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__NOTOC__
=<span style="color:SteelBlue;">'''Current'''=
=<span style="color:DarkGreen;">Computational biology toolboxes=
==<span style="color:DarkGreen;">GFtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|width="40%"|
For modelling the growth of shapes.  <br><br>See [[GFtbox|''Details'']], [[GFtbox Tutorial pages|''Tutorials'']] and [https://sourceforge.net/p/gftbox/ ''Download'']<br><br>
(PC, Mac, Linux, uses Matlab<br>[http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and <br>[http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition])
|width="50%"|  ''GFtbox'' is an implementation of 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 (PLoS Computational Biology, ''in press''). <br>The GPT-framework was used to capture an understanding of (to model) the [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 growing Snapdragon flower]. <br>The Snapdragon model was validated by [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 comparing the results with new mutant flowers.];


=<span style="color:DarkGreen;">Computational biology</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>==
{| border="0" width=100% style="background-color:#000000;"
|-
|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>
==<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>]]
==[[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;"
|-
[[Image:PortraitsMEANSsmaller.jpg|800px]]
|-}
<br>
[[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>
=<span style="color:Navy;">Algorithms=
----
==[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'''==
{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
|}
[[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>==
{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|
[[Image:Colour_sieve.jpg|600px|AAMToolbox]]
|}
|}
==<span style="color:DarkGreen;">VolViewer==
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]
{| border="0" cellpadding="5" cellspacing="5"
 
|- valign="top"
[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>]
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
 
|width="40%"|For viewing and measuring 3D volume images. <br><br>See [[VolViewer|''Details'']], [[VolViewer|''Download'']]<br><br>
[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>]
(Windows, Mac, Linux)
 
|width="50%"|  VolViewer makes extensive use of [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt]. It is open-source and is compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
==[[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>
=[[Andrew personal |  Andrew outside activities]]<br>

Latest revision as of 13:03, 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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