To model custom cell phenotypes and their interactions one should edit Parameters_Phenotypes.m located at Synplex/Synthetic_microenvironment/. In this module there are eight variables that can be tuned:
A cell data structure containing names of the cell phenotypes to be simulated e.g.,
CellPhenotypeNames = {'Stromal cells', 'Tumor cells','Stromal-Immune','Lumen','Stromal fibers'};
- 'Stromal cells', 'Tumor cells', and 'Stromal-Immune' refer to cell phenotype populations
- 'Lumen' refers to the space without cells that can be found in the backbround of the tissue, or between glands
- 'Stromal fibers' referes to the space between cells. This parameter is useful to simulate different levels of tissue compactness and the extracellular matrix.
A matrix of size "n of phenotypes" x "n of phenotypes" x "n of neighborhoods", specifying the interactions between phenotypes within each of the neighborhoods. 1 is attraction, 0.5 is no interaction, and 0 is repulsion. e.g.,
CellPhenotypeInteraction(2,3,1) = 1; CellPhenotypeInteraction(3,2,1) = 1; % Tumor - stromal-immune attraction in the stromal compartment.
A vector specifying the average size of cell phenotypes. e.g.,
PhenoSize = [10,16,13,2,2]; % Nucleus radius in pixels
In the case of 'Lumen' and 'Stromal fibers', these values must be defined.
A vector specifying the ratio between the size of the nucleus and the cell. 1 are cells without cytoplasm, 0.5 are cells with equal nucleus and cytoplasm, 0 are cells without nucleus.
RatioNucleousCellSize = [.6,.9,.7,1,1];
A vector specifying the eccentricity of cell phenotypes. Ranging from 0 (round cells) to 1 (maximally elongated cells). e.g.,
PhenoEccentricity = [.5,.7,.4,1,1];
A vector specifying the complexity of cell phenotypes. Ranging from 0 (uniform ellipsoidal shape) to 1 (highly irregular shape) for each cell phenotype.
PhenoMorphDeviation = [.3,.1,.3,0,0];
A vector specifying the average cell phenotype polarity. Ranging from 0 (nucleus at the center of the cell) to 1 (nucleus touching the contour of the cell).
PhenoPolarity = [0.1,0.2,0.3,0,0];
A matrix specifying the abundances of cell phenotypes within each neighborhood. In percentage. e.g.,
Phenotype_Abundance = [60, 0, 10, 0, 30; ... % 'Stroma' is composed of 60% of 'stromal cells', 10% 'stromal-immune cells' and 30% 'stromal fibers' 0, 95, 0, 0, 5; ... % 'Tumor' 0, 0, 0, 100, 0]; % 'Lumen'