2008-07-24T12:36:24Z

Admin:

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T12:30:35Z

Admin: /* Datasets used in Figures */

File:Figure2.gif

2008-07-24T12:30:13Z

Admin:

"Visualising Plant Development and Gene Expression in 3D using Optical Projection Tomography"

2008-07-24T11:27:22Z

Admin: /* Datasets used in Figures */

File:Figure1.gif

2008-07-24T11:26:32Z

Admin:

"Evolution through genetically controlled allometry space"

2008-07-24T10:55:17Z

Admin:

[[Image:PNAS2005.jpg||300px|right]]
=Abstract=

Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to deﬁne an appropriate genotypic space for a range of species. Here we address this problem by deﬁning a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspeciﬁc cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be deﬁned. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near
to, at least one other species in the space, so that together they deﬁned a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reﬂects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.

=The Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionThroughGeneticallyControlledAllometrySpace_Langlade.pdf “Evolution through genetically controlled allometry space”], ''
N. B. Langlade, X. Feng, T. Dransfield, L. Copsey, A. I. Hanna, C. Thebaud, J. A. Bangham, A. Hudson, and E. S. Coen''

=Downloading the Project and AAMToolbox=

The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionThroughGeneticallyControlledAllometrySpace.zip here]. ''(This contains version 6.5 of the AAMToolbox)''
[[Image:Langlade_2005_PNAS.pdf|Langlade ''et. al'' PNAS, 2005]]
To create the figures shown in the manuscript “Evolution through genetically controlled allometry space”, ''N. B. Langlade, X. Feng, T. Dransfield, L. Copsey, A. I. Hanna, C. Thebaud, J. A. Bangham, A. Hudson, and E. S. Coen'', PNAS, 2005, please follow the instructions below.

These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.

=Installing the AAMToolbox=

To install the toolbox, simply unzip the zip file you downloaded from the section above. In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_PNAS2005’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
>>pathtool
</pre>
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.

=Recreating Figures=

==Figure 1==

This is an image available for download.

==Figure 2==

From the Matlab prompt type
<pre>
>>figure_1_points_around_leaf
</pre>
And select ''LE19.temp_dat'' from the Templates directory. The colours are your choice.

==Figure 3==

From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>

* Select the folder ‘PRJ_PNAS2005\StatisticalModels\LE19\Set_1\ImageList_1’ for the model (not scaled).
* Next choose the PCs you want to display (1 to 3 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).

==Figure 4==

From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is ''LE19\Set_1\ImageList_1'' from the drop down list.
* Next click the ''View Shape Space'' button.
* Next click the ''Open'' button from the Groups panel and select ''Majus_Charidemi_Groups''.
* Next click the ''Load'' button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck ''Group Labels'', ''Group Means'', ''Particles'' from the plot options panel.
* Next check ''Ellipses'' and ''Vectors'' from the plot options panel.
* Next click the ''Choose Shape Axes'' button and select the PCs 1, 2, and 3.
* Next select ''Import'' from the ''Vectors'' menu and select ''QTL_Vectors.xls''.
* (Optional) Select ''Walk'' from the ''Vectors'' to walk along the vectors.

==Figure 5 (a)==
'''UNDER CONSTRUCTION '''

==Figure 5 (b)==

From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is ''LE19\Set_1\ImageList_1'' from the drop down list.
* Next click the ''View Shape Space'' button.
* Next click the ''Open'' button from the Groups panel and select ''Species_Groups.mat''.
* Next click the ''Load'' button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck ''Group Labels'', ''Group Means'', ''Particles'' from the plot options panel.
* Next check ''Ellipses'' from the plot options panel.
* Next click the ''Choose Shape Axes'' button and select the PCs 1, 2, and 3.

== Figure 6==

'''THESE FIGURES WERE CREATED WITH A TOOL NOT AVAILABLE FOR DOWNLOAD'''

"Evolution through genetically controlled allometry space"

2008-07-24T10:54:04Z

Admin: /* The Manuscript */

[[Image:PNAS2005.jpg||300px|right]]
=Abstract=

Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to deﬁne an appropriate genotypic space for a range of species. Here we address this problem by deﬁning a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspeciﬁc cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be deﬁned. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near
to, at least one other species in the space, so that together they deﬁned a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reﬂects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.

