PlantLayout pipeline to model tissue patterning.

Area of Science:

• Developmental Biology
• Computational Biology
• Plant Science

Background:

• Tissue patterning relies on understanding morphogen dynamics in anisotropic environments.
• Morphogens form maxima and gradients, guiding dose-dependent cellular processes.
• Analyzing spatio-temporal regulator dynamics across tissue architecture is crucial.

Purpose of the Study:

• Introduce PlantLayout, a MATLAB pipeline for computational tissue patterning studies.
• Facilitate integrated modeling, simulation, and visualization of developmental regulators.
• Enable analysis of gene network outputs influenced by morphogens in specific cell types.

Main Methods:

• Build 2D tissue structural models within MATLAB.
• Embed tissue models into mathematical models using Ordinary Differential Equations (ODEs).
• Perform numerical simulations and visualize results on a unified platform.

Main Results:

• Enables studying morphogen concentration dynamics over reconstructed cell layouts.
• Facilitates analysis of gene network dynamics and outputs in different cell types.
• Semi-automatically determines cell wall orientation and extracts cell/wall features (e.g., dimensions, neighbors, volume).

Conclusions:

• PlantLayout streamlines computational studies of tissue patterning.
• The pipeline aids in modeling developmental patterns, demonstrated with auxin distribution in plant root tips.
• It provides quantitative and qualitative features essential for accurate biological modeling.