MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis

  • Nature Microbiology 1, Article number: 16077 (2016)
  • doi:10.1038/nmicrobiol.2016.77
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Single-cell analysis of bacteria and subcellular protein localization dynamics has shown that bacteria have elaborate life cycles, cytoskeletal protein networks and complex signal transduction pathways driven by localized proteins. The volume of multidimensional images generated in such experiments and the computation time required to detect, associate and track cells and subcellular features pose considerable challenges, especially for high-throughput experiments. There is therefore a need for a versatile, computationally efficient image analysis tool capable of extracting the desired relationships from images in a meaningful and unbiased way. Here, we present MicrobeJ, a plug-in for the open-source platform ImageJ1. MicrobeJ provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets. It performs the most common intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci and organelles, determines their subcellular localization with subpixel resolution, and tracks them over time. Because a dynamic link is maintained between the images, measurements and all data representations derived from them, the editor and suite of advanced data presentation tools facilitates the image analysis process and provides a robust way to verify the accuracy and veracity of the data.

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The authors thank all members of the Brun laboratory for many discussions. In particular, the authors thank B. LaSarre and C. Ellison for useful feedback about MicrobeJ and D. Kysela and L. Espinosa for discussions and reading the manuscript. The authors thank S. Schlimpert, N. Feirer, C. Grangeasse, T. Doan, P. Brown and B. LaSarre for providing images from S. venezuelae cells, A. tumefaciens, S. pneumoniae, B. subtilis, P. hirshii and R. palustris, respectively. The authors thank M. Thanbichler for the pvan-ftsZ-yfp carrying the Caulobacter strain. This research was supported by National Institutes of Health grants GM51986 and GM113172, and by seed funding from the Indiana University Office of the Vice-President for Research. This project was supported, in part, by the Indiana Clinical and Translational Sciences Institute funded, in part, by grant UL1TR001108 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award.

Author information

Author notes

    • Adrien Ducret

    Present address: Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Université Lyon 1, CNRS, UMR 5086, 7 passage du Vercors, Lyon Cedex 07 69367, France.


  1. Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, Indiana 47405, USA

    • Adrien Ducret
    • , Ellen M. Quardokus
    •  & Yves V. Brun


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A.D. wrote the ImageJ plugin. A.D. and Y.V.B. planned the project. A.D. and E.M.Q. performed the experiments. A.D., E.M.Q. and Y.V.B. analysed the data. A.D., E.M.Q. and Y.V.B. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Adrien Ducret or Yves V. Brun.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Results, Supplementary Figures 1-5, Supplementary Video legends, Supplementary Table 1 and Supplementary References.

  2. 2.

    Supplementary Table 2

    Fields of the MicrobeJ data structure containing particle properties or complementary information based on user-selected options.


  1. 1.

    Supplementary Video 1

    Presentation of the MicrobeJ workflow.

  2. 2.

    Supplementary Video 2

    FtsZ-YFP localization in C. crescentus.

  3. 3.

    Supplementary Video 3

    Example of an advanced image analysis with MicrobeJ in real-time.

  4. 4.

    Supplementary Video 4

    FtsZ-YFP localization in a filamentous C. crescentus cell.

  5. 5.

    Supplementary Video 5

    Example of automated and manual segmentation with MicrobeJ.