=The Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionThroughGeneticallyControlledAllometrySpace_Langlade.pdf “Evolution through genetically controlled allometry space”], ''
N. B. Langlade, X. Feng, T. Dransfield, L. Copsey, A. I. Hanna, C. Thebaud, J. A. Bangham, A. Hudson, and E. S. Coen''

== Downloading the Project and AAMToolbox ==

The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionThroughGeneticallyControlledAllometrySpace.zip here]. ''(This contains version 6.5 of the AAMToolbox)''
[[Image:Langlade_2005_PNAS.pdf|Langlade ''et. al'' PNAS, 2005]]
To create the figures shown in the manuscript “Evolution through genetically controlled allometry space”, ''N. B. Langlade, X. Feng, T. Dransfield, L. Copsey, A. I. Hanna, C. Thebaud, J. A. Bangham, A. Hudson, and E. S. Coen'', PNAS, 2005, please follow the instructions below.

These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.

==Installing the AAMToolbox==
To install the toolbox, simply unzip the zip file you downloaded from the section above. In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_PNAS2005’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
>>pathtool
</pre>
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.

== Recreating Figures ==
=== Figure 1 ===
This is an image available for download.

=== Figure 2 ===
From the Matlab prompt type
<pre>
>>figure_1_points_around_leaf
</pre>
And select ''LE19.temp_dat'' from the Templates directory. The colours are your choice.

=== Figure 3 ===
From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>

* Select the folder ‘PRJ_PNAS2005\StatisticalModels\LE19\Set_1\ImageList_1’ for the model (not scaled).
* Next choose the PCs you want to display (1 to 3 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).

===Figure 4 ===
From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is ''LE19\Set_1\ImageList_1'' from the drop down list.
* Next click the ''View Shape Space'' button.
* Next click the ''Open'' button from the Groups panel and select ''Majus_Charidemi_Groups''.
* Next click the ''Load'' button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck ''Group Labels'', ''Group Means'', ''Particles'' from the plot options panel.
* Next check ''Ellipses'' and ''Vectors'' from the plot options panel.
* Next click the ''Choose Shape Axes'' button and select the PCs 1, 2, and 3.
* Next select ''Import'' from the ''Vectors'' menu and select ''QTL_Vectors.xls''.
* (Optional) Select ''Walk'' from the ''Vectors'' to walk along the vectors.

===Figure 5 (a) ===
'''UNDER CONSTRUCTION '''

===Figure 5 (b) ===
From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is ''LE19\Set_1\ImageList_1'' from the drop down list.
* Next click the ''View Shape Space'' button.
* Next click the ''Open'' button from the Groups panel and select ''Species_Groups.mat''.
* Next click the ''Load'' button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck ''Group Labels'', ''Group Means'', ''Particles'' from the plot options panel.
* Next check ''Ellipses'' from the plot options panel.
* Next click the ''Choose Shape Axes'' button and select the PCs 1, 2, and 3.

=== Figure 6 ===
'''THESE FIGURES WERE CREATED WITH A TOOL NOT AVAILABLE FOR DOWNLOAD'''

"Evolutionary Paths Underlying Flower Color Variation in Antirrhinum"

2008-07-24T10:51:22Z

Admin:

=Abstract=

To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.

=The Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum_Whibley.pdf “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”], ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen''

=Downloading the Project and AAMToolbox=

The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project and the manuscript can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum.zip here]. ''(This contains version 6.5 of the AAMToolbox)''

To create the figures shown in the manuscript “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen'', Science, 313:963-966, 2007, please follow the instructions below.

These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.

==Installing the AAMToolbox==
To install the toolbox, unzip the zip file you downloaded from the section above (some unzippers think the file is locked, WinZip and WinRar seem to handle it just fine). In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Science’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
>>pathtool
</pre>
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.

=Creating Figures=

==Figure 4 (f)==

[[Image:science_wormhole.jpg|300px|thumb|right|An example of the appearance cloud generate for the paper. Figure 4(f)]]
Firstly you must make sure that you have correctly installed the Toolshed from [[Computer_programs | here]]. Secondly, you must have downloaded and saved the project '''PRJ_Science''' to your hard disk. If you have done these steps, then start Matlab. In matlab move to project directory '''PRJ_Science''', from the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
This will start the AAMToolbox and if you are in the correct directory you will be presented with the correct details for the project corresponding to this paper.

