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

Garden Tiger Moth photographed by Gabor PozsgaiThis website has been mothballed.

It is no longer being updated but we've left it here for reference.

Further information

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.