# 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.