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__NOTOC__
=<font size="+2">'''The Bangham Lab'''</font>=


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=<span style="color:DarkGreen;">Computational biology</span>=
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----
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==<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>==
{| border="0" width=100% style="background-color:#000000;"
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|align="center"|  
[[Image:LabelledCropped GPT Snapdragon 2010-000340-0001.png|120px]]
[[Image:LabelledCropped GPT Snapdragon 2010-000490-0001.png|120px]]
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002.png|120px]]
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0007.png|120px]]
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0003 double.png|100px]]
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png|120px]]
|}
|}
<br>
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>


{|cellpadding="5" border="1"
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
||
{| border="0" width=100% style="background-color:#000000;"
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
|-
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|align="center"|
<center>
[[Image:Cs0prxz0.png|32x32px]]
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
[[Image:Leaf_trichomes.png|50px]]
Cycdich.jpg
[[Image:Cs0prxz0.png|50px]]
Arabidopsis_Leaf_ATH8bbg.png
[[Image:GL2_GUS.png|50px]]
Grandison-Simulation.png
[[Image:Leaf5.png|50px]]
PaulProjectPic.png
[[Image:OleosinSeed.png|50px]]
Pierre_project_image.jpg
[[Image:OPT_Leaf_copy.png|50px]]
</sgallery>
[[Image:Seedling_copy.png|50px]]
This is a title
[[Image:Snapdragon_Peloric_mutant.png|50px]]
</center>
[[Image:Tissue.png|50px]]
|}
[[Image:Z9r3j2yx.png|50px]]
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
[[Image:1896_wh_txr_light.png|50px]]
||
[[Image:Ara_flower.png|50px]]
<center>
[[Image:Arableaf_ath8_OPT.png|50px]]
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
|}
Cycdich.jpg
<br>
Arabidopsis_Leaf_ATH8bbg.png
[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]
Grandison-Simulation.png
PaulProjectPic.png
Pierre_project_image.jpg
</sgallery>
This is a title </center>
|}
||
{|align="center" cellpadding="10" cellspacing="5" style= "text-align:left"
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=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. The aim of the lab is to be an interface between biology and computing.


Our research goal is to understand the algorithms underpinning the evolution and growth of plants. In a  collaboration with [http://rico-coen.jic.ac.uk/index.php/Main_Page Prof. Enrico Coen] (in the neighbouring [http://www.jic.ac.uk/corporate/index.htm John Innes Centre]), we lead the computing science behind an integrated plant biology and computing science project to model the growing leaf and meristem. Fluorescent probes are incorporated into plants and imaged in two and three dimensions using optical projection tomography and confocal microscopy. Our visualisation tools include haptics and automatic methods for analysing the results and integrating them with finite element and cell-based models.
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
||
{| border="0" width=100% style="background-color:#000000;"
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
|-
||
[[Image:PortraitsMEANSsmaller.jpg|800px]]
<center>
|-}
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
<br>
Cycdich.jpg
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
Arabidopsis_Leaf_ATH8bbg.png
Have you seen the original paintings?  Do they exist?. <br><br>
Grandison-Simulation.png
PaulProjectPic.png
Pierre_project_image.jpg
</sgallery>
This is a title </center>
|}


{| border="1" cellpadding="5" align="center"  style="background:#fff;"
=<span style="color:Navy;">Algorithms=
||
 
<center>
----
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
==[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'''==
Cycdich.jpg
{| border="0" width=100% style="background-color:#ffffff;"
Arabidopsis_Leaf_ATH8bbg.png
|-
Grandison-Simulation.png
|align="center"|
PaulProjectPic.png
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
Pierre_project_image.jpg
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
</sgallery>
This is a title </center>
|}
|}
|}
|}
<p>
{|cellpadding="5" border="1"
||
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
||
<center>
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
Cycdich.jpg
Arabidopsis_Leaf_ATH8bbg.png
Grandison-Simulation.png
PaulProjectPic.png
Pierre_project_image.jpg
</sgallery>
This is a title
</center>
|}
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
||
<center>
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
Cycdich.jpg
Arabidopsis_Leaf_ATH8bbg.png
Grandison-Simulation.png
PaulProjectPic.png
Pierre_project_image.jpg
</sgallery>
This is a title </center>
|}
||
{|align="center" cellpadding="10" cellspacing="5" style= "text-align:left"
||
=Photos, Algorithms and Art=
The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio UEA D’Arcy Thompson Centre] for computational biology. The aim of the lab is to be an interface between biology and computing.


Our research goal is to understand the algorithms underpinning the evolution and growth of plants. In a  collaboration with [http://rico-coen.jic.ac.uk/index.php/Main_Page Prof. Enrico Coen] (in the neighbouring [http://www.jic.ac.uk/corporate/index.htm John Innes Centre]), we lead the computing science behind an integrated plant biology and computing science project to model the growing leaf and meristem. Fluorescent probes are incorporated into plants and imaged in two and three dimensions using optical projection tomography and confocal microscopy. Our visualisation tools include haptics and automatic methods for analysing the results and integrating them with finite element and cell-based models.
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]
||
 
{| border="1" cellpadding="5" align="center"  style="background:#fff;"
==[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>==
||
{| border="0" width=100% style="background-color:#ffffff;"
<center>
|-
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
|align="center"|
Cycdich.jpg
[[Image:Colour_sieve.jpg|600px|AAMToolbox]]
Arabidopsis_Leaf_ATH8bbg.png
|}
Grandison-Simulation.png
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]
PaulProjectPic.png
 
Pierre_project_image.jpg
[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>]
</sgallery>
 
This is a title </center>
[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>]
|}


{| border="1" cellpadding="5" align="center"  style="background:#fff;"
==[[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;"
<center>
|-
<sgallery width="160" height="120" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
|align="center"|
Cycdich.jpg
[[Image:tentacles_reaction_diffusion.png|400px]]
Arabidopsis_Leaf_ATH8bbg.png
[[Image:tentacles_morphogenesis.png|600px]]
Grandison-Simulation.png
PaulProjectPic.png
Pierre_project_image.jpg
</sgallery>
This is a title </center>
|}
|}
|}
|}
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, Algorithms and Art=
=[[Andrew personal |  Andrew outside activities]]<br>
=Tools and Demonstrations=

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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