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Bangham at UEA

Computational biology toolboxes


Growing complex biological shapes from patterns of gene expression

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Viewing three dimensional 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


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Analysing shapes: faces, leaves and flowers

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Seen the origional paintings? Do they exist?.

Algorithms


MSER's, extrema, Connected-set filters, Sieves and Scale-space

AAMToolbox AAMToolbox

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.

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.

These extrema have been computed using an 'M sieve as opposed to an o' (opening) which appears to underlie the MSER algorithm.

More details on MSER's, sieves and connected set filters More

Reaction-diffusion and morphogenesis - the growth of shapes

Tentacles reaction diffusion.png Tentacles morphogenesis.png


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In 1952 Alan Turing proposed 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 widely known. However, the morphogenesis element of the story has been less widely explored - here we illustrate the process using GFtbox - but also see: plant meristemreview 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 (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 Codebreakers.
More details on reaction-diffusion and morphogenesis