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__NOTOC__
 
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=<span style="color:DarkGreen;">Computational biology</span>=
|width="50%"|<span style="color: DarkSlateGray"><font size="+1">'''The Bangham Lab'''</font><span>
 
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----
||'''Contents'''
 
|- valign="top"
==<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>==
|width="50%"|
{| border="0" width=100% style="background-color:#000000;"
|||<center><small>
|-
{| border="0" cellpadding="0" cellspacing="0"  
|align="center"|  
|width="100pt"|[[Main_Page#Computational Biology|'''GFtbox''']]                 
[[Image:LabelledCropped GPT Snapdragon 2010-000340-0001.png|120px]]
|width="100pt"| [[GFtbox|Details]] 
[[Image:LabelledCropped GPT Snapdragon 2010-000490-0001.png|120px]]
|width="100pt"| [https://sourceforge.net/p/gftbox/ Download ]
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002.png|120px]]
|width="100pt"| [[GFtbox Tutorial pages|Tutorials]]  
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0007.png|120px]]
|-
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0003 double.png|100px]]
|width="100pt"|[[Main_Page#Computational Biology|'''VolViewer''' ]]                    
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png|120px]]
|width="100pt"| [[VolViewer|Details]]  
|width="100pt"|  [[VolViewer|Download]]  
|width="100pt"| [[VolViewerUserManual|Manual]]
<!--|-
|width="100pt"|[[Main_Page#Computational Biology|'''Shapes''']]
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|width="100pt"| 7
|-
|width="100pt"|[[Main_Page#Photos and Art|'''Art''']]
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|width="100pt"| 6
|width="100pt"| 7
|-
|width="100pt"|[[Main_Page#Algorithms, Tools and Demonstrations|'''Algorithms''']]
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|width="100pt"| 7 -->
|}
|}
</small></center>
<br>
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>
 
==<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;"
|-
|align="center"|
[[Image:Cs0prxz0.png|32x32px]]
[[Image:Leaf_trichomes.png|50px]]
[[Image:Cs0prxz0.png|50px]]
[[Image:GL2_GUS.png|50px]]
[[Image:Leaf5.png|50px]]
[[Image:OleosinSeed.png|50px]]
[[Image:OPT_Leaf_copy.png|50px]]
[[Image:Seedling_copy.png|50px]]
[[Image:Snapdragon_Peloric_mutant.png|50px]]
[[Image:Tissue.png|50px]]
[[Image:Z9r3j2yx.png|50px]]
[[Image:1896_wh_txr_light.png|50px]]
[[Image:Ara_flower.png|50px]]
[[Image:Arableaf_ath8_OPT.png|50px]]
|}
|}
<br>
[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]


=<span style="color: DarkGreen">Computational Biology</span>=
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
<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" width=100% style="background-color:#000000;"
{| border="0" cellpadding="5" cellspacing="3"  style="background-color: #000000;"
|-
| <!-- column1-->
[[Image:PortraitsMEANSsmaller.jpg|800px]]
<sgallery width="140" height="200" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000">
|-}
LabelledCropped_GPT_Snapdragon_2010-000250-0001.png
<br>
LabelledCropped_GPT_Snapdragon_2010-000340-0001.png
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
LabelledCropped_GPT_Snapdragon_2010-000490-0001.png
Have you seen the original paintings? Do they exist?. <br><br>
LabelledCropped_GPT_Snapdragon_2010-000570-0002.png
 
LabelledCropped_GPT_Snapdragon_2010-000570-0003.png
=<span style="color:Navy;">Algorithms=
LabelledCropped_GPT_Snapdragon_2010-000570-0004.png
 
LabelledCropped_GPT_Snapdragon_2010-000570-0005.png
----
LabelledCropped_GPT_Snapdragon_2010-000570-0007.png
==[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'''==
LabelledCropped_GPT_Snapdragon_2010-000570-0006.png
{| border="0" width=100% style="background-color:#ffffff;"
LabelledCropped_GPT_Snapdragon_2010-000570-0001.png
|-
</sgallery>
|align="center"|
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More Snapdragon model</span>]] </center>
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
|| <!-- column2-->
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
=<span style="color: Gold">Genes and growing shapes (modelling)</span>=
* <span style="color: LemonChiffon">Observation: patterns of gene activity that regulate tissue 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 (cite). </span>
* <span style="color: LemonChiffon">Implemented in ''GFtbox'' (cite) for developing 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">Grow the canvas in 3D under constraints of tissue continuity</span>
** <span style="color: LemonChiffon">Compare with observed data quantitatively </span><p>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''GFtbox''</span>]] </center>
|| <!-- column3-->
<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
<!--Arabidopsis_Leaf_ATH8bbg.png-->
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on testing models</span>]] </center>
|-  <!-- row2-->
|
<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
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
|| <!-- column2-->
=<span style="color: Gold">Viewing 3D volume images (analysis)<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 OPT (ref) used with fluorescent probes that monitor biological gene activity. </span>
** <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 3D images in both open and proprietary file formats </span>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Download and more details on ''VolViewer''</span>]] </center>
|| <!-- column3-->
<sgallery width="140" height="200"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
Arabidopsis_Leaf_ATH8bbg.png
<!--Grandison-Simulation.png-->
<!--PaulProjectPic.png-->
<!--Pierre_project_image.jpg-->
</sgallery>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on 3D measurement</span>]] </center>
|- <!-- row3-->
| <!-- column1-->
|| <!-- column2-->
|| <!-- column3-->
|}
|}


=Photos and Art=
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]
=Algorithms, Tools and Demonstrations=
 
=About=
==[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>==
<span style="color:DarkSlateGray;">The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio| <span style="color:SlateGray;">UEA D’Arcy Thompson Centre] for computational biology and it's members collaborate closely with [http://rico-coen.jic.ac.uk/index.php/Main_Page|<span style="color:SlateGray;">the Coen Lab, John Innes Centre</span>]
{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|
[[Image:Colour_sieve.jpg|600px|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. [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]
 
[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>]
 
[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>]
 
==[[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>


==<span style="color:DarkSlateGray;">Updated [[User:AndrewBangham|Andrew Bangham]] 09:50, 4 May 2011 (UTC)==
=[[Andrew personal | Andrew outside activities]]<br>

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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