Biological Cybernetics

, Volume 110, Issue 6, pp 417–434 | Cite as

Nonlinear statistical data assimilation for HVC\(_{\mathrm{RA}}\) neurons in the avian song system

  • Nirag Kadakia
  • Eve Armstrong
  • Daniel Breen
  • Uriel Morone
  • Arij Daou
  • Daniel Margoliash
  • Henry D. I. Abarbanel
Original Article


With the goal of building a model of the HVC nucleus in the avian song system, we discuss in detail a model of HVC\(_{\mathrm{RA}}\) projection neurons comprised of a somatic compartment with fast Na\(^+\) and K\(^+\) currents and a dendritic compartment with slower Ca\(^{2+}\) dynamics. We show this model qualitatively exhibits many observed electrophysiological behaviors. We then show in numerical procedures how one can design and analyze feasible laboratory experiments that allow the estimation of all of the many parameters and unmeasured dynamical variables, given observations of the somatic voltage \(V_\mathrm{s}(t)\) alone. A key to this procedure is to initially estimate the slow dynamics associated with Ca, blocking the fast Na and K variations, and then with the Ca parameters fixed estimate the fast Na and K dynamics. This separation of time scales provides a numerically robust method for completing the full neuron model, and the efficacy of the method is tested by prediction when observations are complete. The simulation provides a framework for the slice preparation experiments and illustrates the use of data assimilation methods for the design of those experiments.


Data assimilation Parameter estimation Dynamical systems Spiking neuron models Neuronal dynamics Song system Ion channel properties 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Nirag Kadakia
    • 1
  • Eve Armstrong
    • 2
  • Daniel Breen
    • 1
  • Uriel Morone
    • 1
  • Arij Daou
    • 3
  • Daniel Margoliash
    • 3
  • Henry D. I. Abarbanel
    • 4
  1. 1.Department of PhysicsUniversity of CaliforniaLa JollaUSA
  2. 2.BioCircuits InstituteUniversity of CaliforniaLa JollaUSA
  3. 3.Department of Organismal Biology and AnatomyUniversity of ChicagoChicagoUSA
  4. 4.Marine Physical Laboratory (Scripps Institution of Oceanography), Department of PhysicsUniversity of CaliforniaLa JollaUSA

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