BanghamLab - User contributions [en]

Software

2017-07-14T13:36:40Z

PaulSoutham: /* We developed GFtbox to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form. */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_CurrentBiology_Rebocho_2017/GPT_Antirrhinum_CUP.zip '''''Antirrhinum CUP''''' Rebocho et al 2017] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/PinPoint.zip '''''Download''''' ] 
Sample Project
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2017-07-14T13:35:06Z

PaulSoutham: /* We developed GFtbox to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form. */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2017/GPT_Antirrhinum_CUP.zip '''''Antirrhinum CUP''''' Rebocho et al 2017] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/PinPoint.zip '''''Download''''' ] 
Sample Project
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T15:49:56Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/PinPoint.zip '''''Download''''' ] 
Sample Project
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:45:01Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| Download Tool.
Sample Project
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:43:35Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| Download.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:43:23Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| .
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:43:08Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|Tool for analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:38:13Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"|[[File:PinPoint.jpg]]
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:37:57Z

PaulSoutham: /* Tools and Utilities */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>PinPoint.jpg|100px</imgicon>
[[File:PinPoint.jpg]]
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:37:26Z

PaulSoutham: /* Tools and Utilities */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>PinPoint.jpg|100px|</imgicon>
[[File:PinPoint.jpg]]
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:36:39Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| [[File:PinPoint.jpg]]
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

File:PinPoint.jpg

2016-12-13T14:36:00Z

PaulSoutham:

Software

2016-12-13T14:35:27Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| [[File:Example.jpg]]
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:31:55Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>PinPoint.png|100px|/imgicon>
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:31:30Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>PinPoint.png|100px|BioformatsConverter</imgicon>
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:28:04Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For analysing PIN Signal in cells.

|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:27:49Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For analysing PIN Signal in cells.
(Windows, Mac, Linux)
|width="50%"| This tool does something.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:26:55Z

PaulSoutham: /* PIN Point */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-12-13T14:25:43Z

PaulSoutham: /* Tools and Utilities */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

==PIN Point==

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-11-22T10:11:08Z

PaulSoutham: /* We developed GFtbox to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form. */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Elife_Rebocho_2016/GPT_TissueConflicts.zip '''''Tissue Conflicts''''' Rebocho et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-09-13T13:56:22Z

PaulSoutham: /* We developed GFtbox to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form. */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/GPT_HoodedBarleyWingModels.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

Software

2016-09-12T13:55:37Z

PaulSoutham: /* We developed GFtbox to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form. */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]
 Matlab tip: searching a large data structure for a particular field. Clear the command window. Evaluate the structure to list all the fields, then use the usual control-f search tool on the command window.

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
====We developed ''GFtbox'' to allow us to model the growth of complex shapes with the ultimate goal: to understand the relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PlantCell_Richardson_2016/Barley.zip '''''Barley''''' Richardson et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Dev_Eldridge_2016/Fruit_Shape_Brassicaceae.zip '''''Fruits''''' Eldridge et al 2016] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|width="50%"| ''GFtbox'' is an implementation of the Growing Polarised Tissue Framework (GPT-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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

The key point is how '''outgrowths can be specified by genes'''. 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 putative organisers that generate polariser sinks in the region that becomes the tips of the palette outgrowth. ([http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002071 Kennaway et al 2011]). These hypotheses need to be tested in biological systems.
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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. Written by Jerome Avondo it is open-source and is also compatible with the Open Microscopy Environment ([http://openmicroscopy.org/site OME]) (Chris Allen and Avondo, et. al. ''OMERO: flexible, model-driven data management for experimental biology'' Nature Methods 9, 245–253 (2012)) [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
[[Comparison of Matlab MSER's and 'o' sieve|Comparison of Matlab MSER's and 'o' sieve]] Essentially, no difference.
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

===Finding interest points, features and segmenting images. ===
#[[MSER and Sieve Details|'''Technical briefing''']] MSER's incorporate 'o' sieves.
#[[MSER's and Connected sets|'''The twist''': from restricted median filters to sieves and MSER's]]
#One dimensional sieves (measure length)
##[[Types of 1D sieve|Types of 1D sieve]]
##[[First applied to hydrophobicity plots|First applied to hydrophobicity plots]] but lets exploit their idempotency.
#Two dimensional sieves (measure areas)
##Properties
##Relation to MSER's
#Three dimensional sieves (measure volumes)
##[[Segment by volume|Segment by volume]] instant gratification.




===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster, and ArtMaster itself was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help visitors create 'paintings' from photographs. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.) 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
=====PhotoArtMaster=====
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph [http://www.bbc.co.uk/programmes/galleries/p020hd8s Mists and Reflections] had been Photoshopped replied something like 
"A digital camera delivers an unemotional ''raw'' image of pixels that you have to manipulate to ''create your photograph''" Photographers manipulate as little as possible. 
However there is '''another path one that creates pictures'''. For this you need another piece of software: PhotoArtMaster (ArtMaster). Professional Photographer said ''"'''Forget any comparison whatsoever with the art filters in Photoshop - this software reaches out and enters different stratospheres'''"'' [[Professional Photographer]]. 
Early versions of PhotoArtMaster are still '''available from Amazon''' at low prices (I'm not sure where they come from.)
[http://www.amazon.co.uk/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=photoartmaster] . Some help for both the early versions and the latest version can be found in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this document''''' ]).
=====Links to third party PhotoArtMastered pictures=====
*[https://picasaweb.google.com/113257474829608374943/InTheStyleOf Oliver Bangham] Colouful rounded shapes from, yes, my brother.
*[http://en.wikipedia.org/wiki/Wimbledon_%28film%29 The entry sequence of the comedy film 'Wimbledon']

====The final version of the Windows ArtMaster2.0 [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSource_ArtMaster/ArtMaster2.0Release.zip '''''is downloadable here'''''] with no support.====
Unzip into (for example) the "Program Files" directory then set your system environment to include: ''C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin;'' (You may need help for this. I right clicked 'computer' from the 'Start' menu, then selected 'Advanced system settings', then 'Environment Variables' and finally slid through the System variables until I found and selected 'Path'. This allowed me to edit the path by adding ';C:\Program Files\Pam2.0 Release\jre\bin;C:\Program Files\Pam2.0 Release\bin' to the end). Rather detailed help using the software is available in [http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''this essay''''' ]. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] are described in an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]. These documents were written to support our Fo2Pix company. PhotoArtMaster originally sold >65,000 licences but ill health forced the closure of Fo2Pix.

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===

=Open source systems to which we have contributed=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}
=Historical=
==Robot arm: still in production after 30 years (serving local industry)==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"|[[Image:2014-06-10 14.22.20 small robot.jpg|400px|]]
|width="40%"|For teaching '''production control''' and '''interrupt programming'''. 
1983 and we are in a world of '''Apple II and BBC B computers''' - the ''6502'' processor reigns. Particularly good for real-time control it responded very fast to hardware interrupts from, for example, the timer. To illustrate timer interrupts what better than digital servo-motors? Set up the on-board timers to produce a stream of 'heartbeat' of pulses, one every 20 ms out of the parallel port and control up to eight motors. Pulse widths, from 1 to 2 ms, control the position of each motor arm. Derek Fulton and I made some loose lab. money by writing a series of articles showing exactly how to build and, in particular, control this robot arm.[[Publications#.28G.29_Computer_control.2C_measurement_and_commercial_software |Bangham et al.]].
Our copyright, I took it to a local company LJ-Electronics ([http://www.ljcreate.com/products/product.asp?id=314&program=195&curr=2 now LJ-Creative]) who incorporated it detail for detail into their product line. Originally, they called it the Emu. Still in production: '''Lovely outcome.'''
|}

=Historical=

MyDepFun

2014-02-06T11:59:43Z

PaulSoutham: Created page with ">> help myDepFun Dep_List=myDepFun(name,toolbox) Tool for recursively finding what further functions a function depends on. myDepFun then creates a subdirectory of th..."

>> help myDepFun
Dep_List=myDepFun(name,toolbox)

Tool for recursively finding what further functions a function depends on.
myDepFun then creates a subdirectory of the 'toolbox' directory and copies
all the 'external' functions that it finds into that directory.
It also puts a copy of the full results (.mat file) into that subdirectory.

