This repository contains a collection of scripts that is broadly categorised by analytical theme for the paper:

Single-cell phenomics reveals behavioural and mechanical heterogeneities underpinning collective migration during mouse anterior patterning, bioRxiv, 2023, written by Stower et al.

The scripts were not initially developed as a reusable library in mind. We make it available here organized by analysis theme to serve as a guide reference for the computational analyses described in the main and methods section of the paper so that readers may take snippets from.

These scripts were developed initialy with Python 2.7 and MATLAB 2019b. It was verified to work also with Python 3.6/3.7 with corresponding compatible MATLAB versions on Windows 7/10 and linux (Ubuntu 17) OS systems. The DeepFlow optical flow computation has been tested to be compatible with Python OpenCV 4.5.1.