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.
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.
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 firstname.lastname@example.org.
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. bioRxiv (2018). doi:10.1101/360230
We would like to acknowledge the authors of the following Matlab File Exchange contributions:
- David Sampson and Ben Tordoff GUI Layout Toolbox
- Ben Tordoff Splash Screen
- Manuel Guizar Efficient subpixel image registration by cross-correlation
- Reza Ahmadzadeh isToolboxAvailable
- Ronald Ouwerkerk Neighbour points in a matrix
- Daniel Terry parfor_progressbar
- Adam Auton Red Blue Colormap
- Yair Altman Enable/disable entire figure window & findjobj
- John C. Crocker and David G. Grier Band-pass filter