WARNING: if the function depends on classfiles (in a directory with a name beginning with @)
then please create a subdirectory within the directory 'toolbox' with the following form
'NAME_Dependencies_outside_TOOLBOX' and copy the classfile directories and contents directly
into this new directory, e.g.
AAMToolbox_Dependencies_outside_ShapeModelToolbox

(This is because 'depfun' does not recognise classfile types.)

name, name of function m file inside a toolbox (without the suffix)
toolbox, path and name of the toolbox in which the function resides and which would normally
be expected to contain all the functions needed. Functions outside the toolbox
are 'external' tools
all, default false and the final list excludes functions in the toolbox,
if true then all functions are listed and external files are not copied into a local directory
Dep_List, a list of all the external tools with their DArT_Toolshed paths

Usage
list=myDepFun('AAMToolbox','C:\DArT_Toolshed\Toolboxes\ShapeModelToolbox')

WARNING
at present this does not check each filename to see whether there is an associated
compiled version, i.e. dll, mexx64 etc.
To add a check would be straightforward if there is always an associated .m file

J. Andrew Bangham, 2012

Software

2014-02-06T11:59:27Z

PaulSoutham: /* Tools and Utilities */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
===='''''The first challenge for'' '''GFtbox.''''' To model the growth of a complex, and therefore challenging, shape to test ''GFtbox'' to the limit as we explored the possible relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

Key is how '''outgrowths can be specified by genes'''. 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])
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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] [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

====For finding features in and segmenting images. ====
[[MSER and Sieve Details|'''What? How? Where?''']] 
[[MSER's and Connected sets|'''''Tutorials''''': from the beginning]] 





===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help users create 'paintings'. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] (an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]). These documents were written to support our Fo2Pix company. A Windows version of the software will soon be downloadable from here for free (originally it sold >65,000 licences but Fo2Pix had to be closed primarily due to ill health.)

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0004.flv|GPT_rd_rk_tentacles_20120417-0004_First.png</wikiflv> A simple reaction-diffusion system develops a pattern of spots.
|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0001.flv|GPT_rd_rk_tentacles_20120417-0004.png</wikiflv>
 Two simple growth rules translate the pattern into directed growth. The changing geometry that arises through growth causes the reaction-diffusion patterning to continue to change.
|}

=Open source systems to which we contribute=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on. See [[myDepFun|''Details'']]

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

Software

2014-02-06T11:58:36Z

PaulSoutham: /* Dependency Checking Tool */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
===='''''The first challenge for'' '''GFtbox.''''' To model the growth of a complex, and therefore challenging, shape to test ''GFtbox'' to the limit as we explored the possible relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

Key is how '''outgrowths can be specified by genes'''. 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])
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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] [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

====For finding features in and segmenting images. ====
[[MSER and Sieve Details|'''What? How? Where?''']] 
[[MSER's and Connected sets|'''''Tutorials''''': from the beginning]] 





===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help users create 'paintings'. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] (an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]). These documents were written to support our Fo2Pix company. A Windows version of the software will soon be downloadable from here for free (originally it sold >65,000 licences but Fo2Pix had to be closed primarily due to ill health.)

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0004.flv|GPT_rd_rk_tentacles_20120417-0004_First.png</wikiflv> A simple reaction-diffusion system develops a pattern of spots.
|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0001.flv|GPT_rd_rk_tentacles_20120417-0004.png</wikiflv>
 Two simple growth rules translate the pattern into directed growth. The changing geometry that arises through growth causes the reaction-diffusion patterning to continue to change.
|}

=Open source systems to which we contribute=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

Tool for recursively finding what further functions a function depends on

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

Software

2014-02-06T11:57:53Z

PaulSoutham: /* Tools and Utilities */

__TOC__


'''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.

===Notes on documenting our software===

[[Tricks for documenting software|Notes for Lab members on how to contribute to this Wiki and where to put downloads. ]]

='''Computational biology'''=
==Quantitative understanding of growing shapes: '''GFtbox'''==
===='''''The first challenge for'' '''GFtbox.''''' To model the growth of a complex, and therefore challenging, shape to test ''GFtbox'' to the limit as we explored the possible relationships between genes, growth and form.====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="400"| [[Image:Journal.pbio.1000537.g009.png|350px|Growth of a flower]] Example of a growing snapdragon flower and some mutants ( [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000537 Green et al 2011]). Growth is specified by factors (genes) according to the Growing Polarised Tissue Framework. Colours represent putative gene activity, arrows the polariser gradient and spots clones.
|<wikiflv width="300" height="313" logo="false" loop="true" background="white" position="right" autoplay='true'>GPT_Snapdragon_2010_Green_et_al-0002_1.flv|GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>

|}

{| 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. 

[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 

[[Ready Reference Manual ancillary functions|'''''Ready Reference'for ancillary functions: in '''interaction function''' and external functions'''' Manual]] 

[[GFtbox|'''What? How? Where?''']] Background 
[[GFtbox Tutorial pages|'''''Tutorials''''': from the beginning]] Start here 
[[GFtbox Example pages|'''''Examples''''': from publications]] 

[https://sourceforge.net/p/gftbox/ '''''Download GFTbox''''' from SourceForge] 
'''''Download GFTbox project files:''''' 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_SauretGueto_2013/GPT_Petal_PLoS_20130502.zip '''''Petals''''' Sauret-Güeto et al 2013] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/GPT_ArabidopsisLeafModel_20120207.zip '''''Leaves''''' Kuchen et al 2012] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Kennaway_2011/Kennaway-etal-2011.zip '''''Principles and concepts''''' Kennaway et al 2011] 

[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_PLoS_Green_2011/Green-etal-2010.zip '''''Snapdragon''''' Green et al 2011, Cui et al 2010] 

|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]). 

The GPT-framework was used to capture an understanding of (to model) the growing petal ([http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001550 Sauret-Güeto et al 2013]), leaf ([http://www.sciencemag.org/content/335/6072/1092.abstract 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.] 

Key is how '''outgrowths can be specified by genes'''. 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])
|}

==Viewing and measuring volume images: '''VolViewer'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>VolViewer-logo.png|120px|VolViewer</imgicon>
|width="40%"|For viewing and measuring '''volume images''' on both normal and '''stereo''' screens. Typical images from: confocal microscope and Optical Projection Tomography (OPT) images 
[[VolViewer#Description|'''What? How? Where?''']] 
[[VolViewer#User Documentation|'''''Tutorials''''': from the beginning]] 
[[VolViewer#Download| '''''Download''''']] 
(Windows, Mac, Linux) 
Output from VolViewer has appeared in: 

[http://www.cell.com/cell_picture_show-plantbio Cell: Online Gallery] | [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.americanscientist.org/issues/pub/2013/1/3d-carnivorous-plants American Scientist] | [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.dailymail.co.uk/sciencetech/article-2215052/The-complexity-intricacy-Mother-Nature-revealed-incredible-pictures-plants--seen-inside.html The Daily Mail] | [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]

 
|width="50%"| VolViewer is used as a '''stand-alone''' app. or as a '''viewport for other systems''', e.g. Matlab programs. 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] [[image:Silique.PNG|360px]]).
|}

==Analysing shapes in 2D and 3D: '''AAMToolbox'''==
{| 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. 
[[AAMToolbox Details|'''What? How? Where?''']] 
[[Tutorials on the Shape modelling toolbox|'''''Tutorials''''': from the beginning]] 

[[AAMToolbox Download|'''''Download revised Nov2012''''' ]] 

(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|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 ([http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=982900 Matthews ''et al''. 2002][http://www2.cmp.uea.ac.uk/~sjc/matthews-pami-01.pdf version of pdf]), we have used it extensively for analysing the shapes of leaves ([http://www.pnas.org/content/102/29/10221.short Langlade ''et al'' 2005.],[http://www.tandfonline.com/doi/abs/10.2976/1.2836738 Bensmihen ''et al.'' 2010]) and petals ([http://www.sciencemag.org/content/313/5789/963.short Whibley ''et al'' 2006],[http://www.mssaleshops.info/content/21/10/2999.short Feng ''et al''. 2010]). The analysis can be applied to art, for example, finding systematic differences between portraits by Rembrandt and Modigliani.
|}
==Analysing the shapes of clones: '''SectorAnalysisToolbox'''==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>Sector analysis icon.jpg|120px|SectorAnalysisToolbox</imgicon>
|width="40%"|For analysing the shapes of marked cell clones. 
[[SectorAnalysisToolbox Details|'''What? How? Where?''']] 
[[SectorAnalysisToolbox Documentation|'''''Tutorials''''': from the beginning]] 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/OpenSourceDownload_Science_Paper_2012/SectorAnalysisToolbox.zip '''''Download''''' ] 
(PC, Mac, Linux, uses Matlab no Mathworks toolboxes needed [http://www.mathworks.com/products/matlab/tryit.html Matlab 30 day free trial] and [http://www.mathworks.com/academia/student_version/?s_cid=global_nav student edition]) 
|width="50%"| The SectorAnalysisToolbox enables the user analyse the shapes of marked clones in a sheet of tissue.
|}

='''Algorithms'''=
==MSERs, extrema, connected-set filters and sieves==
====The algorithm finding MSER's starts with a connected-set opening or 'o' sieve====
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="50%"| [[Image:Cameraman_iso_topview.jpg|300px|link=AAMToolbox Details|MSERs]] 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.
|[[Image:cameraman_iso_tree.jpg|300px|link=AAMToolbox Details|MSERs over scale-space]] Isometric view of the cameraman image with superimposed maxima (red) and minima (blue). The trees trace the maxima through increasing scale-space. Large spots have been identified as stable extrema.
|}

====For finding features in and segmenting images. ====
[[MSER and Sieve Details|'''What? How? Where?''']] 
[[MSER's and Connected sets|'''''Tutorials''''': from the beginning]] 





===Art, extrema of light and shade: '''''PhotoArtMaster'''''===

Art created using ArtMaster was featured in an exhibit at the London Victoria and Albert (V&A) Museum exhibition 'Cheating? How to make Perfect Work of Art' (2003). The exhibition centered on the idea of [http://en.wikipedia.org/wiki/Hockney%E2%80%93Falco_thesis Hockney's] that advances in realism and accuracy in the history of Western art since the Renaissance were primarily the result of optical aids such as the camera obscura, camera lucida, and curved mirrors. My exhibit used a touch screen (rare in those days) and ArtMaster to help users create 'paintings'. [http://www.sciencemuseum.org.uk/visitmuseum/galleries/turing.aspx finding its name]. 

