Updated 14 Oct 2020
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.
Hartmann, Raimo, et al. “BacStalk: A Comprehensive and Interactive Image Analysis Software Tool for Bacterial Cell Biology.” Molecular Microbiology, vol. 114, no. 1, Wiley, Apr. 2020, pp. 140–50, doi:10.1111/mmi.14501.
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
Inspired by: GUI Layout Toolbox, SplashScreen, Efficient subpixel image registration by cross-correlation, isToolboxAvailable, Neighbour points in a matrix, parfor_progressbar, Red Blue Colormap, enable/disable entire figure window, findjobj - find java handles of Matlab graphic objects
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