Main Page: Difference between revisions

From BanghamLab
Jump to navigation Jump to search
No edit summary
No edit summary
 
(162 intermediate revisions by 4 users not shown)
Line 1: Line 1:
__NOTOC__
 
<span style="color: DarkSlateGray"><font size="+1"><center>'''The Bangham Lab'''</center></font><span>
 
=<span style="color: DarkGreen">Computational Biology</span>=  
=<span style="color:DarkGreen;">Computational biology</span>=
{| border="1" cellpadding="5" cellspacing="3"  style="background-color: #000000;"
 
| <!-- column1-->
----
<sgallery width="160" height="280" showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="2000">
 
LabelledCropped_GPT_Snapdragon_2010-000250-0001.png
==<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>==
LabelledCropped_GPT_Snapdragon_2010-000340-0001.png
{| border="0" width=100% style="background-color:#000000;"
LabelledCropped_GPT_Snapdragon_2010-000490-0001.png
|-
LabelledCropped_GPT_Snapdragon_2010-000570-0002.png
|align="center"|
LabelledCropped_GPT_Snapdragon_2010-000570-0003.png
[[Image:LabelledCropped GPT Snapdragon 2010-000340-0001.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0004.png
[[Image:LabelledCropped GPT Snapdragon 2010-000490-0001.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0005.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0007.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0007.png|120px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0006.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0003 double.png|100px]]
LabelledCropped_GPT_Snapdragon_2010-000570-0001.png
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png|120px]]
</sgallery>
|}
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on Snapdragon model</span>]] </center>
<br>
|| <!-- column2-->
[[Software#Quantitative understanding of growing shapes: GFtbox|<span style="color:Green;">'''MORE'''</span>]]<br>
=<span style="color: Gold">Genes and growing shapes<span>=  
 
<span style="color: LemonChiffon">The aim is to understand how patterns of gene activity in biological organs influence the developing shape. A key notion is that genes may regulate growth direction independently of growth rate. We formalised our ideas in the Growing Polarised Tissue Framework (ref). To make it easy to develop ideas on the relationship between growth and form we implemented a software package: ''GFtbox''. Using ''GFtbox'' one can start with a simple sheet of tissue (the canvas), lay out experimentally observed, or hypothesised, patterns of regulator activity and then grow the canvas in 3D. The final shape can be compared quantitatively with it's biological counterpart - so testing the hypotheses.</span><p>
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''GFtbox''</span>]] </center>
{| border="0" width=100% style="background-color:#000000;"
||  <!-- column3-->
|-
<sgallery width="160" height="280"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="3000">
|align="center"|
LabelledCropped GPT Snapdragon 2010-000570-0003 double.png
[[Image:Cs0prxz0.png|32x32px]]
LabelledCropped GPT Snapdragon 2010-000570-0002 triple.png
[[Image:Leaf_trichomes.png|50px]]
LabelledCropped GPT Snapdragon 2010-000570-0001-Wildtype.png
[[Image:Cs0prxz0.png|50px]]
<!--Arabidopsis_Leaf_ATH8bbg.png-->
[[Image:GL2_GUS.png|50px]]
<!--Grandison-Simulation.png-->
[[Image:Leaf5.png|50px]]
<!--PaulProjectPic.png-->
[[Image:OleosinSeed.png|50px]]
<!--Pierre_project_image.jpg-->
[[Image:OPT_Leaf_copy.png|50px]]
</sgallery>
[[Image:Seedling_copy.png|50px]]
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on testing models</span>]] </center>
[[Image:Snapdragon_Peloric_mutant.png|50px]]
|- <!-- row2-->
[[Image:Tissue.png|50px]]
|
[[Image:Z9r3j2yx.png|50px]]
<sgallery width="160" height="280"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="1500">
[[Image:1896_wh_txr_light.png|50px]]
Arabidopsis_Leaf_ATH8bbg.png
[[Image:Ara_flower.png|50px]]
Antirrhinum flower small1.jpg
[[Image:Arableaf_ath8_OPT.png|50px]]
Antirrhinum flower small2.jpg
|}
Antirrhinum flower small3.jpg
<br>
Anthers1.jpg
[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;">'''MORE'''</span>]]
MacroOPTIris1.jpg
 
<!--Grandison-Simulation.png-->
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
<!--PaulProjectPic.png-->
{| border="0" width=100% style="background-color:#000000;"
<!--Pierre_project_image.jpg-->
|-
</sgallery>
[[Image:PortraitsMEANSsmaller.jpg|800px]]
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on visualising 3D</span>]] </center>
|-}
|| <!-- column2-->
<br>
=<span style="color: Gold">Working with 3D volume images<span>=
[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''MORE'''</span>]]<br>
<span style="color: LemonChiffon">Three dimensional (3D) volume images are key to understanding the development of shape. They are produced by CT X-ray scanners, MRI and PET. However, biological gene activity is monitored using fluorescent probes and so optical methods are used: confocal microscopy and optical projection microscopy. The resulting images are large and are best viewed using software that exploits powerful graphics processors. We implemented VolViewer which is a viewer of choice in the open microscopy environment.</span>
Have you seen the original paintings? Do they exist?. <br><br>
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">Downloads and more details on ''VolViewer''</span>]] </center>
 
|| <!-- column3-->
=<span style="color:Navy;">Algorithms=
<sgallery width="160" height="280"  showarrows="false" showcarousel="false" showinfopane="false" timed="true" delay="4000">
 
Arabidopsis_Leaf_ATH8bbg.png
----
<!--Grandison-Simulation.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'''==
<!--PaulProjectPic.png-->
{| border="0" width=100% style="background-color:#ffffff;"
<!--Pierre_project_image.jpg-->
|-
</sgallery>
|align="center"|
<center> [[Software#Toolboxes for research|<span style="color:GreenYellow;">More on 3D measurement</span>]] </center>
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
|-  <!-- row3-->
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
| <!-- column1-->
|}
|| <!-- column2-->
 
|| <!-- column3-->
[[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]]
|}
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>


=Photos, Algorithms and Art=
=[[Andrew personal |  Andrew outside activities]]<br>
=Tools and Demonstrations=
=About=
The Bangham Lab is part of the [http://www.uea.ac.uk/cmp/research/cmpbio UEA D’Arcy Thompson Centre] for computational biology.

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

Retrieved from "http://cmpdartsvr3-v.uea.ac.uk/wiki/BanghamLab/index.php?title=Main_Page&oldid=6928"