A tutorial workflow for detecting collective signalling events in microscopy images and accompanies the manuscript published in Methods in Microscopy. The raw data microscopy data required to perform the analysis are deposited on Mendeley Data (1.2 GB).
The biological phenomenon studied here are apoptosis-induced collective ERK activity signalling waves in starved, wild type MCF10A epithelium, published earlier in the journal Developmental Cell. The key computational components of the Jyputer notebook arcos-tutorial.ipynb are:
- StarDist for image segmentation,
- scikit-image for image manipulation,
- btrack for object tracking,
- ARCOS, an algorithm for Automatic Recognition of COllective Signalling, described extensively in the Journal of Cell Biology and available online as R and Python packages, as well as a plugin for the napari image viewer.
