Automated motion estimation of root responses to sucrose in two Arabidopsis thaliana genotypes using confocal microscopy
Root growth is a highly dynamic process influenced by genetic background and environment. This paper reports the development of R scripts that enable root growth kinematic analysis that complements a new motion analysis tool: PlantVis. Root growth of Arabidopsis thaliana expressing a plasma membrane targeted GFP (C24 and Columbia 35S:LTI6b-EGFP) was imaged using time-lapse confocal laser scanning microscopy. Displacement of individual pixels in the time-lapse sequences was estimated automatically by PlantVis, producing dense motion vector fields. R scripts were developed to extract kinematic growth parameters and report displacement to ±0.1 pixel. In contrast to other currently available tools, Plantvis-R delivered root velocity profiles without interpolation or averaging across the root surface and also estimated the uncertainty associated with tracking each pixel. The PlantVis-R analysis tool has a range of potential applications in root physiology and gene expression studies, including linking motion to specific cell boundaries and analysis of curvature. The potential for quantifying genotype × environment interactions was examined by applying PlantVis-R in a kinematic analysis of root growth of C24 and Columbia, under contrasting carbon supply. Large genotype-dependent effects of sucrose were recorded. C24 exhibited negligible differences in elongation zone length and elongation rate but doubled the density of lateral roots in the presence of sucrose. Columbia, in contrast, increased its elongation zone length and doubled its elongation rate and the density of lateral roots.
KeywordsCell expansion Confocal laser scanning microscopy Digital image analysis Motion estimation Root meristem Sucrose
Confocal laser scanning microscopy
Days after germination
Displacement vector field
Elemental growth rate
Particle image velocimetry
Prof. Jim Haseloff (Cambridge University) for the kind donation of A. thaliana. D. White (University of Western Australia) for access to the Cambridge University PIV code. This work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), UK. SCRI receives grant-in-aid from the Scottish Government Rural and Environmental Research and Analysis Directorate (SG-RERAD). Dr. Kath Wright, Dr. Lionel Dupuy and Prof. Philip White for helpful comments on this manuscript.
- Bigün J, Granlund GH (1987) Optimal orientation detection of linear symmetry. In: Proceedings of the first international conference on computer vision, London, 8–11 June 1987. IEEE Computer Society Press, Washington, DC, pp 433–438Google Scholar
- Chavarria-Krauser A, Nagel KA, Palme K, Schurr U, Walter A, Scharr H (2008) Spatio-temporal quantification of differential growth processes in root growth zones based on a novel combination of image sequence processing and refined concepts describing curvature production. New Phytol 177:811–821PubMedCrossRefGoogle Scholar
- Jiang HS, Palaniappan K, Baskin TI (2003) A combined matching and tensor method to obtain high fidelity velocity fields from image sequences of the non-rigid motion of the growth of a plant root. In: Hamza MH (ed) IASTED international conference on biomedical engineering, BioMED 2003. ACTA Press, Calgary, Canada, 386–010, pp 159–165Google Scholar
- van der Weele CM, Jiang HS, Palaniappan KK, Ivanov VB, Palaniappan K, Baskin TI (2003) A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone. Plant Physiol 132:1138–1148PubMedCrossRefGoogle Scholar