This tutorial describes a workflow to detect collective cell signalling 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 Jupyter 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.
The video below illustrates:
- raw microscopy time-lapse images of ERK activity in live MCF10A cells measured with the ERK-KTR biosensor (left),
- segmented nuclei with correlated, collective ERK activity waves indicates with coloured dots (middle),
- noodle plot showing when single cells are participating in collective events indicated by different colours (right).
SuppVideo1_ERK-CEs_small.mp4
The entire analysis can be performed in the arcos-gui, an interactive plugin for the napari image viewer. The 2-minute-long screencast can be watched on YouTube.