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:DegasLightAndShade.jpg|400px]][[Image:Emma_face_Art_C.jpg|300px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of light and shade crisply segmented from a photograph. Likewise, on the right, edges.
|}
 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/Art_For_All_a4a_3_web2.pdf '''''The sieve algorithms underpinning PhotoArtMaster software''''' ] (an extract of the
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/SieveWebPages/a4a_2_screensize.pdf ''''essay''''' ]). These documents were written to support our Fo2Pix company. A Windows version of the software will soon be downloadable from here for free (originally it sold >65,000 licences but Fo2Pix had to be closed primarily due to ill health.)

{| border="0" width=100% style="background-color:#ffffff;"
|-
|align="center"|[[Image:Trees_1.jpg|600px]]
 
Illustration of PhotoArtMaster used to find and 'paint' with regions of colour crisply segmented from a photograph.
|}



==Reaction-diffusion and morphogenesis==
{| border="0" width=100% style="background-color:#000000;"
|-
|align="center"|
[[Image:tentacles_morphogenesis.png|600px]]
|}
Illustration of morphogenesis inspired by Turing's paper. 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/software/GPT_ReactionDiffusionTentacles_20121211.zip Example using growth toolbox GPT_ReactionDiffusionTentacles_20121211.zip]
 
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0004.flv|GPT_rd_rk_tentacles_20120417-0004_First.png</wikiflv> A simple reaction-diffusion system develops a pattern of spots.
|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_rd_rk_tentacles_20120417-0001.flv|GPT_rd_rk_tentacles_20120417-0004.png</wikiflv>
 Two simple growth rules translate the pattern into directed growth. The changing geometry that arises through growth causes the reaction-diffusion patterning to continue to change.
|}

=Open source systems to which we contribute=
==OMERO==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>OMERO_DIAGRAM.jpg|100px|OMERO</imgicon>
|width="40%"|For working with the OME image database. See [http://www.openmicroscopy.org/site/products/omero ''Details''], [http://www.openmicroscopy.org/site/support/omero4/downloads ''Download''] [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] 
(Windows, Mac, Linux)
|width="50%"| [http://openmicroscopy.org/site/support/omero4 Open Microscopy Environment Remote Objects (OMERO).] for visualising, managing, and annotating scientific image data. See also our [http://dmbi.nbi.bbsrc.ac.uk/index.php/OMEROWorkshop OMERO Workshop] training course we ran in April 2011.
|}

=Tools and Utilities=
==BioformatsConverter==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>BioformatsConverterZip.png|100px|BioformatsConverter</imgicon>
|width="40%"|For converting microscope manufacturer proprietary file formats. See [[BioformatsConverter|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| This tool allows for the batch conversion of microscope manufacturer proprietary file formats, to the open source OME-TIFF standard. Uses the [http://www.loci.wisc.edu/software/bio-formats Bioformats] library.
|}
==Dependency Checking Tool==

=In development=
==MTtbox==
{| border="0" cellpadding="5" cellspacing="5"
|- valign="top"
|width="10%"| <imgicon>MTtboxA.jpg|100px|BioformatsConverter</imgicon>
|width="40%"|For modelling the behaviour of microtubules within a cell. 
See [[MTtbox documentation|''Details'']] 
(Windows, Mac, Linux)
|width="50%"| In development. The idea is to be able to model the behaviour of growing microtubules and factors as they react chemically and diffuse within the different cell compartments. 
The icon shows a spherical cell sliced open to show concentric components: cell wall (magenta), plasma-membrane (yellow), cytoplasm (green) and vacuole (yellow). Microtubules (blue) grow in 3D within the cytoplasm.
|}

Tutorial on mapping results into shape space

2013-01-14T11:26:25Z

PaulSoutham:

[[GFtbox Tutorial pages#4 Comparing resultant shapes with observed organ shapes|Return to GFtbox Tutorial pages]] 

Shape space for a growing leaf is computed from a set of labelled leaf outlines - see AAMToolbox. Each outline is captured by a set of landmarks placed around the leaf. To project the output from the GFtbox into a shape space requires landmarks to be placed around the model leaf at corresponding position. In the case of leaves there is a GFtbox function

leaf_profile_monitor

which is tailored to the Arabidopsis leaf. It could be adapted to suit other shapes.

>> help leaf_profile_monitor
function m=leaf_profile_monitor(m,realtime,RegionLabels,Morphogens,start_figno)
monitor morphogen levels at a set of vertices

m, mesh
RegionLabels, vertices to be monitored as designated by cell array of strings, i.e. region labels
Morphogens, cell array of strings, i.e. uppercase morphogen names to
be monitored. There should be one RegionLabels string for each
Morphogens string
Vertlabels, if true then display vertex numbers in each regionlabel on
the mesh default false
start_figno, default figure 1 (Must open a fig even if just monitoring to file)

e.g.
monitor properties of vertices
m=leaf_profile_monitor(m,... % essential
'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential
'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional (one element per REGIONLABEL)
'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')

leaf_profile_monitor is called from the Gftbox interaction function. It writes a DataXXX.mat file, where XXX corresponds to the model step time stamp, to the project directory in ./snapshots.

We now need to convert these DataXXX.mat files into the format read by the AAMToolbox. The function that converts our growing leaf shapes is

kparKperModel

which like leaf_profile_monitor is tailored to the Arabidopsis leaf and the AAMToolbox Arabidopsis leaf template but could be adapted to other shapes.

[tempprojectpath, aamModelType] = fileparts(Cwd);
projectname='GPT_leafFromBullet_20121017';
%projectpath='D:\ab\Matlab stuff';
projectpath='K:\Paul\Karen\growthModels';
[FileName,PathNameA] = uigetfile(fullfile('..','*.m'),...
'Select GFtbox project interaction function m file',fullfile(projectpath,projectname,[lower(projectname),'.m'])) ;

kparKperModel requires three inputs, 1) The Gftbox project name, 2) The AAMToolbox project location and 3) the location of the Gftbox interaction function. This function should write xxx_pm.mat files into the ./pointmodels directory in the AAMToolbox project. These xxx_pm.mat files can be added to an exisiting AAMToolbox project or used to create a new project.

==Example==
Based on the GFtbox project ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???''

Tutorial on mapping results into shape space

2013-01-14T11:25:08Z

PaulSoutham:

[[GFtbox Tutorial pages#4 Comparing resultant shapes with observed organ shapes|Return to GFtbox Tutorial pages]] 

Shape space for a growing leaf is computed from a set of labelled leaf outlines - see AAMToolbox. Each outline is captured by a set of landmarks placed around the leaf. To project the output from the GFtbox into a shape space requires landmarks to be placed around the model leaf at corresponding position. In the case of leaves there is a GFtbox function

leaf_profile_monitor

which is tailored to the Arabidopsis leaf. It could be adapted to suit other shapes.

>> help leaf_profile_monitor
function m=leaf_profile_monitor(m,realtime,RegionLabels,Morphogens,start_figno)
monitor morphogen levels at a set of vertices

m, mesh
RegionLabels, vertices to be monitored as designated by cell array of strings, i.e. region labels
Morphogens, cell array of strings, i.e. uppercase morphogen names to
be monitored. There should be one RegionLabels string for each
Morphogens string
Vertlabels, if true then display vertex numbers in each regionlabel on
the mesh default false
start_figno, default figure 1 (Must open a fig even if just monitoring to file)

e.g.
monitor properties of vertices
m=leaf_profile_monitor(m,... % essential
'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential
'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional (one element per REGIONLABEL)
'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')

leaf_profile_monitor is called from the Gftbox interaction function. It writes a DataXXX.mat file, where XXX corresponds to the model step time stamp, to the project directory in ./snapshots.

