Tracking B Cells from Two-Photon Microscopy Images Using Sequential Monte Carlo

  • David Olivieri
  • Ivan Gomez Conde
  • Jose Faro
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 93)


A python based software package that implements Sequential Monte Carlo (SMC) tracking is used for extracting dynamical information of a large collection of individual cells from two-photon microscopy image sequences.We show how our software tool is useful for quantifying the motility of B cells involved in immune response and for validating computational immunologic models. We describe the theory behind our algorithm and discuss the architecture of our software. Finally, we demonstrate both the functionality and utility using a practical example from videos of the germinal center reactions.


Sequential Monte Carlo Germinal Center Reaction OpenCV Library Principal Class Reference Histogram 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Allen, C.D.C., Okada, T., Tang, H.L., Cyster, J.G.: Imaging of Germinal Center Selection Events During Affinity Maturation. Science 315(5811), 528–531 (2007)CrossRefGoogle Scholar
  2. 2.
    Beltman, J.B., Maree, A.F.M., de Boer, R.J.: Analysing immune cell migration. Nat. Rev. Immunol. 9(11), 789–798 (2009)CrossRefGoogle Scholar
  3. 3.
    Bradski, G.: The OpenCV Library. Dr. Dobb’s Journal of Software Tools (2000)Google Scholar
  4. 4.
    Denk, W., Strickler, J., Webb, W.: Two-photon laser scanning fluorescence microscopy. Science 248(4951), 73–76 (1990)CrossRefGoogle Scholar
  5. 5.
    Doucet, A., de Freitas, N., Gordon, N.: Sequential Monte Carlo methods in practice. Series Statistics for Engineering and Information Science. Springer, Heidelberg (2001)zbMATHGoogle Scholar
  6. 6.
    Hand, A.J., Sun, T., Barber, D.C., Hose, D.R., MacNeil, S.: Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration. J. Microscopy 234, 62–79 (2009)MathSciNetCrossRefGoogle Scholar
  7. 7.
    Hauser, A.E., Junt, T.R., Mempel, T., Sneddon, M.W., Kleinstein, S.H., Henrickson, S.E., von Andrian, U.H., Shlomchik, M.J., Haberman, A.M.: Definition of germinal-center b cell migration in vivo reveals predominant intrazonal circulation patterns. Immunity 26(5), 655–667 (2007)CrossRefGoogle Scholar
  8. 8.
    Isard, M., Blake, A.: Condensation - conditional density propagation for visual tracking. International Journal of Computer Vision 29, 5–28 (1998)CrossRefGoogle Scholar
  9. 9.
    Meyer-Hermann, M.E., Maini, P.K.: Interpreting two-photon imaging data of lymphocyte motility. Phys. Rev. E 71(6), 061912 (2005)CrossRefGoogle Scholar
  10. 10.
    Miller, M.J., Wei, S.H., Parker, I., Cahalan, M.D.: Two-photon imaging of lymphocyte motility and antigenresponse in intact lymph node. Science 296(5574), 1869–1873 (2002)CrossRefGoogle Scholar
  11. 11.
    Moreira, J.S., Faro, J.: Re-evaluating the recycling hypothesis in the germinal centre. Immunol. Cell. Biol. 84, 404–410 (2006)CrossRefGoogle Scholar
  12. 12.
    Moreira, J.S., Faro, J.: Modelling two possible mechanisms for the regulation of the germinal centre dynamics. J. Immunol. 177, 3705–3710 (2006)Google Scholar
  13. 13.
    O’Connor, M.J., Hauser, A.E., Haberman, A.M., Kleinstein, S.H.: Activated germinal-center b cells undergo directed migration. In: IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009, November 2009, pp. 327–331 (2009)Google Scholar
  14. 14.
    Perelson, A.S., Weisbuch, G.: Immunology for physicists. Rev. Mod. Phys. 69(4), 1219–1268 (1997)CrossRefGoogle Scholar
  15. 15.
    Schwickert, T.A., Lindquist, R.L., Shakhar, G., Livshits, G., Skokos, D., Kosco-Vilbois, M.H., Dustin, M.L., Nussenzweig, M.C.: In vivo imaging of germinal centres reveals a dynamic open structure. Nature 446, 83–87 (2007)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • David Olivieri
    • 1
  • Ivan Gomez Conde
    • 1
  • Jose Faro
    • 2
  1. 1.Computer ScienceU. VigoSpain
  2. 2.Fac. BiologyU. VigoSpain

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