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 acquisition

Data analysis

  • FibrilTool, A. Boudaoud, A. Burian, D. M. Borowska-Wykret, M. Uyttewaal, R. Wrzalik, D. Kwiatkowska and O. Hamant (2014). FibrilTool, an ImageJ plugin to quantify fibrillar structures in raw microscopy images. NATURE PROTOCOLS 9, 457.
  • AFM_plugin, an ImageJ plugin for AFM data (Vincent Mirabet)
  • 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, anisotropic diffusion filters (Annamaria Kiss)


  • 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).

For unpublished tools see here.


Manager: Annamaria Kiss