We now need to convert these DataXXX.mat files into the format read by the AAMToolbox. The function that converts our growing leaf shapes is

kparKperModel

which like leaf_profile_monitor is tailored to the Arabidopsis leaf and the AAMToolbox Arabidopsis leaf template but could be adapted to other shapes.

[tempprojectpath, aamModelType] = fileparts(Cwd);
projectname='GPT_leafFromBullet_20121017';
%projectpath='D:\ab\Matlab stuff';
projectpath='K:\Paul\Karen\growthModels';
[FileName,PathNameA] = uigetfile(fullfile('..','*.m'),...
'Select GFtbox project interaction function m file',fullfile(projectpath,projectname,[lower(projectname),'.m'])) ;

kparKperModel requires three inputs, 1) The Gftbox project name, 2) The AAMToolbox project location and 3) the location of the Gftbox interaction function. This function should write xxx_pm.mat files into the ./pointmodels directory in the AAMToolbox project.

==Example==
Based on the GFtbox project ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???''

Tutorial on mapping results into shape space

2013-01-14T11:19:48Z

PaulSoutham:

[[GFtbox Tutorial pages#4 Comparing resultant shapes with observed organ shapes|Return to GFtbox Tutorial pages]] 

Shape space for a growing leaf is computed from a set of labelled leaf outlines - see AAMToolbox. Each outline is captured by a set of landmarks placed around the leaf. To project the output from the GFtbox into a shape space requires landmarks to be placed around the model leaf at corresponding position. In the case of leaves there is a GFtbox function

leaf_profile_monitor

which is tailored to the Arabidopsis leaf. It could be adapted to suit other shapes.

>> help leaf_profile_monitor
function m=leaf_profile_monitor(m,realtime,RegionLabels,Morphogens,start_figno)
monitor morphogen levels at a set of vertices

m, mesh
RegionLabels, vertices to be monitored as designated by cell array of strings, i.e. region labels
Morphogens, cell array of strings, i.e. uppercase morphogen names to
be monitored. There should be one RegionLabels string for each
Morphogens string
Vertlabels, if true then display vertex numbers in each regionlabel on
the mesh default false
start_figno, default figure 1 (Must open a fig even if just monitoring to file)

e.g.
monitor properties of vertices
m=leaf_profile_monitor(m,... % essential
'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential
'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional (one element per REGIONLABEL)
'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')

leaf_profile_monitor is called from the Gftbox interaction function. It writes a DataXXX.mat file, where XXX corresponds to the model step time stamp, to the project directory in ./snapshots.

We now need to convert these DataXXX.mat files into the format read by the AAMToolbox. The function that converts our growing leaf shapes is

kparKperModel

==Example==
Based on the GFtbox project ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???''

Tutorial on mapping results into shape space

2013-01-14T11:08:54Z

PaulSoutham:

Tutorial on mapping results into shape space

2013-01-14T11:06:16Z

PaulSoutham:

GFtbox Tutorial pages

2013-01-14T11:04:00Z

PaulSoutham:

[[GFtbox|''GFtbox'' Details]] 
[[Notes from a new user|Notes from a new user]] 
[[Running example models and using a cluster|Running example models and using a cluster]] 
[[GFtbox Example pages|Examples from our papers]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]] 
([[Full freshly minted interaction function|A newly created interaction function is shown here - the green comments are another ready reference.]]) 
[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 

__NOTOC__
The models shown in these tutorials illustrate features of the GFtbox software. They are not designed to understand the Growing Polarised Tissue Framework which is better done with [[GFtbox Example pages|Examples from our papers]]. 
Viewing these pages. Some versions of ''Firefox'' and ''Explorer'' do not create satisfactory prints even though you can view the pages with no problems. ''Chrome'' does appear to produce good printouts.
=Three ways to use ''GFtbox''=
1) [[GFtbox Tutorial pages#1 Modelling using the Graphical User Interface| '''Do everything from the Graphical User Interface (GUI).''']] 
2) [[GFtbox Tutorial pages#2 Modelling using a combination of GUI and interaction function|'''Do only some things from the GUI.''']] Use the GUI to generate the mesh (canvas) and create growth factors, but capturing your ideas on how the regulatory processes work by writing Matlab code in what we call the interaction function. 
3) [[GFtbox Tutorial pages#3 Running models without the GUI|'''Without the GUI.''']] For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We use this extensively once we have roughed out the basic ideas of a model interactively.
=Hints and Tips=
#[[Ready Reference Manual|Ready Reference Manual]] worth printing it includes details on taking snapshots and movies (and solving problems)
#[[Ready Reference Manual#Snapshots|Multiple Figures for publication]] '''colours and viewpoints.'''
#[[Ready Reference Manual#Movies|Movies for publication and web]] '''codecs compression and Powerpoint.'''
#'''Quality and accuracy'''
##[[Mesh: tradeoff |Mesh: tradeoff]] between memory/speed and accuracy. '''Increasing the number of vertices in specific regions'''
##[[Time: tradeoff|Time: tradeoff]] between speed and accuracy. '''Checking that time steps are small enough'''.
##[[Tolerances: tradeoff|Tolerances: tradeoff]] between speed and accuracy. '''Checking that tolerances are tight enough.'''
#Measuring model growth
##[[Measuring using interaction function subroutines| '''Measuring''' using interaction function subroutines]]
#[[DemoCutting intraction function|Mesh: cutting and flattening]] '''Dissecting a mesh and flattening the parts'''
='''1''' Modelling using the Graphical User Interface=
== Isotropic growth==
'''How to use the tutorial.''' Open GFtbox and attempt to repeat the results shown.
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Uniform|Tutorial on uniform growth.]] Consider a disc shaped canvas (tissue) in which the '''specified growth is uniform''', isotropic and on both sides. '''Into what shape will the disc grow?''' This model is as simple as it gets. Notice that, during growth, the mesh is automatically subdivided. Notice also that the final surface is not quite flat. This is because, to allow it to deform in 3D, it is not flat initially. There are options to initialise a flat mesh and others to force it to remain flat - see options on the GUI (hover over controls to get prompts). 
In the absence of a polariser (there is no polariser in this example) growth will be isotropic, in other words growth in the plane of the canvas will be the average of what is specified for ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0003.flv|GPT_tut_uniform_20110527-0003_Last.png</wikiflv>
|}
===1 B===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning non-uniform|Tutorial on non-uniform growth.]] Consider a disc shaped canvas (tissue) in which the''' non-uniform specified growth''' increases in proportion to the distance from the centre. '''Into what shape will the disc grow?''' Already we are into the realms of modelling biological systems. Compare this result with the discussion of Lily petals and Gaussian curvature ([http://www.pnas.org/content/early/2011/03/14/1007808108.abstract Lianga and Mahadevana],[http://www.americanscientist.org/issues/feature/leaves-flowers-and-garbage-bags-making-waves Sharon, Marder and Swinney],[http://rico-coen.jic.ac.uk/uploads/0/0f/Nath_Science.pdf Nath, Crawford, Carpenter and Coen] ).
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0006.flv|GPT_tut_uniform_20110527-0006_First.png</wikiflv>
|}

==Adding polariser==
===1 C===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Growing a cone|Tutorial on uniform growth with non-uniform polariser.]] 
In the presence of polariser, ''GFtbox'' growth will be anisotropic, in other words growth in the plane of the canvas can be different parallel and perpendicular to the axis of the polariser: ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
We now''' add polariser'''. Start with example A - uniform growth - and add a radial polarising gradient. Arrows show the direction of the gradient. They are turned on using the Panel:Plot option:Pol. grad. tick box. The gradient defines local directions and local growth can be specifed either parallel to (''Kpar'') or perpendicular to (''Kper'') that direction. 
Given a '''uniform pattern of specified growth parallel''' to the polariser and '''zero specified growth perpendicular''' to the polariser. '''What will be the final shape?''' 
Note: the gradient of the polariser, green to cyan, is shown using the arrows. Specified growth rate parallel to the arrows, red, is uniform.

|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_in_the_beginning_2_20110510-0003.flv|GPT_in_the_beginning_2_20110510-0003_First.png</wikiflv>
|}

='''2''' Modelling using a combination of GUI and interaction function=
'''How to use these tutorials.''' Use a combination of the GUI to set up the Mesh structure and editing the associated interaction function to repeat the results shown. Full listings of the interaction functions are given from which you can copy the key, editable, elements. 
The '''full specification''' of a ''GFtbox'' model is stored in a combination of the mesh data structure ('''Mesh''') and the '''interaction function'''. The Mesh stores all the physical properties of the system: spatial structure, mechanical properties, etc. It is usually set up using the GUI. The Mesh is stored on disc as a Matlab data file (.mat) and in memory as a data structure (m). The '''interaction function''' (a Matlab program file ''.m'') contains all the details of the growth regulation system: morphogen concentrations, signal interactions etc.
 
