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=[http://www.uea.ac.uk/computing/People/Honorary/Andrew+Bangham Bangham at UEA]=
=<span style="color:DarkGreen;">Computational biology</span>=
=<span style="color:Indigo;">Bangham Lab - Home=
 
<span style="color: DarkGreen">'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.</span>
=<span style="color:DarkGreen;">Computational biology toolboxes=


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==<span style="color:DarkGreen;">Growing complex biological shapes from patterns of gene expression</span>==
==<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>==
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[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>


Movies: [http://www.youtube.com/watch?v=7Uu5dHxyEwk Model Snapdragon flower movie], [http://www.youtube.com/watch?feature=endscreen&v=kZ45R1UlohM&NR=1 Bees and why the Snapdragon flower shape is so complex]<br><br>
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
 
The growth of a complex ''snapdragon flower shape''. Key to the model, is an hypothesis on'' how organisers control the axes'' along which growth occurs. The organisers are shown in cyan and green. On the right are the shapes of two symmetrical mutants computed from the same model (hypotheses).<br><br>
The Growing Polarised Tissue Framework for understanding and modelling the relationship between gene activity and the growth of shapes such leaves, flowers and animal embryos is introduced in ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). The GPT-framework was used to capture an understanding of (to model) the Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.]<br><br>
The GPT-framework was also used to model the developing shape of ''Arabidopsis'' leaves as they grow ([http://www.sciencemag.org/content/335/6072/1092.abstract Kuchen et al 2012]) a model that was extended to include ''Arabidopsis'' petals [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip  Sauret-Güeto et al 2013].
 
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:DarkGreen;">More details on growth </span>]]<br><br>
 
==<span style="color:DarkGreen;">Viewing three dimensional images==
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[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]<br><br>
[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]


Images of plants, plant organs and cells.<br><br>
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
''VolViewer'' uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and  optical projection tomography images. It is open-source and is compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).<br><br>
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Movies of [http://www.youtube.com/user/InnerWorldsJIC carnivorous plants]
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[[Image:PortraitsMEANSsmaller.jpg|800px]]
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[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
Have you seen the original paintings?  Do they exist?. <br><br>


[[Software#Viewing and measuring volume images: VolViewer|<span style="color:DarkGreen;">More details on viewing three dimensional images</span>]]<br><br>
=<span style="color:Navy;">Algorithms=


==<span style="color:DarkGreen;">Analysing shapes: faces, leaves and flowers==
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[[Image:PortraitsMEANSsmaller.jpg|800px]]
==[http://cmpdartsvr3.cmp.uea.ac.uk/wiki/BanghamLab/index.php/Software#Art.2C_extrema_of_light_and_shade:_PhotoArtMaster<span style="color:Navy;">'''Vision''':] MSER's, extrema, filter-banks, Sieves and '''Scale-space'''==
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[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
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Seen the origional paintings?  Do they exist?. <br><br>
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[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
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The ''AAMToolbox'' is used to analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.<br><br>
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:DarkGreen;">More details on analysing shapes</span>]]<br><br>


=<span style="color:Navy;">Algorithms=
==[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:Chocolate;">The algorithm finding MSER's starts with a connected-set opening or 'o' sieve</span>==
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|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] Cameraman image. Superimposed red spots are maximal extrema and blue spots are minima. Irregular cyan, blue and yellow regions illustrate regions associated with maxima and the magenta region is a minimum.
[[Image:Colour_sieve.jpg|600px|AAMToolbox]]
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]]<br>Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
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[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Chocolate;">'''MORE''' </span>]]<br><br>
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]
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[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>]


==<span style="color:Navy;">Reaction-diffusion and morphogenesis - the growth of shapes==
==[[Software#Reaction-diffusion and morphogenesis| <span style="color:Navy;"> '''Reaction-diffusion'''</span>]] <span style="color:Navy;">and morphogenesis - the growth of shapes==
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[[Image:tentacles_morphogenesis.png|600px]]
[[Image:tentacles_morphogenesis.png|600px]]
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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>
[[Software#Reaction-diffusion and morphogenesis|<span style="color:Navy;">'''MORE'''</span>]]<br><br>
In 1952 Alan Turing proposed [http://rstb.royalsocietypublishing.org/content/237/641/37.abstract The chemical basis of Morphogenesis] - "... suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis. Such a system, although it may originally be quite homogeneous, may later develop a pattern or structure due to an instability of the homogeneous equilibrium, which is triggered off by random disturbances. ..." Such patterning is now [http://en.wikipedia.org/wiki/Reaction%E2%80%93diffusion_system widely known]. However, the morphogenesis element of the story has been less widely explored - here we illustrate the process using ''GFtbox'' - but also see: [http://www.sciencedirect.com/science/article/pii/S1360138507000611 plant meristem][http://home.thep.lu.se/~henrik/mnxa09/Jonsson2012.pdf review related plant stuff]
Two chemical substances react and diffuse to dynamically develop a pattern of spots (top row). We have added two simple growth rules ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 based on our hypotheses on the growth of shapes]) to dynamically translate the pattern into a pattern of growth (bottom row). The changing geometry arising through growth which in turn feeds back on the reaction-diffusion system to modulate patterning. One of the morphogenesis rules uses the chemical concentration gradient to set the axes for anisotropic growth (arrows in third panel).
This model was featured in a video interview exhibit in the London Science Museum 'Codebreakers' exhibition [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx Codebreakers]. <br>
[[Software#Reaction-diffusion and morphogenesis|<span style="color:Navy;">More details on reaction-diffusion and morphogenesis</span>]]<br><br>

Latest revision as of 11:57, 14 April 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

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