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Robustness_Microfluidics


NOTE. This collection of scripts and macros has been developed for the following publication:
Quantifying microbial robustness in dynamic environments using microfluidic single-cell cultivation.
Blöbaum, L., Torello Pianale, L., Olsson, L., Grünberger, A.. Microb Cell Fact 23, 44 (2024).
https://doi.org/10.1186/s12934-024-02318-z


Collection of scripts to analyse microfluidics data:
  • Pipeline for semi-automated analysis of images (using Fiji)
  • Script for data analysis (performance and orbustness) deriving from Fiji (using R).

Getting started:

  1. Install R (https://cran.r-project.org/), RStudio (https://posit.co/download/rstudio-desktop/) and then the RMarkdown package in R (https://rmarkdown.rstudio.com/). No need to pre-install other packages needed for the scripts as they will be installed automatically (if they are not already).
  2. Install Fiji (Fiji: https://imagej.net/software/fiji/downloads), if microscopy images need to be analysed.
  3. Always check the data organisation in the example files provided.
  4. Follow the directions in the scripts and macros (details before each chunk and important sections of scripts).
  5. Make changes upon need (replace grouping variables, way of importing data, etc.).

Luca Torello Pianale, [email protected]

Chalmers University of Technology, Department of Life Sciences, Industrial Biotechnology Division.

Created: December, 2023.

The scripts were tested with:

  1. R Version 4.3.1 (2021-11-01)
  2. RStudio (2021.09.2 Build 382)
  3. ImageJ 1.54j

Acknowledgment of support: This material is based upon work supported by the Novo Nordisk Foundation grant DISTINGUISHED INVESTIGATOR 2019 - Research within biotechnology-based synthesis & production (#0055044).