Fig. 3. Representation of the PlantLayout pipeline on the example of building the model for the study of phytohormone auxin distribution within the plant root tip.

a, pre-processed confocal image of the root tip; b, identifying the cells as connected components and getting unique indexes for each cell; c, quantification of cells features; d, identification of the cell walls between each two cells as connected components; e, estimation of the quantitative and qualitative characteristics for the cell walls; f, definition of the cell wall orientations; g, embedding the quantitative and qualitative characteristics of the 2D structural model into the mathematical model; h, steady state solution of the mathematical model, auxin distribution in the plant root tip.