This repository contains scripts required to reproduce the results in the publication of Grädel et al. Tracking Coordinated Cellular Dynamics in Time-Lapse Microscopy with ARCOS.px (link).

ARCOS.px is a computational method to identify and track clusters of correlated cell signaling in time-lapse microscopy images. It is the latest addition to the ARCOS ecosystem developed in the Cellular Dynamics Lab at the University of Bern. ARCOS.px is a Python software package, and a dedicated interactive plugin for the napari image viewer.

The scripts folder contains the following Python scripts and Jupyter notebooks.

Python scripts to simulate circular & directional waves, and target & chaotic patterns using cellular automaton.

The scripts reproduce Figure S3 and Movies S1−S5.

Python scripts to simulate merges and splits.

The scripts reproduce Figure S4A,B and Movie S6.

Python script to analyze optogenetically induced synthetic RhoA activity wave in REF52 cells. Cells express a RhoA activity sensor 2xrGBD and the optogenetic actuator optoLARG.

The script reproduces Figure 1B,C and Movie S7.

Python script to track podosomes in REF52 cells; reproduces Figure 2A−D and Movie S8.

R scripts to analyze lineage length and split/merge rate in cells treated with blebbistatin, latrunculin B and Y-27632; reproduce Figures 2E,F & S4C-E, and Movie S9.

Python script to track active wave-like dynamics in REF52 cells; reproduces Figure 3 and Movie S10.

Python script to process images of MCF10A WT epithelial monolayer treated with increasing dosages of Doxorubicin; reproduces Figure 4 and Movie S11.

Python notebook to demonstrate two methods to initiate spatial clusters:

1. A custom clustering function that performs instance segmentation instead of clustering. Arcos then utilises this to track clusters.
2. Initialise the tracker using a seed image, priming it for specific cluster ID propagation. implemented in the ImageTracker class.

The data folder is a placeholder for files stored on the BioImage Archive due to GitHub's size restrictions. Use this link to download and unpack the data into that folder. Once in place, the scripts can process the data and reproduce the figures.