The lab is involved in the development of analysis tools and databases. Here you can find some examples of them.

Rosa sp. Transcriptome Database

The database provides useful information on Rosa sp. expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy, and represents a valuable prerequisite to the sequencing of the rose genome.

The Petunia Platform

The Petunia Platform promotes the main object of research of its participating members, Petunia, and in a broader sense research on Solanaceous species. The tools that you can find on the platform will greatly facilitate the use of Petunia as a plant model in genetics and molecular biology.

MARS-ALT on Openalea

MARS-ALT is a pipeline designed to track cell lineages at different time steps. It provides algorithms for three-dimensional reconstruction and cell segmentation, as well as for automated lineage tracking. This gives the basis of 4D analysis of plant organ development at cellular level. The method is described in Fernandez R. et al. (2010) Imaging plant growth in 4D : robust tissue reconstruction and lineaging at cell resolution. Nat Methods. 7(7):547-53.


FibrilTool is used to analyse image texture, it computes the mean fibril orientation on a surface. There is a 2D version working on ImageJ A. Boudaoud et al. (2014) FibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Nature Protocols 9, 457–463, as well as a version adapted for 3D surfaces, that is working on MorphoGraphX, an open source application for the visualization and analysis of 4D biological datasets P. Barbier de Reuille et al. (2015) MorphoGraphX : A platform for quantifying morphogenesis in 4D. eLife 4:e05864.


The lsm3d tool allows to segment 3D images of plant tissues at multiple scales using the level set method. It detects for instance the outer surface of the tissue. It can be used to segment cells in the tissue as well as nuclei in the cells. The method and the tool are described in A. Kiss et al. (2017) Segmentation of 3D images of plant tissues at multiple scales using the level set method. Plant Methods, 13, 114

Articles de cette rubrique

  • Protocols

    , par BioPhysics

    Analysis of 3D gene expression patterns in plants using whole-mount RNA in situ hybridisation
    Frédérique Rozier, Vincent Mirabet, Teva Vernoux, and Pradeep Das
    Nature Protocols (in press)
    Analyse en 3 dimensions de l’expression des gènes vizualisation of a 3D stack
    The method allows the (...)

  • Liens

    , par yfesseli

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