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=[http://www.uea.ac.uk/computing/People/Honorary/Andrew+Bangham Bangham at UEA]=
 
=<span style="color:DarkGreen;">Computational biology toolboxes=
 
=<span style="color:DarkGreen;">Computational biology</span>=


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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>


==<span style="color:DarkGreen;">Viewing three dimensional images==
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
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<br>
<br>
[[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>]]


==<span style="color:DarkGreen;">Analysing shapes: faces, leaves and flowers==
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
[[Image:PortraitsMEANSsmaller.jpg|800px]]
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[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
Seen the origional paintings?  Do they exist?. <br><br>
Have you seen the original paintings?  Do they exist?. <br><br>
 
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#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:DarkGreen;">More details on analysing shapes</span>]]<br><br>


=<span style="color:Navy;">Algorithms=
=<span style="color:Navy;">Algorithms=


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==<span style="color:Navy;">MSER's, extrema, Connected-set filters, Sieves and '''Scale-space'''==
==[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'''==
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Left: 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. <br>
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]
 
==[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>==
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[[Image:Colour_sieve.jpg|600px|AAMToolbox]]
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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]


Right: Isometric view of the cameraman image with superimposed maxima and minima. The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.<br><br>
[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>]
These extrema have been computed using an ''''''M''' sieve as opposed to an '''o'''''' (opening) which appears to underlie the MSER algorithm.


[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">More details on MSER's, sieves and connected set filters</span> More]]
[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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<br>
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:Green;">'''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>
=[[Andrew personal | Andrew outside activities]]<br>
[[Software#Reaction-diffusion and morphogenesis|<span style="color:Navy;">More details on reaction-diffusion and morphogenesis</span>]]<br><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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