When a new project is first edited''' the interaction function is generated automatically'''. Thereafter, it is automatically kept in synchrony with the GUI. It is divided into several sections. Some are generated automatically and should not be edited. Others are set aside for the user to specify the model. To ensure that the automatic and manual edits are synchronised '''always invoke the Editor from the GUI''' (Panel: Interaction Function: Edit).

===2 A===
'''Basic interaction function'''
The patterns of morphogens A and B are set up by 

id_a_p(m.nodes(:,1) < -0.03) = 1;
id_b_p(m.nodes(:,2) < -0.01) = 1;

where ''id_a_p'' is the A morphogen. ''m.node(:,1)'' refers to the ''x'' coordinates of all nodes (vertices) in the mesh 
The expression ''(m.nodes(:,1) < -0.03)'' means find all vertices with ''x'' coordinates that are less than -0.03. 
Similarly, ''(m.nodes(:,2) < -0.01)'' means find all vertices with ''y'' coordinates that are less than -0.01. 

And the pattern of polariser (P) is set up by 

P((m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)) = 1;
Where ''(m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)'' means find all vertices with ''x,y'' coordinates that are less than -0.05 and greater than 0.03 respectively 
Thus the full code describing the model is:
if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
id_a_p(m.nodes(:,1) < -0.03) = 1; % setup region for A where identity factor A is represented by id_a_p
id_b_p(m.nodes(:,2) < -0.01) = 1; % setup region for B
else
% @@KRN Growth Regulatory Network
kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
kaper_p(:) = kapar_p; % isotropic growth
kbpar_p(:) = kapar_p; % same on both sides of the sheet
kbper_p(:) = kapar_p; % same
knor_p(:) = 0; % thickness not growing
end
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the basic interaction function|Tutorial on a basic interaction function.]] 
The tutorial explains how the code shown above appears in the interaction function. 
To create the interaction function, first create and save a project (see above) then click Panel:Interaction function:Edit. The interaction function will contain all the default variables and any patterns of variables (''Kapar'', etc.) that have already been set through the GUI.
[[Types of morphogens and factors| Types of morphogens and factors are given here]].
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_why_matlab-2011-05-05-0005.flv|GPT_why_matlab-2011-05-05-0005_First.png‎</wikiflv>
|-align="top"
|
||<center>Play and the mesh will grow and subdivide. Normally we do not want to see the mesh. Red is growth rate</center>
|}
===2 B===
'''Interaction function in detail''' 
([[Full freshly minted interaction function|A newly created interaction function is shown here - this one has two, user specified morphogens: ''id_a'' and ''id_b''.]]) 
There are two submodels. An identical growth pattern and polariser pattern is specified in both, but only the specified growth in the second is anisotropic and so uses the axiality specified by the polariser gradient. The gradient is zero in the region where the polariser is held at a constant value of one - and therefore growth in the region without arrows is isotropic. 

{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the interaction function details|Tutorial on the interaction function details.]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]]. 
Submodel 1
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
|- valign="top"
|Submodel 2. Growth in the region that has no arrows is isotropic and, as result, the outgrowth is blunt.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0007.flv|GPT_tut_interaction_example_20110601-0006_Last.png‎</wikiflv> 
|}
===2 C Illustrating independent ways to form shapes and the use of submodels. ===
Conclusion: interesting shapes can be generated either by '''patterns of differential growth''' or''' patterns of local growth axe'''s. 
[[Tutorial on different ways of specifying the growth of shapes|Tutorial on different ways of specifying the growth of shapes.]] 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|Submodel 1. Uniform specified polariser ('''no polariser gradient'''). Creating a shape using a specified pattern of isotropic growth. 
'''Result''': simple patterns of differential growth can readily produce blobby shapes. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0001.flv|GPT_TwoWayHeart_20110531-0001_Last.png‎</wikiflv> 
<center>Play submodel 1. Pattern of isotropic specified growth (no polariser)</center>
|- valign="top"
|Submodel 2.'''Uniform specified growth'''. Creating a shape using a specified pattern of diffusable polariser. 
'''Result''': simple patterns organising a diffusable polariser can readily produce sharp shapes. 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="bottom"
|width="150pt"|[[Image:Heartdrawingtransparent.png|Heartdrawing]]
|width="150pt"| [[Image:Heartshaped.jpg|200px|Heartdrawing]] 
|}
 Outputs from these models bear only a romantic relation to hearts, flowers and lepidoptra. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0002.flv|GPT_TwoWayHeart_20110531-0002_Last.png‎</wikiflv> 
<center>Play submodel 2. Pattern of specified polariser levels (green-cyan). Polariser can diffuse and the gradient is arrowed. Uniform specified growth (red).</center>
|}
===2 D===
'''Retaining strain and cutting the mesh''' 
There are two submodels. They are the same except that in the first strain is not retained from step to step whereas in the second strain is fully retained. The shape changes during growth look similar, the difference is only revealed when the mesh is cut. The behaviour of plant tissue can be similar. 
[[Tutorial on retaining residual strain and cutting|Tutorial on retaining residual strain and cutting]]
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|
[[Image:GPT_RetainStrainAndCut_20110603-000050-0005.png|300px|none]]Strain not retained after each step. In plant tissue terms this would appear to be equivalent to there being a homeostatic mechanism that operates such as to re-strengthen the cell walls after they have been weakened to the point that they yield under turgor pressure during growth.
|width="120pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0006.flv|GPT_RetainStrainAndCut_20110603-0006.png‎</wikiflv> 
<center>Play submodel 1</center>
 
|- valign="top"
|width="200pt"| [[Image:GPT_RetainStrainAndCut_20110603-000050-0003.png|300px|none]]Retaining the strain from step to step allows the growth on the inside to force the mesh as a whole to grow more than when strain is not retained.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0004.flv|GPT_RetainStrainAndCut_20110603-0004.png‎</wikiflv>
<center>Whilst the frame rate relates directly to growth rate, the relaxation rate after cutting does not. After cutting the computation has to be done in smaller steps and the rate at which the sides bend back shown here is too slow.</center>
|}

='''3''' Cluster runs and batch mode: running models without the GUI=
Having developed the concepts underpinning a pattern of growth in an interaction function it is often desirable to explore a range of model parameters. Given that each run of the model can take between 5 minutes and hour it is appropriate to run the models in batch mode on the desktop or, better, in parallel on a computing cluster. (Each node of the cluster to be used by ''GFtbox'' needs to be licensed to run Matlab - however for the purpose of running on a cluster without the GUI we are exploring the possibility of making ''GFtbox'' compatible with [http://www.gnu.org/software/octave/ Octave].) 
'''Batch mode and cluster runs.''' 
'''How to use these tutorials.''' First ensure that your model is working as you would expect using the GUI. Then run the model from the Matlab command line. Finally, run the models in batch mode or submit the project to the linux computing cluster with one or more ranges of parameters.
For further details [[Running example models and using a cluster|Running example models and using a cluster]] 
='''4''' Comparing resultant shapes with observed organ shapes=
===4 A===
[[Tutorial on mapping results into shape space|Tutorial on mapping results into shape space]]
{| border="1" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Image:wikiModelShapespace.png|400px|none]]
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
<left>(Marks) The shape of growing ''Arabidopsis'' leaves projected into a shape space represented by the two principal components. (Lines) The shape of a computational model of a growing ''Arabidopsis'' leaf projected into the same space.</center>
|}

GFtbox Tutorial pages

2013-01-14T11:03:17Z

PaulSoutham:

[[GFtbox|''GFtbox'' Details]] 
[[Notes from a new user|Notes from a new user]] 
[[Running example models and using a cluster|Running example models and using a cluster]] 
[[GFtbox Example pages|Examples from our papers]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]] 
([[Full freshly minted interaction function|A newly created interaction function is shown here - the green comments are another ready reference.]]) 
[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 