* Click the ''View Shape Space'' button.
* Click the ''Open'' button from the ''Group'' panel.
* Select ''SciencePaperGroups.mat'' and click ''Open''.
* Click the ''Load'' button from the ''Group'' panel.

a dialog box with the text ''Loading Group Data, Please Wait..'' will appear, when this dialog box closes you have loaded your groups.

* Select ''Tools->Units->Standard Deviations''
* Click the ''Choose App. Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Click the ''Choose Shape Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Uncheck ''Group Labels'' from the ''Plot Options'' panel

* Set dx=30, dy=30 and dz=30 in the ''Surface Quantization'' panel
* Click the ''Fit Surface'' button from the ''Display Options Panel''

a dialog box will appear telling you that the surface has been fitted, close this by clicking ''Ok''.

* Check ''Iso-Surface'' box from the ''Plot Options'' panel
* Slide the ''Isosurface Level'' slider to 3 in the ''Isosurface Pane''
* Bring the Appearance window to the front to see the surface.

"Evolutionary Paths Underlying Flower Color Variation in Antirrhinum"

2008-07-24T10:50:47Z

Admin: /* The Manuscript */

__TOC__
=Abstract=

To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.

=The Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum_Whibley.pdf “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”], ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen''

== Downloading the Project and AAMToolbox ==

The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project and the manuscript can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum.zip here]. ''(This contains version 6.5 of the AAMToolbox)''

To create the figures shown in the manuscript “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen'', Science, 313:963-966, 2007, please follow the instructions below.

These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.

==Installing the AAMToolbox==
To install the toolbox, unzip the zip file you downloaded from the section above (some unzippers think the file is locked, WinZip and WinRar seem to handle it just fine). In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Science’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
>>pathtool
</pre>
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.

==Creating Figures==

===Figure 4 (f)===
[[Image:science_wormhole.jpg|300px|thumb|right|An example of the appearance cloud generate for the paper. Figure 4(f)]]
Firstly you must make sure that you have correctly installed the Toolshed from [[Computer_programs | here]]. Secondly, you must have downloaded and saved the project '''PRJ_Science''' to your hard disk. If you have done these steps, then start Matlab. In matlab move to project directory '''PRJ_Science''', from the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
This will start the AAMToolbox and if you are in the correct directory you will be presented with the correct details for the project corresponding to this paper.

* Click the ''View Shape Space'' button.
* Click the ''Open'' button from the ''Group'' panel.
* Select ''SciencePaperGroups.mat'' and click ''Open''.
* Click the ''Load'' button from the ''Group'' panel.

a dialog box with the text ''Loading Group Data, Please Wait..'' will appear, when this dialog box closes you have loaded your groups.

* Select ''Tools->Units->Standard Deviations''
* Click the ''Choose App. Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Click the ''Choose Shape Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Uncheck ''Group Labels'' from the ''Plot Options'' panel

* Set dx=30, dy=30 and dz=30 in the ''Surface Quantization'' panel
* Click the ''Fit Surface'' button from the ''Display Options Panel''

a dialog box will appear telling you that the surface has been fitted, close this by clicking ''Ok''.

* Check ''Iso-Surface'' box from the ''Plot Options'' panel
* Slide the ''Isosurface Level'' slider to 3 in the ''Isosurface Pane''
* Bring the Appearance window to the front to see the surface.

"Mutational spaces for leaf shape and size"

2008-07-24T10:48:37Z

Admin:

=Abstract=
A key approach to understanding how genes control growth and form is to analyze mutants in which shape and size have been perturbed. Although many
mutants of this kind have been described in plants and animals, a general quantitative framework for describing them has yet to be established. Here we describe an approach based on Principal Component Analysis of organ landmarks and outlines. Applying this method to a collection of leaf shape mutants in Arabidopsis and Antirrhinum allows low-dimensional spaces to be constructed that capture the key variations in shape and size. Mutant phenotypes can be represented as vectors in these allometric spaces, allowing additive gene interactions to be readily described. The principal axis of each allometric space reﬂects size variation and an associated shape change. The shape change is similar to that observed during the later stages of normal development, suggesting that many phenotypic differences involve modulations in the timing of growth arrest. Comparison between allometric mutant spaces from different species reveals a similar range of phenotypic possibilities. The spaces therefore provide a general quantitative framework for exploring and comparing the development and evolution of form.

