djimenezsanchez / synplex Goto Github PK

Hi There,
I'm a graduate student at the Harvard University School Of Engineering And Applied Sciences. I'm currently looking into ways of generating synthetic multiplexed imaging data, ideally at a sub-cellular resolution.
I'm trying to run Synplex out of the box without changing anything and am encountering some issues:
I've had to comment out many of the visualization components because of out-of-index errors
e.g.

Error in Parameters_Visualization_Phenotypes (line 6)
    h = heatmap(CellPhenotypeNames([4,6,7]),CellPhenotypeNames([4,6,7]),CellPhenotypeInteraction([4,6,7],[4,6,7],2),'Colormap',jet,'ColorLimits',[0 1]);

once I do this, I'm able to train the model, but am now getting the following error, which seems to think there are more than 3 rows in the Phenotype_Abundance matrix

Index in position 1 exceeds array bounds. Index must not exceed 3.

Error in Modeling_phenotypes (line 88)
        CellCellInter(:,:,iNb) = CellPhenotypeInteraction(:,:,iNb).*(((Phenotype_Abundance(iNb,:)*100)./Perc_Nb_Pheno(iNb,2:end)).^3);

Error in main (line 30)
    last_step_phenotypes = Modeling_phenotypes(BasefolderName,LoadfolderName,...

Do you have any guidance to get this working? Happy to provide more information if necessary.
-Simon