__NOTOC__
The models shown in these tutorials illustrate features of the GFtbox software. They are not designed to understand the Growing Polarised Tissue Framework which is better done with [[GFtbox Example pages|Examples from our papers]]. 
Viewing these pages. Some versions of ''Firefox'' and ''Explorer'' do not create satisfactory prints even though you can view the pages with no problems. ''Chrome'' does appear to produce good printouts.
=Three ways to use ''GFtbox''=
1) [[GFtbox Tutorial pages#1 Modelling using the Graphical User Interface| '''Do everything from the Graphical User Interface (GUI).''']] 
2) [[GFtbox Tutorial pages#2 Modelling using a combination of GUI and interaction function|'''Do only some things from the GUI.''']] Use the GUI to generate the mesh (canvas) and create growth factors, but capturing your ideas on how the regulatory processes work by writing Matlab code in what we call the interaction function. 
3) [[GFtbox Tutorial pages#3 Running models without the GUI|'''Without the GUI.''']] For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We use this extensively once we have roughed out the basic ideas of a model interactively.
=Hints and Tips=
#[[Ready Reference Manual|Ready Reference Manual]] worth printing it includes details on taking snapshots and movies (and solving problems)
#[[Ready Reference Manual#Snapshots|Multiple Figures for publication]] '''colours and viewpoints.'''
#[[Ready Reference Manual#Movies|Movies for publication and web]] '''codecs compression and Powerpoint.'''
#'''Quality and accuracy'''
##[[Mesh: tradeoff |Mesh: tradeoff]] between memory/speed and accuracy. '''Increasing the number of vertices in specific regions'''
##[[Time: tradeoff|Time: tradeoff]] between speed and accuracy. '''Checking that time steps are small enough'''.
##[[Tolerances: tradeoff|Tolerances: tradeoff]] between speed and accuracy. '''Checking that tolerances are tight enough.'''
#Measuring model growth
##[[Measuring using interaction function subroutines| '''Measuring''' using interaction function subroutines]]
#[[DemoCutting intraction function|Mesh: cutting and flattening]] '''Dissecting a mesh and flattening the parts'''
='''1''' Modelling using the Graphical User Interface=
== Isotropic growth==
'''How to use the tutorial.''' Open GFtbox and attempt to repeat the results shown.
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Uniform|Tutorial on uniform growth.]] Consider a disc shaped canvas (tissue) in which the '''specified growth is uniform''', isotropic and on both sides. '''Into what shape will the disc grow?''' This model is as simple as it gets. Notice that, during growth, the mesh is automatically subdivided. Notice also that the final surface is not quite flat. This is because, to allow it to deform in 3D, it is not flat initially. There are options to initialise a flat mesh and others to force it to remain flat - see options on the GUI (hover over controls to get prompts). 
In the absence of a polariser (there is no polariser in this example) growth will be isotropic, in other words growth in the plane of the canvas will be the average of what is specified for ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0003.flv|GPT_tut_uniform_20110527-0003_Last.png</wikiflv>
|}
===1 B===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning non-uniform|Tutorial on non-uniform growth.]] Consider a disc shaped canvas (tissue) in which the''' non-uniform specified growth''' increases in proportion to the distance from the centre. '''Into what shape will the disc grow?''' Already we are into the realms of modelling biological systems. Compare this result with the discussion of Lily petals and Gaussian curvature ([http://www.pnas.org/content/early/2011/03/14/1007808108.abstract Lianga and Mahadevana],[http://www.americanscientist.org/issues/feature/leaves-flowers-and-garbage-bags-making-waves Sharon, Marder and Swinney],[http://rico-coen.jic.ac.uk/uploads/0/0f/Nath_Science.pdf Nath, Crawford, Carpenter and Coen] ).
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0006.flv|GPT_tut_uniform_20110527-0006_First.png</wikiflv>
|}

==Adding polariser==
===1 C===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Growing a cone|Tutorial on uniform growth with non-uniform polariser.]] 
In the presence of polariser, ''GFtbox'' growth will be anisotropic, in other words growth in the plane of the canvas can be different parallel and perpendicular to the axis of the polariser: ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
We now''' add polariser'''. Start with example A - uniform growth - and add a radial polarising gradient. Arrows show the direction of the gradient. They are turned on using the Panel:Plot option:Pol. grad. tick box. The gradient defines local directions and local growth can be specifed either parallel to (''Kpar'') or perpendicular to (''Kper'') that direction. 
Given a '''uniform pattern of specified growth parallel''' to the polariser and '''zero specified growth perpendicular''' to the polariser. '''What will be the final shape?''' 
Note: the gradient of the polariser, green to cyan, is shown using the arrows. Specified growth rate parallel to the arrows, red, is uniform.

|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_in_the_beginning_2_20110510-0003.flv|GPT_in_the_beginning_2_20110510-0003_First.png</wikiflv>
|}

='''2''' Modelling using a combination of GUI and interaction function=
'''How to use these tutorials.''' Use a combination of the GUI to set up the Mesh structure and editing the associated interaction function to repeat the results shown. Full listings of the interaction functions are given from which you can copy the key, editable, elements. 
The '''full specification''' of a ''GFtbox'' model is stored in a combination of the mesh data structure ('''Mesh''') and the '''interaction function'''. The Mesh stores all the physical properties of the system: spatial structure, mechanical properties, etc. It is usually set up using the GUI. The Mesh is stored on disc as a Matlab data file (.mat) and in memory as a data structure (m). The '''interaction function''' (a Matlab program file ''.m'') contains all the details of the growth regulation system: morphogen concentrations, signal interactions etc.
 
When a new project is first edited''' the interaction function is generated automatically'''. Thereafter, it is automatically kept in synchrony with the GUI. It is divided into several sections. Some are generated automatically and should not be edited. Others are set aside for the user to specify the model. To ensure that the automatic and manual edits are synchronised '''always invoke the Editor from the GUI''' (Panel: Interaction Function: Edit).

===2 A===
'''Basic interaction function'''
The patterns of morphogens A and B are set up by 

id_a_p(m.nodes(:,1) < -0.03) = 1;
id_b_p(m.nodes(:,2) < -0.01) = 1;

where ''id_a_p'' is the A morphogen. ''m.node(:,1)'' refers to the ''x'' coordinates of all nodes (vertices) in the mesh 
The expression ''(m.nodes(:,1) < -0.03)'' means find all vertices with ''x'' coordinates that are less than -0.03. 
Similarly, ''(m.nodes(:,2) < -0.01)'' means find all vertices with ''y'' coordinates that are less than -0.01. 

And the pattern of polariser (P) is set up by 

P((m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)) = 1;
Where ''(m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)'' means find all vertices with ''x,y'' coordinates that are less than -0.05 and greater than 0.03 respectively 
Thus the full code describing the model is:
if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
id_a_p(m.nodes(:,1) < -0.03) = 1; % setup region for A where identity factor A is represented by id_a_p
id_b_p(m.nodes(:,2) < -0.01) = 1; % setup region for B
else
% @@KRN Growth Regulatory Network
kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
kaper_p(:) = kapar_p; % isotropic growth
kbpar_p(:) = kapar_p; % same on both sides of the sheet
kbper_p(:) = kapar_p; % same
knor_p(:) = 0; % thickness not growing
end
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the basic interaction function|Tutorial on a basic interaction function.]] 
The tutorial explains how the code shown above appears in the interaction function. 
To create the interaction function, first create and save a project (see above) then click Panel:Interaction function:Edit. The interaction function will contain all the default variables and any patterns of variables (''Kapar'', etc.) that have already been set through the GUI.
[[Types of morphogens and factors| Types of morphogens and factors are given here]].
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_why_matlab-2011-05-05-0005.flv|GPT_why_matlab-2011-05-05-0005_First.png‎</wikiflv>
|-align="top"
|
||<center>Play and the mesh will grow and subdivide. Normally we do not want to see the mesh. Red is growth rate</center>
|}
===2 B===
'''Interaction function in detail''' 
([[Full freshly minted interaction function|A newly created interaction function is shown here - this one has two, user specified morphogens: ''id_a'' and ''id_b''.]]) 
There are two submodels. An identical growth pattern and polariser pattern is specified in both, but only the specified growth in the second is anisotropic and so uses the axiality specified by the polariser gradient. The gradient is zero in the region where the polariser is held at a constant value of one - and therefore growth in the region without arrows is isotropic. 

{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the interaction function details|Tutorial on the interaction function details.]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]]. 
Submodel 1
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
|- valign="top"
|Submodel 2. Growth in the region that has no arrows is isotropic and, as result, the outgrowth is blunt.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0007.flv|GPT_tut_interaction_example_20110601-0006_Last.png‎</wikiflv> 
|}
===2 C Illustrating independent ways to form shapes and the use of submodels. ===
Conclusion: interesting shapes can be generated either by '''patterns of differential growth''' or''' patterns of local growth axe'''s. 
[[Tutorial on different ways of specifying the growth of shapes|Tutorial on different ways of specifying the growth of shapes.]] 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|Submodel 1. Uniform specified polariser ('''no polariser gradient'''). Creating a shape using a specified pattern of isotropic growth. 
'''Result''': simple patterns of differential growth can readily produce blobby shapes. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0001.flv|GPT_TwoWayHeart_20110531-0001_Last.png‎</wikiflv> 
<center>Play submodel 1. Pattern of isotropic specified growth (no polariser)</center>
|- valign="top"
|Submodel 2.'''Uniform specified growth'''. Creating a shape using a specified pattern of diffusable polariser. 
'''Result''': simple patterns organising a diffusable polariser can readily produce sharp shapes. 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="bottom"
|width="150pt"|[[Image:Heartdrawingtransparent.png|Heartdrawing]]
|width="150pt"| [[Image:Heartshaped.jpg|200px|Heartdrawing]] 
|}
 Outputs from these models bear only a romantic relation to hearts, flowers and lepidoptra. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0002.flv|GPT_TwoWayHeart_20110531-0002_Last.png‎</wikiflv> 
<center>Play submodel 2. Pattern of specified polariser levels (green-cyan). Polariser can diffuse and the gradient is arrowed. Uniform specified growth (red).</center>
|}
===2 D===
'''Retaining strain and cutting the mesh''' 
There are two submodels. They are the same except that in the first strain is not retained from step to step whereas in the second strain is fully retained. The shape changes during growth look similar, the difference is only revealed when the mesh is cut. The behaviour of plant tissue can be similar. 
[[Tutorial on retaining residual strain and cutting|Tutorial on retaining residual strain and cutting]]
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|
[[Image:GPT_RetainStrainAndCut_20110603-000050-0005.png|300px|none]]Strain not retained after each step. In plant tissue terms this would appear to be equivalent to there being a homeostatic mechanism that operates such as to re-strengthen the cell walls after they have been weakened to the point that they yield under turgor pressure during growth.
|width="120pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0006.flv|GPT_RetainStrainAndCut_20110603-0006.png‎</wikiflv> 
<center>Play submodel 1</center>
 
