A Code availability

All code that we used in each phase of the project can be located on Github. Below we listed the repositories used as well as a brief description of their content.

Table A.1: Github repositories used for this project.
Repository Description
https://github.com/ccg-esb-lab/uJ It contains a series of programs in \(\mu \mathrm{J}\), which consist of an \(ImageJ\) macro library for quantifying unicellular bacterial dynamics in microfluidic devices. Besides, it includes all the Python code used for the image analysis processing and our developed custom Napari cell-viewer (see Chapter 1).
https://github.com/jvelezmagic/undergraduate_research_project It contains all the files necessary to reproduce this document in its entirety. In addition, it includes the code used in R to analyze the tabular data of the experiments (see Chapter 2).
https://github.com/jvelezmagic/CellFilamentation In includes all the Julia code used to create the mathematical filamentation model exposed in Chapter 3.