This repository includes the code written for the analysis and quantification of long-range cell-cell mechnaical communication as presented in the paper: https://www.biorxiv.org/content/10.1101/2020.07.30.223149v1

figures.py includes all figures generated for the paper by order.

fiji_scripts includes all scripts used in Fiji software.

fiber_density folder includes all methods for analyses made based on quantification of the fibrin channel for both simulations and experiments.

libs folder includes all methods used during the analysis process, including configurations and paths. Simulations-specific and experiments-specific methods are located in the inner folders.

methods folder includes all methods used in the pre-processing such as creating new cell pairs, fake pairs, tracking of cells, printing data and computing the normalization parameters for z-score calculation.

plotting folder mainly include a modified version that uses plotly lib for creating and saving figures.

data folder includes the quantified windows of cell pairs for simulations and experiments in CSV format. Update: example raw data was added.