|- valign="top"
|width="200pt"| [[Image:GPT_RetainStrainAndCut_20110603-000050-0003.png|300px|none]]Retaining the strain from step to step allows the growth on the inside to force the mesh as a whole to grow more than when strain is not retained.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0004.flv|GPT_RetainStrainAndCut_20110603-0004.png‎</wikiflv>
<center>Whilst the frame rate relates directly to growth rate, the relaxation rate after cutting does not. After cutting the computation has to be done in smaller steps and the rate at which the sides bend back shown here is too slow.</center>
|}

='''3''' Cluster runs and batch mode: running models without the GUI=
Having developed the concepts underpinning a pattern of growth in an interaction function it is often desirable to explore a range of model parameters. Given that each run of the model can take between 5 minutes and hour it is appropriate to run the models in batch mode on the desktop or, better, in parallel on a computing cluster. (Each node of the cluster to be used by ''GFtbox'' needs to be licensed to run Matlab - however for the purpose of running on a cluster without the GUI we are exploring the possibility of making ''GFtbox'' compatible with [http://www.gnu.org/software/octave/ Octave].) 
'''Batch mode and cluster runs.''' 
'''How to use these tutorials.''' First ensure that your model is working as you would expect using the GUI. Then run the model from the Matlab command line. Finally, run the models in batch mode or submit the project to the linux computing cluster with one or more ranges of parameters.
For further details [[Running example models and using a cluster|Running example models and using a cluster]] 
='''4''' Comparing resultant shapes with observed organ shapes=
===4 A===
[[Tutorial on mapping results into shape space|Tutorial on mapping results into shape space]]
{| border="1" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Image:wikiModelShapespace.png|300px|none]]
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
<left>(Marks) The shape of growing ''Arabidopsis'' leaves projected into a shape space represented by the two principal components. (Lines) The shape of a computational model of a growing ''Arabidopsis'' leaf projected into the same space.</center>
|}

GFtbox Tutorial pages

2013-01-14T11:02:46Z

PaulSoutham:

[[GFtbox|''GFtbox'' Details]] 
[[Notes from a new user|Notes from a new user]] 
[[Running example models and using a cluster|Running example models and using a cluster]] 
[[GFtbox Example pages|Examples from our papers]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]] 
([[Full freshly minted interaction function|A newly created interaction function is shown here - the green comments are another ready reference.]]) 
[[Ready Reference Manual|'''''Ready Reference''''' Manual]] 

__NOTOC__
The models shown in these tutorials illustrate features of the GFtbox software. They are not designed to understand the Growing Polarised Tissue Framework which is better done with [[GFtbox Example pages|Examples from our papers]]. 
Viewing these pages. Some versions of ''Firefox'' and ''Explorer'' do not create satisfactory prints even though you can view the pages with no problems. ''Chrome'' does appear to produce good printouts.
=Three ways to use ''GFtbox''=
1) [[GFtbox Tutorial pages#1 Modelling using the Graphical User Interface| '''Do everything from the Graphical User Interface (GUI).''']] 
2) [[GFtbox Tutorial pages#2 Modelling using a combination of GUI and interaction function|'''Do only some things from the GUI.''']] Use the GUI to generate the mesh (canvas) and create growth factors, but capturing your ideas on how the regulatory processes work by writing Matlab code in what we call the interaction function. 
3) [[GFtbox Tutorial pages#3 Running models without the GUI|'''Without the GUI.''']] For example, run many examples (instances) of a pre-existing project on a cluster. This is the best way to explore the parameter space of a model for comparison with biological observations. We use this extensively once we have roughed out the basic ideas of a model interactively.
=Hints and Tips=
#[[Ready Reference Manual|Ready Reference Manual]] worth printing it includes details on taking snapshots and movies (and solving problems)
#[[Ready Reference Manual#Snapshots|Multiple Figures for publication]] '''colours and viewpoints.'''
#[[Ready Reference Manual#Movies|Movies for publication and web]] '''codecs compression and Powerpoint.'''
#'''Quality and accuracy'''
##[[Mesh: tradeoff |Mesh: tradeoff]] between memory/speed and accuracy. '''Increasing the number of vertices in specific regions'''
##[[Time: tradeoff|Time: tradeoff]] between speed and accuracy. '''Checking that time steps are small enough'''.
##[[Tolerances: tradeoff|Tolerances: tradeoff]] between speed and accuracy. '''Checking that tolerances are tight enough.'''
#Measuring model growth
##[[Measuring using interaction function subroutines| '''Measuring''' using interaction function subroutines]]
#[[DemoCutting intraction function|Mesh: cutting and flattening]] '''Dissecting a mesh and flattening the parts'''
='''1''' Modelling using the Graphical User Interface=
== Isotropic growth==
'''How to use the tutorial.''' Open GFtbox and attempt to repeat the results shown.
===1 A===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Uniform|Tutorial on uniform growth.]] Consider a disc shaped canvas (tissue) in which the '''specified growth is uniform''', isotropic and on both sides. '''Into what shape will the disc grow?''' This model is as simple as it gets. Notice that, during growth, the mesh is automatically subdivided. Notice also that the final surface is not quite flat. This is because, to allow it to deform in 3D, it is not flat initially. There are options to initialise a flat mesh and others to force it to remain flat - see options on the GUI (hover over controls to get prompts). 
In the absence of a polariser (there is no polariser in this example) growth will be isotropic, in other words growth in the plane of the canvas will be the average of what is specified for ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
|width="300pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0003.flv|GPT_tut_uniform_20110527-0003_Last.png</wikiflv>
|}
===1 B===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning non-uniform|Tutorial on non-uniform growth.]] Consider a disc shaped canvas (tissue) in which the''' non-uniform specified growth''' increases in proportion to the distance from the centre. '''Into what shape will the disc grow?''' Already we are into the realms of modelling biological systems. Compare this result with the discussion of Lily petals and Gaussian curvature ([http://www.pnas.org/content/early/2011/03/14/1007808108.abstract Lianga and Mahadevana],[http://www.americanscientist.org/issues/feature/leaves-flowers-and-garbage-bags-making-waves Sharon, Marder and Swinney],[http://rico-coen.jic.ac.uk/uploads/0/0f/Nath_Science.pdf Nath, Crawford, Carpenter and Coen] ).
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_tut_uniform_20110527-0006.flv|GPT_tut_uniform_20110527-0006_First.png</wikiflv>
|}

==Adding polariser==
===1 C===
{| border="0" cellpadding="5" cellspacing="3"
|- valign="top"
|width="700pt"|[[In the beginning Growing a cone|Tutorial on uniform growth with non-uniform polariser.]] 
In the presence of polariser, ''GFtbox'' growth will be anisotropic, in other words growth in the plane of the canvas can be different parallel and perpendicular to the axis of the polariser: ''Kapar'' and ''Kaper'' (''A'' side) and ''Kbpar'' and ''Kbper'' (''B'' side). 
We now''' add polariser'''. Start with example A - uniform growth - and add a radial polarising gradient. Arrows show the direction of the gradient. They are turned on using the Panel:Plot option:Pol. grad. tick box. The gradient defines local directions and local growth can be specifed either parallel to (''Kpar'') or perpendicular to (''Kper'') that direction. 
Given a '''uniform pattern of specified growth parallel''' to the polariser and '''zero specified growth perpendicular''' to the polariser. '''What will be the final shape?''' 
Note: the gradient of the polariser, green to cyan, is shown using the arrows. Specified growth rate parallel to the arrows, red, is uniform.

|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true" background="white">GPT_in_the_beginning_2_20110510-0003.flv|GPT_in_the_beginning_2_20110510-0003_First.png</wikiflv>
|}

='''2''' Modelling using a combination of GUI and interaction function=
'''How to use these tutorials.''' Use a combination of the GUI to set up the Mesh structure and editing the associated interaction function to repeat the results shown. Full listings of the interaction functions are given from which you can copy the key, editable, elements. 
The '''full specification''' of a ''GFtbox'' model is stored in a combination of the mesh data structure ('''Mesh''') and the '''interaction function'''. The Mesh stores all the physical properties of the system: spatial structure, mechanical properties, etc. It is usually set up using the GUI. The Mesh is stored on disc as a Matlab data file (.mat) and in memory as a data structure (m). The '''interaction function''' (a Matlab program file ''.m'') contains all the details of the growth regulation system: morphogen concentrations, signal interactions etc.
 
