THOTH software
Classification of the trajectories in a single micro-patterned (crossbow) cell :
Rab11a-GFP protein in TIRF-2D fluorescence microscopy (courtesy of UMR 144 CNRS-Institut Curie).
In blue Brownian motion, in green subdiffusion, in red superdiffusion.
Overview
THOTH (Testing HypOtheses for diffusion TricHotomy) is a method for classifying particle trajectories into three groups of diffusion corresponding to different biological contexts:
- Free diffusion (or Brownian motion) : the particle evolves freely inside the cytosol.
- Subdiffusion : the particle is confined in a domain or evolves in an open but crowded area.
- Superdiffusion : the particle is transported actively via molecular motors along the cytoskeleton.
We use a three-decision statistical test to make this classification. We develop :
- a single test procedure to test a single trajectory.
- a multiple test procedure which tests a collection of trajectories at the same time for reducing the number of false alarms (number of Brownian trajectories falsely labeled as non-Brownian.)
Software distribution
Matlab source code is freely ditributed under Affero GPL v3.0 license: thoth.zip
Reference
- V. Briane, C. Kervrann, M. Vimond. Statistical analysis of particle trajectories in living cells, Phys. Rev. E 97, 062121 (doi:10.1103/PhysRevE.97.062121), 2018 (arXiv) (HAL-INRIA-01557705)
- V. Briane, M. Vimond, C. Kervrann. An overview of diffusion models for intracellular dynamics analysis, bbz052, Briefings in Bioinformatics, HAL-INRIA-0196682, 2019
