Main Page: Difference between revisions

From BanghamLab
Jump to navigation Jump to search
No edit summary
No edit summary
 
(90 intermediate revisions by 2 users not shown)
Line 1: Line 1:
__NOTOC__
=Bangham Lab - Home=


<span style="color: DarkGreen">'''Current activity: a collaboration''' with the [http://rico-coen.jic.ac.uk/index.php/Main_Page CoenLab] with the aim of understanding how patterns of gene activity in biological organs influence the developing shape. The BanghamLab is focussed on the conceptual underpinning: concepts captured in computational growth models, experimental data visualisation and analysis.</span>
 
=<span style="color:DarkGreen;">Computational biology toolboxes=
=<span style="color:DarkGreen;">Computational biology</span>=


----
----


==<span style="color:DarkGreen;">GFtbox==
==<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" cellpadding="5" cellspacing="5"
{| border="0" width=100% style="background-color:#000000;"
|- valign="top"
|-
|width="10%"| <imgicon>GPT_thumbnail2.png|120px|GFtbox</imgicon>
|align="center"|  
|width="40%"|
[[Image:LabelledCropped GPT Snapdragon 2010-000340-0001.png|120px]]
For modelling the growth of shapes. <br><br>
[[Image:LabelledCropped GPT Snapdragon 2010-000490-0001.png|120px]]
[[GFtbox|'''What? How? Where?''']]<br><br>
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0002.png|120px]]
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]]<br><br>
[[Image:LabelledCropped GPT Snapdragon 2010-000570-0007.png|120px]]
[[GFtbox Example pages|'''''Examples''''': from publications]]<br><br>
[[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>


[https://sourceforge.net/p/gftbox/ <span style="color: Gray">'''''Download GFTbox''''' from SourceForge</span>]<br>
==<span style="color:DarkGreen;">[[Software#Viewing and measuring volume images: VolViewer|<span style="color:Green;"> '''Viewing''']] three dimensional volume (microscopy) images==
<small><span style="color: Gray">'''''Download GFTbox project files:''''' </span></small><br>
{| border="0" width=100% style="background-color:#000000;"
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip <small><span style="color: Gray">'''''Leaves''''' Kuchen et al 2012</span></small>]<br>
|-
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip <small><span style="color: Gray">'''''Principles and concepts''''' Kennaway et al 2011</span></small>]<br>
|align="center"|
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip <small><span style="color: Gray">'''''Snapdragon''''' Green et al 2011, Cui et al 2010</span></small>]<br><br>
[[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>]]


[[Ready Reference Manual|'''''Ready Reference''''' Manual]]<br><br>
==[[Software#Analysing shapes in 2D and 3D: AAMToolbox|<span style="color:Green;">'''Analysing'''</span>]] shapes: faces, leaves and flowers==
(PC, Mac, Linux, uses Matlab<br>no Mathworks toolboxes needed<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])<br><br>
{| 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>


|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 ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). <br><br>The GPT-framework was used to capture an understanding of (to model) the growing leaf (Kuchen et al 2012) and Snapdragon flower [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]. The Snapdragon model was validated by comparing the results with other mutant and transgenic flowers [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000538 Cui et al 2010.]<br><br>The icon shows an asymmetrical outgrowth. Conceptually, it is specifed by two independent patterns under genetic control: a pattern of growth and a pattern of organisers. The outgrowth arises from a region of extra overall growth. Growth is aligned along axes set by two interacting systems. Organisers at the ends of the mesh create a lengthwise gradient. This gradient interacts with the second due to an organiser that generates polariser in a region that becomes the tip of the outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011])
=<span style="color:Navy;">Algorithms=
|}


