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Extracting intracellular diffusive states and transition rates from single-molecule tracking data

Nature Methods volume 10, pages 265269 (2013) | Download Citation


We provide an analytical tool based on a variational Bayesian treatment of hidden Markov models to combine the information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. The method identifies the number of diffusive states and the state transition rates. Using this method we have created an objective interaction map for Hfq, a protein that mediates interactions between small regulatory RNAs and their mRNA targets.

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We thank I. Barkefors for her careful and critical reading of the manuscript. M.L. is grateful to C.H. Wiggins and J.-W. van de Meent for insightful discussions. This work was supported by the European Research Council (J.E.), the Knut and Alice Wallenberg Foundation (J.E.), Vetenskapsrådet (J.E.), the Göran Gustafsson Foundation (J.E.), the Wenner-Gren Foundations (M.L.) and the Center for Biomembrane Research (M.L.).

Author information

Author notes

    • Fredrik Persson
    •  & Martin Lindén

    These authors contributed equally to this work.


  1. Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

    • Fredrik Persson
    • , Cecilia Unoson
    •  & Johan Elf
  2. Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

    • Martin Lindén


  1. Search for Fredrik Persson in:

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J.E. and M.L. conceived the method, M.L. designed the vbSPT algorithm, M.L. and F.P. implemented and tested the algorithm, F.P. designed and implemented the image analysis and particle-tracking algorithms, and C.U. cloned and characterized the bacterial strains. F.P. and J.E. built the optical setup. F.P., C.U. and J.E. designed the experiments, and C.U. and F.P. performed the experiments. F.P., M.L., C.U. and J.E. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Johan Elf.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Tables 1–7 and Supplementary Notes 1–5

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    Supplementary Software

    vbSPT (variational Bayes single-particle tracking) software

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