Lionel Dupuy

Honorary Associate
Ecological Sciences
E: Lionel.Dupuy@hutton.ac.uk
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

Journals

Conference papers

  • Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.J.; Schmidt, S.; White, P.; Bengough, G. (2015) Tools and techniques for phenotyping plant:soil interactions., Integrated Plant and Algal Phenomics (IPAP) Meeting, Prague, Czech Republic, 27-30 June 2015.
  • Valentine, T.A.; Upton, C.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: transparent soil and rhizotubes., ISSR 2015. 9th International Symposium of the ISRR. “Roots down under – Belowground solutions to global challenges”, Canberra, Australia, 6-9 October 2015. Paper O-23.
  • Valentine, T.A.; Bengough, A.G.; Dupuy, L.X.; Hallett, P.; Karley, A.J.; McKenzie, B.M.; Newton, A.; Schmidt, S.; Stobart, R.; Squire, G.; Young, M.; Hawes, C. (2015) Evaluating interactions at the plant:soil interface., UK-India Initiative in Agroecology, Centre for Pollination Studies, Calcutta University, Kolkata, India, 21-23 February 2015.
  • Valentine, T.A.; Upton, C.; Binnie, K.; Dupuy, L.X.; Karley, A.K.; Schmidt, S.; White, P.; Bengough, A.G. (2015) Tools and techniques for phenotyping plant:soil interactions. , International Plant and Algal Phenomics Meeting, Prague, Czech Republic, 27-30 June 2015.
  • Valentine, T.A.; Upton, C.M.; Bentley, S.; Greenland, A.; Otten, W.; Schmidt, S.; Squire, G.; Dupuy, L.X.; Karley, A.J. (2015) Recent developments in root phenotyping pipelines of cereal crops: Transparent soil and rhizotubes., 9th International Symposium of the International Society of Root Research, Roots Down Under – Belowground Solutions to Global Chanllenges, Canberra, Australia 6-9 October 2015.
  • Upton, C.M., Dupuy, L.X.; Schmidt, S.; Downie, H.; Otten, W.; Valentine, T.A. (2014) Quantifying 3D root system architecture of roots grown in transparent soil – current progress, challenges and future work., Society for Experimental Biology (SEB) Conference, University of Manchester, July 2014. Scientific Session – Roots for global food security (a tribute to Bill Davies).
    Http://www.sebiology.org/meetings/Manchester/sessions.html
  • Brown, L.K.; George, T.S.; Dupuy, L.; White, P.J. (2014) A conceptual model of root hair ideotypes for future agricultural environments., Phosphorus in Soils and Plants, 5th International Symposium, 4th Sustainable Phosphorus Summit, Montpellier, France, 26 August – 3 September 2014.
  • Adu, M.O.; Broadley, M.R.; Bennett, M.J.; White, P.J.; Dupuy, L.X. (2013) Developing a low cost high throughput root phenotyping system for selection of phosphorus efficient Brassica rapa lines., In: XVII International Plant Nutrition Colloquium and Boron Satellite Meeting, Sabanci University, Istanbul, Turkey, 19-22 August 2013. Proceedings, pp227-228.
  • Dupuy, L.X.; Bengough, A.G.; Draye, X.; Kalogiros, D.; Ptashnyk, M. (2013) Density-based approaches to interface models and data in root biology., Annual Meeting of the Society for Experimental Biology, Valencia, Spain, 3-6 July 2013.
  • Thomas, C.L.; Neugebauer, K.; Graham, N.S.; Hayden, R.; Hammond, J.P.; Nightingale, M.; Meacham, M.C.; White, P.J.; Dupuy, L.; Broadley, M.R. (2013) Developing root phenotyping techniques for Brassica napus., In: XVII International Plant Nutrition Colloquium and Boron Satellite Meeting, Sabanci University, Istanbul, Turkey, 19-22 August 2013. Proceedings, pp290-291.
  • Adu, M.; Bennett, M.; Hammond, J.; White, P.; Dupuy, L.; Broadley, M. (2012) High throughput imaging and analysis of Brassica rapa root system architecture in response to (P) ext., The 8th Symposium of the International Society of Root Research (ISRR); Roots to the Future, The James Hutton Institute, Dundee, 26-29 June 2012.