----
----
{| border="0" width=100% style="background-color:#000000;"
==[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"|
|align="center"|
[[Image:Cs0prxz0.png|32x32px]]
[[Image:Cameraman_iso_topview.jpg|300px|AAMToolbox]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Cameraman_iso_tree.jpg|300px|AAMToolbox]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:Cs0prxz0.png|32x32px]]
[[Image:GL2_GUS.png|32x32px]]
[[Image:Leaf_trichomes.png|32x32px]]
[[Image:Leaf5.png|32x32px]]
[[Image:LFY_GUS_Arabidopsis_inflorescence_512.png|32x32px]]
[[Image:OleosinSeed.png|32x32px]]
[[Image:OPT_Leaf_copy.png|32x32px]]
[[Image:Seedling_copy.png|32x32px]]
[[Image:Senecio_floret_copy.png|32x32px]]
[[Image:Snapdragon_Peloric_mutant.png|32x32px]]
[[Image:Tissue.png|32x32px]]
[[Image:Z9r3j2yx.png|32x32px]]
[[Image:Zeds48ci.png|32x32px]]
[[Image:1896_wh_txr_light.png|32x32px]]
[[Image:Ara_flower.png|32x32px]]
[[Image:Arableaf_ath8_OPT.png|32x32px]]
[[Image:Arableaf_young_ath8_OPT.png|32x32px]]
[[Image:Enhby820.png|32x32px]]
|}
==<span style="color:DarkGreen;">VolViewer==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring biological images. <br><br>
[[VolViewer#Description|'''What? How? Where?''']]<br><br>
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]]<br><br>
[[VolViewer#Download| '''''Download''''']]<br><br>
(Windows, Mac, Linux)<br><br>
Output from VolViewer has appeared in:<br>
[http://www.amazon.co.uk/Handbook-Plant-Science-Keith-Roberts/dp/0470057238/ref=sr_1_19?s=books&ie=UTF8&qid=1289321357&sr=1-19 Front cover: Handbook of Plant Science] | [http://www.plantcell.org/content/18/9.toc Front cover: The Plant Cell] | [http://www.rms.org.uk/Resources/Royal%20Microscopical%20Society/infocus/Edgar%20article.pdf  Royal Microscopical Society: Infocus Magazine] | [http://www.bioptonics.com/Home.htm Bundled with the Bioptonic 3001 scanner: Bioptonics Viewer] | [http://www.guardian.co.uk/science/gallery/2007/sep/04/fruitflybrain#/?picture=330675671&index=1 The Guardian newspaper: 3D Fruit fly] | [http://qt.nokia.com/qt-in-use/ambassadors/project?id=a0F20000006LZ2pEAG Qt Ambassador program] | [http://www.triffidnurseries.co.uk/special3.php Triffid Nurseries website]
<br><br>
|width="50%"|  VolViewer uses [http://www.opengl.org/ OpenGL] and [http://qt.nokia.com/products/ Qt] to provide a user friendly application to interactively explore and quantify multi-dimensional biological images. It has been successfully used in our lab to explore and quantify confocal microscopy and  optical projection tomography images. It is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]).
|}
|}


[[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]


==<span style="color:DarkGreen;">AAMToolbox==
[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>]
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>AAMToolbox_logo.jpg|120px|AAMToolbox</imgicon>
|width="40%"|For analysing populations of shapes and colours within the shapes using principal component analysis. <br><br>
[[AAMToolbox Details|'''What? How? Where?''']]<br><br>
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]]<br><br>


[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/ShapeModelToolbox.zip <span style="color: Gray">'''''Download''''' </span>]<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>]


(PC, Mac, Linux, uses Matlab<br>no Mathworks toolboxes needed<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])<br><br>
==[[Software#Reaction-diffusion and morphogenesis| <span style="color:Navy;"> '''Reaction-diffusion'''</span>]] <span style="color:Navy;">and morphogenesis - the growth of shapes==
|width="50%"| The AAMToolbox enables the user analyse the shape and colour of collections of similar objects. Originally developed to analyse face shapes for lipreading, we have used it extensively for analysing the shapes of leaves and petals. The analysis can be applied to art, for example, finding systematic differences between portraits by, for example, Rembrandt and Modigliani.
{| 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 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"