Software and associated data provided here support Perng et al, 2026 (https://doi.org/10.64898/2026.04.16.719078).

The folder "VCell_models" contains Virtual Cell reaction-diffusion models referenced the manuscript. 


MATLAB source code and software compiled for Windows 11 and Mac PCs are provided for the programs listed below. 

The compiled MATLAB programs require installation of MATLAB Runtime(R2023a). 
Download and install the Mac or Windows version of the MATLAB Runtime for R2023a from the following link on the MathWorks website:

    https://www.mathworks.com/products/compiler/mcr/index.html


"Fast_Rx_Dif" models immunohistochemistry (IHC) reaction-diffusion kinetics, according to parameters provided by the user, by rapid interpolation using previously calculated reaction data.

"Standalone_curve_fit" objectively finds reaction parameters most consistent IHC time course data provided by the user.

"ML_Rx_dif_batch" models IHC kinetics for one or more reactions based on parameters provided by the user in a separate .csv file.

"Wasserstein_flow" calculates a scale-invariant metric of spatial heterogeneity in a square image.

The folder "Image_analysis_demo_code" contains a set of MATLAB and ImageJ programs to process experimental Keyence .tif image data (download representative images from https://data.mendeley.com/datasets/hvgwj9mn92/1) to obtain IHC reaction time course and reaction parameters.

All MATLAB programs require files found in the "Program_Data" folder. 

User guides for all programs are provided.