=The Manuscript=

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/MutationalSpacesForLeafShapeAndSize_Bensmihen.pdf “Mutational spaces for leaf shape and size”], ''S. Bensmihen, A. I. Hanna, N. B. Langlade, J. L. Micol, A. Bangham, and E. S. Coen''

=Downloading the Project and AAMToolbox=

[[Image:HFSP.jpg|thumb||right]]
The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/MutationalSpacesForLeafShapeAndSize.zip here]. ''(This contains version 6.5 of the AAMToolbox)''

To create the figures shown in the manuscript “Mutational spaces for leaf shape and size”, ''S. Bensmihen, A. I. Hanna, N. B. Langlade, J. L. Micol, A. Bangham, and E. S. Coen'', HFSP Journal, 2008, please follow the instructions below.

These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.

=Installing the AAMToolbox=

To install the toolbox, simply unzip the zip file you downloaded from the section above. In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Arabid_Antirrh’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
>>pathtool
</pre>
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.

=Creating Figures=

==Figure 1==

From the Matlab prompt type
<pre>
>>figure_1_points_around_leaf
</pre>

And select ''LE50template_04_05_06.temp_dat'' from the ''Templates'' directory. The colours are your choice.

==Figure 2==

From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>

* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_18’ for model (Ler only, not scaled).
* Next choose the PCs you want to display (1 to 5 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).

==Figure 3==

From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is “LE50Template_04_05_06\Set_1\ImageList_18” from the drop down list.
* Next click the “View Shape Space” button.
* Next click the “Open” button from the Groups panel and select “all_groups_no_tsk”.
* Next click the “Load” button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck the “Group Labels” from the plot options panel.
* Next click the “Choose Shape Axes” button and select the PC 1. (To view another PC click the “Choose Shape Axes” button and choose the PC of interest (in our case PC1, PC2, PC3, PC4).)

==Figure 4==

'''UNDER CONSTRUCTION'''

==Figure 5==

From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>
* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_17’ for model (Ler only, scaled).
* Next choose the PCs you want to display (1 to 4 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).

==Figure 6==

From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>
* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_21’ for model (_epure= cleaned form double mutant and flower effect mutants).
* Next choose the PCs you want to display (1 to 4 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).

==Figure 7==

'''UNDER CONSTRUCTION'''

==Figure 8==

From the Matlab prompt type
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is “LE50Template LE50Template_04_05_06\Set_1\ImageList_21” from the drop down list.
* Next click the “View Shape Space” button.
* Next click the “Open” button from the Groups panel and select “ran_re _double”.
* Next click the “Load” button from the Groups panel.
* Next click the “Choose Shape Axes” button.
* Next select PCs 1 and 2 and hit “Ok”
* Next uncheck “Particles” and “Group Labels” from the “Plot Options” panel.
(The leaf pictures originated from the original pictures (observed). Vectors were added in the Adobe Illustrator CS2 software)

==Figure 9==

* Top panel: the outlines of young and mature Arabidopsis and antirrhinum leaves from Yvette’s pictures (for Munderman et al.?) were cut and filled (using the magic stick from Adobe Photoshop). Pictures were copied to Adobe Illustrator CS2 and scaled (selecting your shape, using then from the bar menu: object, transformation, scaling (“mise à l’échelle” in the French version).
* Bottom panel: the outlines of the Arabidopsis and Antirrhinum mean shapes, plus or minus 2SD, were created using the figure_2_pc_effects script as described for Figure 2. The file was saved as .eps and opened in Adobe Illustrator CS2 and the same scaling procedure was used.

=Creating Tables=

* Table 1 originates from the ranked t-test analysis described above performed on all the Arabidopsis Ler groups (on Image List 18 model). Groups were arranged and sorted in XL.
* Table 2 originates from the ranked t-test analysis (from Image List 21 model) of the antirrhinum groups (E_groups) using as wild type a group of 3 flower mutant groups (“flower_only_formean” group).