The Biophysics and Development Team is part of the RDP Lab. It focuses on morphogenesis at the shoot apex. Our research is conducted along four axes: Mechanics of morphogenesis; Floral Growth Patterns; Mechanical Feedbacks; Modelling Plant Morphogenesis.

The following projects gather tools we developed in order to be able to tackle these subjects.

Data analysis

  • FibrilTool, A. Boudaoud, A. Burian, D. M. Borowska-Wykret, M. Uyttewaal, R. Wrzalik, D. Kwiatkowska and O. Hamant. FibrilTool, an ImageJ plugin to quantify fibrillar structures in raw microscopy images. NATURE PROTOCOLS 9, 457. (2014).
  • lsm3D, A. Kiss, T. Moreau, V. Mirabet, C. I. Calugaru, A. Boudaoud, P. Das. Segmentation of 3D images of plant tissues at multiple scales using the level set method. Plant Methods, 13, 114 ( 2017)
  • AniFilters, Yuchen Long, Ibrahim Cheddadi, Gabriella Mosca, Vincent Mirabet, Mathilde Dumond, Annamaria Kiss, Jan Traas, Christophe Godin, Arezki Boudaoud Cellular Heterogeneity in Pressure and Growth Emerges from Tissue Topology and Geometry. Curr Biol. 30(8):1504-1516.e8. doi: 10.1016 (2020)
  • AFM_plugin, an ImageJ plugin for AFM data (Vincent Mirabet)


  • AFM_plane, a SOFA plugin for a simulated Atomic Force Microscope acting on a plane. R. Malgat, F. Faure & A. Boudaoud*. A mechanical model to interpret cell-scale indentation experiments on plant tissues in terms of cell wall elasticity and turgor pressure. Front. Plant Sci. 7, 1351 (2016).
  • Cell Division Rule, M. Louveaux, J.-D. Julien, V. Mirabet, A. Boudaoud* & O. Hamant*. A cell division rule based on tensile stress in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 113, E4294–E4303 (2016).
  • Vascular Networks in Growing Leaves, Y. Bar-Sinai, J.-D. Julien, E. Sharon*, S. Armon, N. Nakayama, M. Adda-Bedia & A. Boudaoud*. Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves. PLoS Comput. Biol. 4, e1004819 (2016).
  • Dandelion, FreeFem script for dandelion morphing simulation used in "Madeleine Seale, Annamaria Kiss, Simone Bovio, Ignazio Maria Viola, Enrico Mastropaolo, Arezki Boudaoud, Naomi Nakayama, Dandelion pappus morphing is actuated by radially patterned material swelling, doi: https://doi.org/10.1101/2021.08.23.457337"

For unpublished tools see here.


Manager: Annamaria Kiss