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__NOTOC__
 
<span style="color: DarkSlateGray"><font size="+1"><center>'''The Bangham Lab'''</center></font><span>
 
=<span style="color: DarkGreen">Computational Biology=
=<span style="color:DarkGreen;">Computational biology</span>=
<span style="color: DarkGreen"><font size="+1">The aim </font><span>is to understand how patterns of gene activity in biological organs influence the developing shape. </span><p></p><p></p>
 
{| border="0" cellpadding="5" cellspacing="3"  style="background-color: #000000;"
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<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000">
==<span style="color:DarkGreen;">[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;"> '''Growing''']] complex biological shapes from patterns of gene expression</span>==
LabelledCropped_GPT_Snapdragon_2010-000250-0001.png
{| border="0" width=100% style="background-color:#000000;"
LabelledCropped_GPT_Snapdragon_2010-000340-0001.png
|-
LabelledCropped_GPT_Snapdragon_2010-000490-0001.png
|align="center"|
LabelledCropped_GPT_Snapdragon_2010-000570-0002.png
[[Image:LabelledCropped GPT Snapdragon 2010-000340-0001.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0003.png
[[Image:LabelledCropped GPT Snapdragon 2010-000490-0001.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0004.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0005.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0007.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0007.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0003 double.png|100px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0006.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0001.png
|}
</sgallery>
<br>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>
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=<span style="color: Gold">Genes and growing shapes</span>=
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
* <span style="color: LemonChiffon">Observed: patterns of gene activity regulate tissue growth.</span>
{| border="0" width=100% style="background-color:#000000;"
* <span style="color: LemonChiffon">Hypothesis: gene activity independently regulates direction of growth.</span>
|-
* <span style="color: LemonChiffon">Formalised in the Growing Polarised Tissue Framework (cite). </span>
|align="center"|
* <span style="color: LemonChiffon">Implemented in ''GFtbox'' (cite) for developing ideas on growth and form.</span>
[[Image:Cs0prxz0.png|32x32px]]
** <span style="color: LemonChiffon">Start with a sheet of tissue (the canvas) with observed, or hypothetical patterns of growth factor activity. </span>
[[Image:Leaf_trichomes.png|50px]]
** <span style="color: LemonChiffon">Grow the canvas in 3D under constraints of tissue continuity</span>
[[Image:Cs0prxz0.png|50px]]
** <span style="color: LemonChiffon">Compare with observed data quantitatively </span><p>
[[Image:GL2_GUS.png|50px]]
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''GFtbox''</span>]] </center>
[[Image:Leaf5.png|50px]]
|| <!-- column3-->
[[Image:OleosinSeed.png|50px]]
<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
[[Image:OPT_Leaf_copy.png|50px]]
LabelledCropped GPT Snapdragon 2010-000570-0003 double.png
[[Image:Seedling_copy.png|50px]]
LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png
[[Image:Snapdragon_Peloric_mutant.png|50px]]
LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png
[[Image:Tissue.png|50px]]
<!--Arabidopsis_Leaf_ATH8bbg.png-->
[[Image:Z9r3j2yx.png|50px]]
<!--Grandison-Simulation.png-->
[[Image:1896_wh_txr_light.png|50px]]
<!--PaulProjectPic.png-->
[[Image:Ara_flower.png|50px]]
<!--Pierre_project_image.jpg-->
[[Image:Arableaf_ath8_OPT.png|50px]]
</sgallery>
|}
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on testing models</span>]] </center>
<br>
|- <!-- row2-->
[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]
|
 
<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500">
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
Arabidopsis_Leaf_ATH8bbg.png
{| border="0" width=100% style="background-color:#000000;"
Antirrhinum flower small1.jpg
|-
Antirrhinum flower small2.jpg
[[Image:PortraitsMEANSsmaller.jpg|800px]]
Antirrhinum flower small3.jpg
|-}
Anthers1.jpg
<br>
MacroOPTIris1.jpg
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
<!--Grandison-Simulation.png-->
Have you seen the original paintings? Do they exist?. <br><br>
<!--PaulProjectPic.png-->
 
<!--Pierre_project_image.jpg-->
=<span style="color:Navy;">Algorithms=
</sgallery>
 
