This repository contains supporting Jupyter Notebook for paper "Quantifying emergence and self-organisation of Enterobacter cloacae microbial communities"
To reproduce the results, clone this repository and install python dependencies using conda:
git clone https://github.com/valeriu-balaban/bacteria-emergence
cd bacteria-emergence
conda create -n bacteria-emergence python=3 jupyterlab scikit-image scipy seaborn matplotlib pandas numpy
conda activate bacteria-emergence
jupyter lab
Next, access jupyter lab webpage in browser to run the code to analyze bacteria images in processed data folder.