Phytocomp - new computing tools for plant science | The James Hutton Institute

Publications and posters

Posters describing areas of this work

In-vivo segmentation and tracking of cells using confocal microscopy.

Optical flow analysis of time-lapse confocal microscopy images.


Archiroot website - quantitative methods in root architecture analysis


Wuyts, N., Bengough, A.G., Roberts, T.J., Du, C., Bransby, M.F., McKenna, S.J. & Valentine, T.A. 2011. Automated motion estimation of root responses to sucrose in two Arabidopsis thaliana genotypes using confocal microscopy. Planta 234, 769-784.

Dupuy, L., Gregory, P.J. & Bengough, A.G. 2010. Root growth models: Towards a new generation of continuous approaches. Journal of Experimental Botany 61, 2131-2143.

Bengough, A. G., J. Hans, M. F. Bransby & T. A. Valentine (2010) PIV as a Method for Quantifying Root Cell Growth and Particle Displacement in Confocal Images. Microscopy Research and Technique, 73, 27-36.

Roberts, T. J., S. J. McKenna, C. J. Du, N. Wuyts, T. A. Valentine & A. G. Bengough (2010) Estimating the motion of plant root cells from in vivo confocal laser scanning microscopy images. Machine Vision and Applications, 21, 921-939.

Roberts, T.J., McKenna, S.J., Wuyts, N., Valentine, T.A. and Bengough, A.G. 2007. Performance of low-level motion estimation methods for confocal microscopy of plant cells in vivo. Institute of Electrical and Electronics Engineers Workshop on Applications of Computer Vision, Austin, Texas, 21-22 February 2007. 372-382.

Roberts, T.J., McKenna, S.J., Hans, J., Valentine, T.A. and Bengough, A.G. 2006. Part-based multiframe registration for estimation of the growth of cellular networks in plant roots. 18th International Conference on Pattern Recognition, Hong Kong, 20-24 August 2006. 378-382.

Dupuy, L.X., Mackenzie, J and Haseloff, J. A biomechanical model for the study of plant morphogenesis: Coleochaete orbicularis. Proceedings of the 5th Plant Biomechanics Conference. Stockholm. (2006)

Dupuy L, Mackenzie J, Rudge T, Haseloff J. A system for modelling cell- cell interactions during plant morphogenesis. Annals of Botany101:1255-1265 (2008)

Bengough, A.G., Bransby, M.F., Hans, J., McKenna, S.J., Roberts, T.J. and Valentine, T.A. 2006. Root responses to soil physical conditions; growth dynamics from field to cell. Journal of Experimental Botany 57, 437-447.