Lionel Dupuy

Honorary Associate
Ecological Sciences
T: +44 (0)344 928 5428 (*)

I graduated in Timber Engineering from the École Supérieure du Bois (Nantes, France) in 2000 and was awarded a PhD in 2003 from the University of Bordeaux (School of Physics and Engineering Sciences) where I was developing biomechanical models of tree uprooting at the Laboratoire de Rheologie du Bois de Bordeaux (now Institute of Mechanics and Engineering of Bordeaux). I developed software for digitising the architecture of root systems and constructed finite element models of root soil interactions. In 2005 I took a post-doctoral position in Jim Haseloff's laboratory (University of Cambridge) to work on computational methods to analyse plant cell morphogenesis. I developed image analysis methods to track cell expansion and division from live microscopy data, and used these measurements to construct models that integrated genetic and biomechanical processes into dynamic multicellular architectures. 

Research

I develop models that predict how crops utilise environmental resources to grow and produce yield. I design experimental systems where such processes can be observed and quantified. For example, recent work has focused on the development of novel transparent soils that are suitable for the culture and live imaging of soil biological organisms.

My research also focuses on quantitative imaging to improve data resolution and throughput for models. I use techniques such as Optical Projection Tomography (OPT), Single Plane Illumination Microscopy (SPIM, in collaboration with Mike MacDonald), and Biospeckle Laser (BSL, in collaboration with Roberto Braga), and web-cam and scanner based systems to construct low cost high throughput phenotyping (Michael Adu, co-supervisors Martin Broadley, Malcolm Bennett, Philip White).

The main objective is to construct simple models that can be understood, calibrated easily using available data and integrated with existing software. To achieve this objective, I develop continuous models (PDE) where fundamental growth processes can be incorporated explicitly into conservation equations (in collaboration with Glyn Bengough, Xavier Draye, Tim George and Philip White).

See group pages for more information.

Software development
Archiroot: Software for the acquisition and visualisation of root architecture
BalloonPlugin: Fiji plugin for the segmentation of cell architecture
CellModeller2.0: Software platform for multicellular analysis modelling and computation
SIMUL3R : simulation of root architectures dynamics
More descriptions at: http://www.archiroot.org.uk/doku.php/navigation/architools

 

Publications

The following Publications have not yet been migrated to the James Hutton Institute's Pure service and relate to the research outputs from the two legacy organisations: The Macaulay Land Use Research Institute and The Scottish Crop Research Institute.

Journals

Conference papers

  • Adu M.; Bennett M.; Hammond, J.P.; White, P.J.; Dupuy, L.; Broadley, M.R. (2011) Variation in root system architecture of a single genotype of Brassica rapa., Joint Meeting of BSSS Scottish Soils Discussion Group and the Scottish Root Group, Edinburgh, 2 November 2011.
  • Dupuy, L.X. (2011) Modelling root systems using oriented density distributions., 9th International Conference of Numerical Analysis and Applied Mathematics, Halkidiki, Greece, 19-25 September 2011. AIP Conference Proceedings, 1389, p726.
  • Dupuy, L. (2010) Modelling root systems using continuous deformable plant models (CDPM)., 6th International Workshop on Functional – Structural Plant Models (FSPM). University of California, Davis, California, USA, 12-17 September 2010 (Talk).
  • Dupuy, L. (2009) New approaches for the modelling of root architecture., The 20th International Conference on Arabidopsis Research. EICC, Edinburgh, 30 June-4 July 2009 (Invited talk).
  • Dupuy, L.; Vignes, M. (2009) Simplified root architectural models using continuous deformable domains., IEEE, 3rd International Symposium Plant Growth Modeling, Simulation, Visualization and Applications. Beijing, China, 9-13 November 2009 (Talk).
  • Dupuy, L.; Vignes, M.; McKenzie, B.M.; White, P.J. (2009) The dynamics of plant root meristems., French Annual Meeting of Biology, Informatics and Mathematics, Nantes, France, 9-11 June 2009.
  • Bengough, A.G.; Roberts, T.J.; Wuyts, N.; Hans, J.; McKenna, S.J.; Valentine, T.A.; Bransby, M.F.; Dupuy, L.; Haseloff, J. (2007) Computer visualisation and modelling of plant morphogenesis: Motion analysis of time-lapse confocal microscopy images., BBSRC Joint Bioinformatics and e-Science, Proteomics and Cell Function Grantholders Workshop, Cheshire, 8-10 January 2007.
  • Valentine, T.A.; Bengough, A.G.; Bransby, F.; Dupuy, L.; Hans, J.; Haseloff, J.; McKenna, S.; Roberts, T.J. (2005) Computer visualisation and modelling of plant morphogenesis: Optical flow analysis of time-lapse confocal microscopy images., BBSRC/SCRI Bioinformatics and Escience Workshop, Manchester, 18-19 October 2005.
  • Roberts, T.J.; Bengough, A.G.; Bransby, F.; Dupuy, L.; Hans, J.; Haseloff, J.; McKenna, S.; Valentine, T.A. (2005) Computer visualisation and modelling of plant morphogenesis: in-vivo segmentation and tracking of cells using confocal microscopy., BBSRC/SCRI Bioinformatics and Escience Workshop, Manchester, 18-19 October 2005.

Conference posters / abstracts

  • George, T.S.; Brown, L.K.; Barrett, G.; Dupuy, L.; White, P.J. (2010) Genotypic variation in the ability of barley to tolerate multiple abiotic stresses., SEB Annual Main Meeting 2010, Prague, Czech Republic, 30 June-3 July 2010 (Poster).
  • Gill, A.S.; Bengough, A.G.; Grinev, D.V.; Dupuy, L. (2009) Imaging the 3D kinematics of circummutation in maize roots., Society for Experimental Biology Annual Main Meeting, Glasgow, 28 June – 1 July 2009 (Poster).
  • Dupuy, L.; Braga, R.A.; Federici, F.; Haseloff, J.; McKenzie, B.M.; Vignes, M.; White, P.J. (2009) Root models to improve crop performance. From cell to field., KnowledgeScotland Stakeholder Event, Forestry Commission, Edinburgh, 27 October 2009. (Poster)
  • Federici, F.; Dupuy, L.; Haseloff, J. (2008) Novel tools for plant tissue engineering., Synthetic Biology 4.0. The Fourth International Meeting on Synthetic Biology, University of Science & Technology, Kowloon, Hong Kong, 10-12 October 2008 (Poster).

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