Interactive software for tracking and modeling the motions of plant organs

Link to the source code and installation guidelines :

https://forgemia.inra.fr/felix.hartmann/interekt

Interekt (INTERactive Exploration of Kinematics and Tropisms) is a software dedicated to the semi-automatic phenotyping of growth and/or tropical movements of plant organs. The organ must be approximately one-dimensional, typically a stem or a root.

Interekt takes as input a sequence of 2D images of a plant organ growing and/or undergoing a tropic movement. A quasi-automatic procedure allows to extract the shape of the organ on each image. It is then possible to compute and visualize its geometric characteristics (length, radius, angles, curvatures) as well as its kinematics (growth rate, angle variations, curvature variations).

In addition to the quantitative description of the movement, Interekt integrates mathematical models of gravitropic and proprioceptive response. Semi-automatic procedures allow to estimate the value of these parameters for each image sequence, and thus to quickly perform model-assisted phenotyping.

Implementation

Interekt is written in Python 3, with a Tkinter graphical interface. It depends on the library Numpy, Scipy, Matplotlib, Pandas, Scikit-image and h5py.

Contact : Félix Hartmann (felix.hartmann@inrae.fr)

Reference

Hartmann F.P., Chauvet-Thiry H. et al. (2022) Methods for a Quantitative Comparison of Gravitropism and Posture Control Over a Wide Range of Herbaceous and Woody Species. In Plant Gravitropism, Humana, New York.

https://hal.inrae.fr/hal-03400916