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__NOTOC__
=<span style="color:DarkGreen;">Computational biology</span>=
='''Overview of Research Programme'''=


Some text describing the research programme for the Bangham Lab.
----


=='''Visualization, Quantification and Data Management of Microscopy Images'''==
==<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>==
[[Image:Arabidopsis_Leaf_ATH8bbg.png|thumb|left|128px|Volume render of an ''Arabidopsis'' leaf with ATH8::GUS expression in the veins (red).]]
{| 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>


'''Jerome Avondo''' - [mailto:jerome.avondo@uea.ac.uk email]
==<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>]]


The field of biological imaging has seen incredible advances due to new imaging techniques and molecular markers. These advances in data aquisition result in the creation of multidimensional images. How these images are to be visualized, quantified and data managed remains an open challenge.  
==[[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>


To visualize and quantify multidimensional images I research the field of real time volume rendering and the use of the graphics processing unit (GPU). This allows the creation of rendering algorithms for the interactive visualization of microscopy images through space, spectral channels and time.
=<span style="color:Navy;">Algorithms=


By using interactive visualization, it is also possible to create simple intuitive interfaces to equip biologists with tools to quantify their biological data. All results from my work is available to the community as a free open source application called [[Software|VolViewer]].
----
==[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'''==
{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
|}


Due to the large amounts of data being produced by bio-image data acquisition systems, such as a confocal microscope, it is possible for a single lab to generate many terabytes of imaging data. To address the data management issues involved with such large data sets I am working in collaboration with the [http://openmicroscopy.org/site  Open Microscopy Environment] team lead by [http://www.lifesci.dundee.ac.uk/groups/jason_swedlow/ Jason Sweldow] at the [http://www.dundee.ac.uk/ Univeristy of Dundee].
[[Software#MSERs.2C_extrema.2C_connected-set_filters_and_sieves|<span style="color:Navy;">'''MORE'''</span>]]


Together we are working on integrating the VolViewer application as an addon package to the [http://openmicroscopy.org/site  Open Microscopy Environment] platform. Work is also being conducted to offer a customized OMERO system as part of the [http://www.jic.ac.uk/corporate/services-and-products/resources/bioimaging.htm John Innes Centre Bio-Imaging] platform service. This work is being conducted to promote advanced visualisation, data management and image processing at the [http://www.jic.ac.uk John Innes Centre]. Research from this work can be found on the [http://dmbi.nbi.bbsrc.ac.uk DMBI project wiki].
==[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]


<br style="clear: both" />
[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>]


=='''Modelling and analysis of growing plant tissues. Application to flower development'''==
[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>]


[[Image:Pierre_project_image.jpg|left|thumb|128px|No caption]]
==[[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;"
'''Pierre Barbier-De-Reuille''' - [mailto:pierre.barbier-de-reuille@bbsrc.ac.uk email]
|-
 
|align="center"|
My main research project is about methods and tools for the modelling and the analysis of growing plant tissues.
[[Image:tentacles_reaction_diffusion.png|400px]]
 
[[Image:tentacles_morphogenesis.png|600px]]
For the modelling part, I am developing VVe, a modelling environment for the modelling of 2D structures in 3D space. VVe includes specialized tools for dealing with the development of plant tissues at the cellular scale, but can also be used to model tissue considered as a continuum. It is already distributed, as it is used by Sarah Robinson in our lab, in the lab of the professor Prusinkiewicz in Calgary and in the lab of the professor Kuhlemeier in Bern.
|}
 
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>
For the data analysis, I am developing digitizing and computation tools. I am in particular working on tracking cell growth and division, and extracting useful information from this (i.e. growth tensor, division rate, ...).
[[Software#Reaction-diffusion and morphogenesis|<span style="color:Navy;">'''MORE'''</span>]]<br><br>
 
Currently, my developments aim at helping the understanding of the growth patterns in the mature petal of Arabidopsis.
 
<br style="clear: both" />
 
=='''Modelling microtubule dynamics'''==
 
[[Image:Grandison-Simulation.png|thumb|left|128px|A frame from a microtubule simulation.]]
 
'''Scott Grandison''' - [mailto:s.grandison@uea.ac.uk email]
 
Microtubules are small, filamentous polymers that perform a variety of important developmental functions that have an impact, not only within the cell, but on a macroscopic scale.  They help to provide structural integrity to the cell, by guiding the mechanisms which lay down cellulose microfibrils.  If these microfibrils are laid down with a preferential direction then the cell can be encouraged to grow anisotropically which is important when forming complex shapes during development.  Another important role for microtubules is their role in determining where exactly a cell will divide during mitosis.
 
I'm interesting in studying these functions by making accurate mathematical and computer simulations of microtubule dynamics.  I work closely with Dr. Jordi Chan and Dr. Paul Southam who are interesting in the experimental and image processing part of the project.
 
<br style="clear: both" />
 
=='''Modelling Growth at the Tissue Scale'''==
 
[[Image:Cycdich.jpg|thumb|left|128px|Model for Snapdragon cyc dich mutant]]
 
'''Richard Kennaway'''  - [mailto:r.kennaway@uea.ac.uk email]
 
I am developing finite element methods for modelling the growth and development of curved two-dimensional tissues such as leaves and petals. The interactive software tool I am developing, called GFtbox, is [http://cmpdartsvr1.cmp.uea.ac.uk/wiki/LabGuide/index.php/Growth_Toolbox available for download].
 
<br style="clear: both" />
 
=='''Image Processing for Biological Development'''==
 
[[Image:PaulProjectPic.png|thumb|left|128px| 3D segmentation of cells (green) from a volumetric image (Arabdidopsis leaf).]]
 
'''Paul Southam''' - [mailto:paul.southam@uea.ac.uk email]
 
Extracting quantitative measurements from image data is a fundamental step towards understanding how biological forms develop and evolve. I work on a number of projects including:
 
Modelling microtubule dynamics during growth and division - Jordi Chan & Scott Grandison.
 
Modelling Dynamic Growth Maps of Leaf Development - Samantha Fox.
 
Capturing plant development in 3D with Optical Projection Tomography - Karen Lee.
 
I am also interested in cell segmentation, cell registration, leaf classification and texture analysis.
 
 
<br style="clear: both" />

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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