Current activity: a collaboration with the 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
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.
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.
|Example of a growing snapdragon flower and some mutants ( 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.||GPT_Snapdragon_2010_Green_et_al-0002.png</wikiflv>|
For modelling the growth of shapes.
Viewing and measuring volume images: VolViewer
Analysing shapes in 2D and 3D: AAMToolbox
Analysing the shapes of clones: SectorAnalysisToolbox
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 Essentially, no difference.
Finding interest points, features and segmenting images.
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 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. finding its name. (It is entirely different in principle from the software more recently used by Hockney to paint with an iPad.)
Saturday 07/06/2014: Inspired Photographer of the Year 2013 Tony Bennett when asked whether his photograph Mists and Reflections had been Photoshopped replied something like
Links to third party PhotoArtMastered pictures
The final version of the Windows ArtMaster2.0 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 'this essay .
Reaction-diffusion and morphogenesis
Illustration of morphogenesis inspired by Turing's paper.
Open source systems to which we have contributed
Tools and Utilities
Dependency Checking Tool
Tool for recursively finding what further functions a function depends on. See Details
Robot arm: still in production after 30 years (serving local industry)