Code Supplement to: Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis (Kasahara et. al) (submitted)

This repository provides reproducible microscopy image analysis to reproduce the reported data in our paper.

Microscopy Data

Our microscopy data is available here but it is described in the next section how to download it automatically for reproduction.

Segmentation and Fluorescence Analysis

In order to reproduce the result extraction from the microscopy images we provide the analysis scripts. Please follow the steps below to reproduce our results:

1. Clone our repo

   git clone https://github.com/JuBiotech/Supplement-to-Kasahara-et-al.-2023a.git Supplement-to-Kasahara-et-al
   cd Supplement-to-Kasahara-et-al

2. Download the microscopy data

   wget -O data.zip https://fz-juelich.sciebo.de/s/KTBjtTZBZawpClS/download
   unzip data.zip

3. Create the analysis environment using anaconda:

   conda env create -f conda.yml
   conda activate oxygen-analysis

4. Start the jupyter notebook server

   jupyter notebook
   

   and navigate to the MetaScript.ipynb file. Executing the cells in the file will reproduce and plot the fluorescence intensity developments reported in our paper.