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
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==[http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves <span style="color:Navy;">'''Vision''':] MSER's, extrema, filter-banks, Sieves and '''Scale-space'''==
=<span style="color: Gold">Working with 3D volume images<span>=
{| border="0" width=100% style="background-color:#ffffff;"
*<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>
|align="center"|
** <span style="color: LemonChiffon">CT X-ray scanners, MRI and PET.</span>
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
** <span style="color: LemonChiffon">Confocal microscopy and OPT (cite) used with fluorescent probes that monitor biological gene activity. </span>
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
** <span style="color: LemonChiffon">Huge amounts of data potentially make viewing slow, but...</span>
|}
* <span style="color: LemonChiffon">To interact with the images we implemented '''VolViewer''' (cite) which 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>
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''VolViewer''</span>]] </center>
 
|| <!-- column3-->
==[http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Software#Art.2C_extrema_of_light_and_shade:_PhotoArtMaster <span style="color:Navy;">'''Applications'''</span>]' <span style="color:Navy;">of non-linear filter banks (sieves) and the art of light and shade</span>==
<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
{| border="0" width=100% style="background-color:#ffffff;"
Arabidopsis_Leaf_ATH8bbg.png
|-
<!--Grandison-Simulation.png-->
|align="center"|
<!--PaulProjectPic.png-->
[[Image:Colour_sieve.jpg|600px|AAMToolbox]]
<!--Pierre_project_image.jpg-->
|}
</sgallery>
These images were produced from photographs using '''ArtMaster''' (formally known as '''PhotoArtMaster'''). The software received many favourable reviews when it was released (e.g. [http://graphicssoft.about.com/cs/photoart/gr/photoartmasterg.htm  "This software can give you a lot of satisfaction from your everyday photos"], [http://graphicssoft.about.com/library/products/aafpr_photoartmaster1.htm]
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on 3D measurement</span>]] </center>
 
|- <!-- row3-->
[http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Software#The_final_version_of_the_Windows_ArtMaster2.0_is_downloadable_here_with_no_support The final (so far unpublished) version of ArtMaster including code is downloadable from here.] I cannot provide support but quite of lot of documentation is available within  [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf <span style="color: Chocolate">''''this document''''' </span>]
| <!-- column1-->
 
|| <!-- column2-->
[http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Software#Art.2C_extrema_of_light_and_shade:_PhotoArtMaster <span style="color:Navy;">'''MORE'''</span>]
|| <!-- column3-->
 
==[[Software#Reaction-diffusion and morphogenesis| <span style="color:Navy;"> '''Reaction-diffusion'''</span>]] <span style="color:Navy;">and morphogenesis - the growth of shapes==
{| border="0" width=100% style="background-color:#000000;"
  |-
|align="center"|
[[Image:tentacles_reaction_diffusion.png|400px]]
[[Image:tentacles_morphogenesis.png|600px]]
|}
|}
This image forms part of a 'journey' in the Science Museum of London's 'Journeys of Invention' [http://www.sciencemuseum.org.uk/journeys iPad app.]<br><br>
[[Software#Reaction-diffusion and morphogenesis|<span style="color:Navy;">'''MORE'''</span>]]<br><br>


=Photos and Art=
=[[Andrew personal | Andrew outside activities]]<br>
=Algorithms, Tools and Demonstrations=
=About=
The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio| <span style="color:DarkSlateGray;">UEA D’Arcy Thompson Centre<!span>] for computational biology and collaborates closely with [[http://rico-coen.jic.ac.uk/index.php/Main_Page|<span style="color:DarkSlateGray;">the Coen Lab, John Innes Centre</span>]]
--[[User:AndrewBangham|Andrew]] 09:50, 4 May 2011 (UTC)

Latest revision as of 12:03, 27 October 2014


Computational biology

Growing complex biological shapes from patterns of gene expression

LabelledCropped GPT Snapdragon 2010-000340-0001.png LabelledCropped GPT Snapdragon 2010-000490-0001.png LabelledCropped GPT Snapdragon 2010-000570-0002.png LabelledCropped GPT Snapdragon 2010-000570-0007.png LabelledCropped GPT Snapdragon 2010-000570-0003 double.png LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png


MORE

Viewing three dimensional volume (microscopy) images

Cs0prxz0.png Leaf trichomes.png Cs0prxz0.png GL2 GUS.png Leaf5.png OleosinSeed.png OPT Leaf copy.png Seedling copy.png Snapdragon Peloric mutant.png Tissue.png Z9r3j2yx.png 1896 wh txr light.png Ara flower.png Arableaf ath8 OPT.png


MORE

Analysing shapes: faces, leaves and flowers

PortraitsMEANSsmaller.jpg
MORE
Have you seen the original paintings? Do they exist?.

Algorithms

Vision: MSER's, extrema, filter-banks, Sieves and Scale-space

AAMToolbox AAMToolbox

MORE

Applications' of non-linear filter banks (sieves) and the art of light and shade

AAMToolbox

These images were produced from photographs using ArtMaster (formally known as PhotoArtMaster). The software received many favourable reviews when it was released (e.g. "This software can give you a lot of satisfaction from your everyday photos", [1]

The final (so far unpublished) version of ArtMaster including code is downloadable from here. I cannot provide support but quite of lot of documentation is available within 'this document

MORE

Reaction-diffusion and morphogenesis - the growth of shapes

Tentacles reaction diffusion.png Tentacles morphogenesis.png

This image forms part of a 'journey' in the Science Museum of London's 'Journeys of Invention' iPad app.

MORE

= Andrew outside activities

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