Laboratoire RDP » Biophysics Team » FLORIVAR

This is a repository for image analysis and morphological quantification codes used for the article Diego A. Hartasánchez, Annamaria Kiss, Virginie Battu, Mathilde Dumond, Charline Soraru, Abigail Delgado-Vaquera, Florian Massinon, Marina Brasó-Vives, Corentin Mollier, Nelly Dubrulle, Fabien Sénéchal, Marie-Laure Martin-Magniette, Arezki Boudaoud, Françoise Monéger, Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall
10.24072/pcjournal.327 - Peer Community Journal, Volume 3 (2023), article no. e93.

The pipeline detects, orients and quantifies some morpholigical features (curved length and width, adaxial and abaxial areas, transverse and longitudinal curvatures, ...) on sepals. For detailed information on the usage please see the Wiki.

Dependencies¶

The pipeline is based on different type of scripts :
- ImageJ macros
- python scripts making use of MorphoGraphX
- python scripts that make use of TimageTk

Timagetk is used here through a python module called "titk_tools". Please follow the instructions of this page in order to install a conda environment with timagetk and the module titk_tools in it.

Download¶

In a terminal go to the directory where you wish to download these tools

cd Path_to_your_directory

and then download using svn

svn checkout http://forge.cbp.ens-lyon.fr/svn/florivar

The scripts will be in the florivar/bin folder. Add this folder to your PATH by adding in your .bashrc file

export PATH=$PATH:Path_to_your_directory/florivar/bin