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LabelledCropped_GPT_Snapdragon_2010-000570-0001.png
LabelledCropped_GPT_Snapdragon_2010-000570-0001.png
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<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on Snapdragon model</span>]] </center>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
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=<span style="color: Gold">Genes and growing shapes</span>=  
=<span style="color: Gold">Genes and growing shapes</span>=  
* <span style="color: LemonChiffon">Observed: patterns of gene activity regulate tissue growth.</span>
* <span style="color: LemonChiffon">Observed: patterns of gene activity regulate tissue growth.</span>
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
* <span style="color: LemonChiffon">Formalised in the Growing Polarised Tissue Framework (ref). </span>
* <span style="color: LemonChiffon">Formalised in the Growing Polarised Tissue Framework (cite). </span>
* <span style="color: LemonChiffon">Implemented in ''GFtbox'' to make it easy to develop ideas on growth and form.</span>
* <span style="color: LemonChiffon">Implemented ''GFtbox'' (cite) to develop ideas on growth and form.</span>
* <span style="color: LemonChiffon">Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity. </span>
* <span style="color: LemonChiffon">Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity. </span>
* <span style="color: LemonChiffon">Grow the canvas in 3D under constraints of tissue continuity</span>
* <span style="color: LemonChiffon">Grow the canvas in 3D under constraints of tissue continuity</span>
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<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500">
Arabidopsis_Leaf_ATH8bbg.png
Arabidopsis_Leaf_ATH8bbg.png
Antirrhinum flower small1.jpg
Antirrhinum flower small1.jpg
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=<span style="color: Gold">Working with 3D volume images<span>=  
=<span style="color: Gold">Working with 3D volume images<span>=  
<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. They are produced by CT X-ray scanners, MRI and PET. However, biological gene activity is monitored using fluorescent probes and so optical methods are used: confocal microscopy and optical projection microscopy. The resulting images are large and are best viewed using software that exploits powerful graphics processors. We implemented VolViewer which is a viewer of choice in the open microscopy environment.</span>  
*<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. </span>
* <span style="color: LemonChiffon">Produced by</span>
** <span style="color: LemonChiffon">CT X-ray scanners, MRI and PET.</span>
** <span style="color: LemonChiffon">Confocal microscopy and optical projection microscopy (cite) used to view fluorescent probes probes that monitor biological gene activity. </span>
* <span style="color: LemonChiffon">'''VolViewer''' (cite) exploits powerful graphics processors.</span>
* <span style="color: LemonChiffon">Works with [[Software#Toolboxes for research|<span style="color:GreenYellow;">BioformatsConverter</span>]] to read open and proprietary file formats </span>  
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''VolViewer''</span>]] </center>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''VolViewer''</span>]] </center>
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<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
Arabidopsis_Leaf_ATH8bbg.png
Arabidopsis_Leaf_ATH8bbg.png
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=About=
=About=
The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio UEA D’Arcy Thompson Centre] for computational biology.
The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio UEA D’Arcy Thompson Centre] for computational biology.
--[[User:AndrewBangham|Andrew]] 09:50, 4 May 2011 (UTC)

Revision as of 10:50, 4 May 2011

The Bangham Lab

Computational Biology

The aim is to understand how patterns of gene activity in biological organs influence the developing shape.

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000"> LabelledCropped_GPT_Snapdragon_2010-000250-0001.png LabelledCropped_GPT_Snapdragon_2010-000340-0001.png LabelledCropped_GPT_Snapdragon_2010-000490-0001.png LabelledCropped_GPT_Snapdragon_2010-000570-0002.png LabelledCropped_GPT_Snapdragon_2010-000570-0003.png LabelledCropped_GPT_Snapdragon_2010-000570-0004.png LabelledCropped_GPT_Snapdragon_2010-000570-0005.png LabelledCropped_GPT_Snapdragon_2010-000570-0007.png LabelledCropped_GPT_Snapdragon_2010-000570-0006.png LabelledCropped_GPT_Snapdragon_2010-000570-0001.png </sgallery>

More Snapdragon model

Genes and growing shapes

  • Observed: patterns of gene activity regulate tissue growth.
  • Hypothesis: gene activity independently regulates direction of growth.
  • Formalised in the Growing Polarised Tissue Framework (cite).
  • Implemented GFtbox (cite) to develop ideas on growth and form.
  • Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity.
  • Grow the canvas in 3D under constraints of tissue continuity
  • Compare with observed data quantitatively

Downloads and more details on GFtbox

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000"> LabelledCropped GPT Snapdragon 2010-000570-0003 double.png LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png </sgallery>

More on testing models

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500"> Arabidopsis_Leaf_ATH8bbg.png Antirrhinum flower small1.jpg Antirrhinum flower small2.jpg Antirrhinum flower small3.jpg Anthers1.jpg MacroOPTIris1.jpg </sgallery>

More on visualising 3D

Working with 3D volume images

  • Three dimensional (3D) volume images are key to understanding the development of shape.
  • Produced by
    • CT X-ray scanners, MRI and PET.
    • Confocal microscopy and optical projection microscopy (cite) used to view fluorescent probes probes that monitor biological gene activity.
  • VolViewer (cite) exploits powerful graphics processors.
  • Works with BioformatsConverter to read open and proprietary file formats
Downloads and more details on VolViewer

<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000"> Arabidopsis_Leaf_ATH8bbg.png </sgallery>

More on 3D measurement

Photos, Algorithms and Art

Tools and Demonstrations

About

The Bangham Lab is part of the UEA D’Arcy Thompson Centre for computational biology. --Andrew 09:50, 4 May 2011 (UTC)

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