This page contains various pieces of code that may be of use to the community:

Packing Analyzer [1] is a software package for detecting the geometry of epithelial tissue. One slightly annoyance with the package is the way that, following segmentation, the ‘bd_fate’ files are placed in separate folders and not labelled by time point. I have written a shell script that copies the bd_fate files into one folder and renames them with time information.

To use:
Download the script and place it in the folder containing the individual folders for the bd_fate files: PA_rename_bd_fate

Turn the file into an executable by typing the following into your terminal (only needs to be done the first time you use it):
mv “PA_rename_bd_fate.txt” “PA_rename_bd_fate”
chmod 755 PA_rename_bd_fate

Run the file:

[1] B. Aigouy, R. Farhadifar, D. B. Staple, A. Sagner, J.-C. Röper, F. Jülicher,
and S. Eaton. “Cell Flow Reorients the Axis of Planar Polarity in the Wing
Epithelium of Drosophila”. In: Cell 142.5 (2010), pp. 773–786.