When a new project is first edited''' the interaction function is generated automatically'''. Thereafter, it is automatically kept in synchrony with the GUI. It is divided into several sections. Some are generated automatically and should not be edited. Others are set aside for the user to specify the model. To ensure that the automatic and manual edits are synchronised '''always invoke the Editor from the GUI''' (Panel: Interaction Function: Edit).

===2 A===
'''Basic interaction function'''
The patterns of morphogens A and B are set up by 

id_a_p(m.nodes(:,1) < -0.03) = 1;
id_b_p(m.nodes(:,2) < -0.01) = 1;

where ''id_a_p'' is the A morphogen. ''m.node(:,1)'' refers to the ''x'' coordinates of all nodes (vertices) in the mesh 
The expression ''(m.nodes(:,1) < -0.03)'' means find all vertices with ''x'' coordinates that are less than -0.03. 
Similarly, ''(m.nodes(:,2) < -0.01)'' means find all vertices with ''y'' coordinates that are less than -0.01. 

And the pattern of polariser (P) is set up by 

P((m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)) = 1;
Where ''(m.nodes(:,1) < -0.05) & (m.nodes(:,2) > 0.03)'' means find all vertices with ''x,y'' coordinates that are less than -0.05 and greater than 0.03 respectively 
Thus the full code describing the model is:
if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code.
id_a_p(m.nodes(:,1) < -0.03) = 1; % setup region for A where identity factor A is represented by id_a_p
id_b_p(m.nodes(:,2) < -0.01) = 1; % setup region for B
else
% @@KRN Growth Regulatory Network
kapar_p(:) = id_a_l .* inh(1,id_b_l); % growth rate
kaper_p(:) = kapar_p; % isotropic growth
kbpar_p(:) = kapar_p; % same on both sides of the sheet
kbper_p(:) = kapar_p; % same
knor_p(:) = 0; % thickness not growing
end
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the basic interaction function|Tutorial on a basic interaction function.]] 
The tutorial explains how the code shown above appears in the interaction function. 
To create the interaction function, first create and save a project (see above) then click Panel:Interaction function:Edit. The interaction function will contain all the default variables and any patterns of variables (''Kapar'', etc.) that have already been set through the GUI.
[[Types of morphogens and factors| Types of morphogens and factors are given here]].
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_why_matlab-2011-05-05-0005.flv|GPT_why_matlab-2011-05-05-0005_First.png‎</wikiflv>
|-align="top"
|
||<center>Play and the mesh will grow and subdivide. Normally we do not want to see the mesh. Red is growth rate</center>
|}
===2 B===
'''Interaction function in detail''' 
([[Full freshly minted interaction function|A newly created interaction function is shown here - this one has two, user specified morphogens: ''id_a'' and ''id_b''.]]) 
There are two submodels. An identical growth pattern and polariser pattern is specified in both, but only the specified growth in the second is anisotropic and so uses the axiality specified by the polariser gradient. The gradient is zero in the region where the polariser is held at a constant value of one - and therefore growth in the region without arrows is isotropic. 

{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|[[Tutorial on the interaction function details|Tutorial on the interaction function details.]] 
[[Types of morphogens and factors| Types of morphogens and factors are given here]]. 
Submodel 1
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
|- valign="top"
|Submodel 2. Growth in the region that has no arrows is isotropic and, as result, the outgrowth is blunt.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0007.flv|GPT_tut_interaction_example_20110601-0006_Last.png‎</wikiflv> 
|}
===2 C Illustrating independent ways to form shapes and the use of submodels. ===
Conclusion: interesting shapes can be generated either by '''patterns of differential growth''' or''' patterns of local growth axe'''s. 
[[Tutorial on different ways of specifying the growth of shapes|Tutorial on different ways of specifying the growth of shapes.]] 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|Submodel 1. Uniform specified polariser ('''no polariser gradient'''). Creating a shape using a specified pattern of isotropic growth. 
'''Result''': simple patterns of differential growth can readily produce blobby shapes. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0001.flv|GPT_TwoWayHeart_20110531-0001_Last.png‎</wikiflv> 
<center>Play submodel 1. Pattern of isotropic specified growth (no polariser)</center>
|- valign="top"
|Submodel 2.'''Uniform specified growth'''. Creating a shape using a specified pattern of diffusable polariser. 
'''Result''': simple patterns organising a diffusable polariser can readily produce sharp shapes. 
{| border="0" cellpadding="15" cellspacing="3"
|- valign="bottom"
|width="150pt"|[[Image:Heartdrawingtransparent.png|Heartdrawing]]
|width="150pt"| [[Image:Heartshaped.jpg|200px|Heartdrawing]] 
|}
 Outputs from these models bear only a romantic relation to hearts, flowers and lepidoptra. 
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_TwoWayHeart_20110531-0002.flv|GPT_TwoWayHeart_20110531-0002_Last.png‎</wikiflv> 
<center>Play submodel 2. Pattern of specified polariser levels (green-cyan). Polariser can diffuse and the gradient is arrowed. Uniform specified growth (red).</center>
|}
===2 D===
'''Retaining strain and cutting the mesh''' 
There are two submodels. They are the same except that in the first strain is not retained from step to step whereas in the second strain is fully retained. The shape changes during growth look similar, the difference is only revealed when the mesh is cut. The behaviour of plant tissue can be similar. 
[[Tutorial on retaining residual strain and cutting|Tutorial on retaining residual strain and cutting]]
{| border="0" cellpadding="15" cellspacing="3"
|- valign="top"
|width="400pt"|
[[Image:GPT_RetainStrainAndCut_20110603-000050-0005.png|300px|none]]Strain not retained after each step. In plant tissue terms this would appear to be equivalent to there being a homeostatic mechanism that operates such as to re-strengthen the cell walls after they have been weakened to the point that they yield under turgor pressure during growth.
|width="120pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0006.flv|GPT_RetainStrainAndCut_20110603-0006.png‎</wikiflv> 
<center>Play submodel 1</center>
 
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|width="200pt"| [[Image:GPT_RetainStrainAndCut_20110603-000050-0003.png|300px|none]]Retaining the strain from step to step allows the growth on the inside to force the mesh as a whole to grow more than when strain is not retained.
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_RetainStrainAndCut_20110603-0004.flv|GPT_RetainStrainAndCut_20110603-0004.png‎</wikiflv>
<center>Whilst the frame rate relates directly to growth rate, the relaxation rate after cutting does not. After cutting the computation has to be done in smaller steps and the rate at which the sides bend back shown here is too slow.</center>
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='''3''' Cluster runs and batch mode: running models without the GUI=
Having developed the concepts underpinning a pattern of growth in an interaction function it is often desirable to explore a range of model parameters. Given that each run of the model can take between 5 minutes and hour it is appropriate to run the models in batch mode on the desktop or, better, in parallel on a computing cluster. (Each node of the cluster to be used by ''GFtbox'' needs to be licensed to run Matlab - however for the purpose of running on a cluster without the GUI we are exploring the possibility of making ''GFtbox'' compatible with [http://www.gnu.org/software/octave/ Octave].) 
'''Batch mode and cluster runs.''' 
'''How to use these tutorials.''' First ensure that your model is working as you would expect using the GUI. Then run the model from the Matlab command line. Finally, run the models in batch mode or submit the project to the linux computing cluster with one or more ranges of parameters.
For further details [[Running example models and using a cluster|Running example models and using a cluster]] 
='''4''' Comparing resultant shapes with observed organ shapes=
===4 A===
[[Tutorial on mapping results into shape space|Tutorial on mapping results into shape space]]
{| border="1" cellpadding="15" cellspacing="3"
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|width="400pt"|[[Image:GPT_RetainStrainAndCut_20110603-000050-0005.png|300px|none]]
|width="200pt"|<wikiflv width="300" height="300" logo="false" loop="true">GPT_tut_interaction_example_20110601-0002.flv|GPT_tut_interaction_example_20110601-0002.png‎</wikiflv> 
<left>(Marks) The shape of growing ''Arabidopsis'' leaves projected into a shape space represented by the two principal components. (Lines) The shape of a computational model of a growing ''Arabidopsis'' leaf projected into the same space.</center>
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File:WikiModelShapespace.png

2013-01-14T11:02:15Z

PaulSoutham: