Welcome to the BacStalk documentation!

BacStalk is an interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species (e.g. Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, etc.) and stalk-forming bacteria (e.g. Caulobacter crescentus, Hyphomonas neptunium, Brevundimonas aveniformis, etc.). BacStalk uses phase contrast, brightfield, and/or fluorescence images to segment bacteria and generate demographs, kymographs, histograms, scatterplots. For stalked bacteria, BacStalk can also identify hardly-visible bacterial stalks to observe stalk formation dynamics and bud cell growth. Fluorescence images can be used to measure protein expression patterns along cells and stalks.

Example image from BacStalk

BacStalk uses a very intuitive and modern graphical user interface (GUI, see Screenshots) and provides all tools required for file-handling, metadata extraction, cell/stalk/bud segmentation, cell tracking, data analysis and visualization. BacStalk generates publication-grade figures with only a few clicks. Although BacStalk is based on the Matlab-software, it does not require any programming knowledge to use.

Video tutorials

Contact us!

BacStalk was developed by Raimo Hartmann and Muriel van Teeseling at the Max Planck Institute for Terrestrial Microbiology and Phillips-Universität in Marburg in the labs of Knut Drescher and Martin Thanbichler. You can reach us at bacstalk@gmail.com.

How to cite

Please use the following reference for citing this software after you have used it:

  • Hartmann, R., van Teeseling, M. C. F., Thanbichler, M. & Drescher, K. BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology. Molecular Microbiology (2020). doi:10.1111/mmi.14501


We would like to acknowledge the authors of the following Matlab File Exchange contributions: