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.

BacStalk uses a very intuitive and modern graphical user interface 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.