  • 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.; Giles, C.D.; Boitt, G.; Dupuy, L.; Brown, L.K.; Condron, L. (2018) Quantitative measurement of phosphatase activity distribution in the rhizosphere – impact of root hairs., 6th Symposium on Phosphorus in Soils and Plants, PSP6, Leuven, Belgium, 10-13 September 2018. Book of Abstracts, p157.
  • Pongrac, P.; Duncan, J.; Wishart, J.; Loades, K.; Dupuy, L.; Bengough, G.; Bingham, I.; Kelemen, M.; Vavpetic, P.; Pelicon, P.; Shelef, O.; White, P.J. (2017) The beauty of roots., CECHR Annual Symposium, West Park Conference Centre, Dundee, 22 February 2017.
  • Dupuy, L.X.; Silk, W.K. (2016) Mechanisms of early establishment of bacterial population in the rhizosphere., 10th European Conference on Mathematical and Theoretical Biology, University of Nottingham, 11-15 July 2016.
  • Upton, C.; Dupuy, L.X.; Schmidt, S.; Otten, W.; Valentine, T.A. (2015) Visualization and quantification of root responses to soil strength and pore structure: Utility of transparent soil., ISSR 2015. 9th International Symposium of the ISRR. “Roots down under – Belowground solutions to global challenges”., Canberra, Australia, 6-9 October 2015. (Poster).
  • Upton, C.; Downie, H.; Schmidt, S.; Dupuy, L.X.; Otten, W.; Valentine, T.A. (2015) Visualization and quantification of root response to soil strength and pore structure: Utility of transparent soil., SEB (Society of Experimental Biology) Annual Main Meeting, Prague, Czech Republic, 30 June – 3 July 2015. Poster P2.71.
  • Thomas, C.L.; Hayden, R.; Graham, N.S.; Neugebauer, K.; Zhang, Y.; Shi, L.; White, P.J.; Dupuy, L.X.; Nightingale, M.; Broadley, M.R. (2015) High throughput root screens are a proxy for field performance in Brassica napus and can be used to identify novel genetic loci., The 9th Symposium of the International Society of Root Research, (ISRR-9) Roots Down Under: Belowground Solutions to Global Challenges. Canberra, Australia, 6-9 October 2015.
  • Stutter, M.I.; Aitkenhead, M.; Robertson, J.; Perez-Fernandez, E.; Dupuy, L.; Prashar, A. (2015) Sensing for food and environmental security., Centre of Innovation for Sensing, CENSIS Event, Glasgow, June 2015.
  • O’Callaghan, F.; Dupuy, L.; Neilson, R.; MacFarlane, S. (2015) 3D imaging of root-nematode interactions: transparent soil for visualizing host-pathogen processes., Potato Council Meeting on Biofumigation, Harper Adams University, 9 September 2015.
  • White, P.J.; Adu, M.; Broadley, M.R.; Brown, L.; Dupuy, L.; George, T.S.; Graham, N.S.; Hammond, J.P.; Hayden, R.; Neugebauer, K.; Nightingale, M.; Ramsay, G.; Thomas, C.; Thompson, J.A.; Wishart. J.; Wright, G. (2014) The importance of juvenile root traits for crop yields., EGU General Assembly, Vienna, Austria, 27 April – 2 May 2014. EGU2014-2337 Abstract.
  • Thomas, C.L.; Neugebauer, K.; Hayden, R.; Graham, N.S.; White, P.J.; Dupuy, L.; Hammond, J.P.; Broadley, M.R. (2014) High throughput phenotyping of Brassica napus root architecture., 19th Crucifer Genetics Workshop, Wuhan, China, March 2014.
  • Adu M.; Bennett, M.; Hammond J.; White, P.J.; Dupuy, L.; Broadley, M. (2012) Variation in root system architecture of a single genotype of Brassica rapa., British Society of Soil Science – Scottish Soil Discussion Group, Edinburgh, 2 November 2012 (Poster).
  • Adu, M.; Bennett, M.; White, P.J.; Dupuy, L.; Broadley, M. (2012) A high-throughput root phenotyping (HTP) system for Brassica rapa., CPIB Summer School Course, Image Analysis for Biologists, University of Nottingham, 3-5 September 2012. (Poster)
  • Adu, M.; Bennett, M.; Broadley, M.; White, P.; Dupuy, L. (2012) High throughput imaging and analysis of Brassica rapa root system architecture., Crop World Global 2012, London, 6-7 November 2012. (Poster).
  • 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).