.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/astrocytes/astrocyte_interaction.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_astrocytes_astrocyte_interaction.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_astrocytes_astrocyte_interaction.py:


A tripartite interaction between two neurons and one astrocyte
--------------------------------------------------------------

.. only:: html

----

 Run this example as a Jupyter notebook:

  .. card::
    :width: 25%
    :margin: 2
    :text-align: center
    :link: https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator-examples&urlpath=lab%2Ftree%2Fnest-simulator-examples%2Fnotebooks%2Fnotebooks%2Fastrocytes%2Fastrocyte_interaction.ipynb&branch=main
    :link-alt: JupyterHub service

    .. image:: https://nest-simulator.org/TryItOnEBRAINS.png


.. grid:: 1 1 1 1
   :padding: 0 0 2 0

   .. grid-item::
     :class: sd-text-muted
     :margin: 0 0 3 0
     :padding: 0 0 3 0
     :columns: 4

     See :ref:`our guide <run_jupyter>` for more information and troubleshooting.

----


This script simulates a tripartite interaction between two neurons and one
astrocyte. This interaction is part of the astrocyte biology described in
[1]_ that involves the neuron-astrocyte glutamate signaling and the astrocytic
calcium dynamics.

``astrocyte_lr_1994`` is used to model the astrocyte, which implements the
dynamics in the astrocyte based on the articles [2]_, [3]_, and [4]_.
``tsodyks_synapse`` is used to create connections from the presynaptic neuron
to the postsynaptic neuron, and from the presynaptic neuron to the astrocyte.
``sic_connection`` is used to create a connection from the astrocyte to the
postsynaptic neuron. Recordings are made for the following variables: membrance
voltage of the presynaptic neuron, inositol 1,4,5-trisphosphate (IP3), and
calcium in the astrocyte, and slow inward current (SIC) in the postsynaptic
neuron. The result demonstrates a tripartite interaction where the presynaptic
spikes induce changes in IP3 and calcium in the astrocyte, which then induces
the generation of SIC in the postsynaptic neuron.

See Also
~~~~~~~~

:doc:`astrocyte_single`

References
~~~~~~~~~~

.. [1] Bazargani, N., & Attwell, D. (2016). Astrocyte calcium signaling: the
       third wave. Nature neuroscience, 19(2), 182-189. DOI:
       https://doi.org/10.1038/nn.4201

.. [2] Li, Y. X., & Rinzel, J. (1994). Equations for InsP3 receptor-mediated
       [Ca2+]i oscillations derived from a detailed kinetic model: a
       Hodgkin-Huxley like formalism. Journal of theoretical Biology, 166(4),
       461-473. DOI: https://doi.org/10.1006/jtbi.1994.1041

.. [3] De Young, G. W., & Keizer, J. (1992). A single-pool inositol
       1,4,5-trisphosphate-receptor-based model for agonist-stimulated
       oscillations in Ca2+ concentration. Proceedings of the National Academy
       of Sciences, 89(20), 9895-9899. DOI:
       https://doi.org/10.1073/pnas.89.20.9895

.. [4] Nadkarni, S., & Jung, P. (2003). Spontaneous oscillations of dressed
       neurons: a new mechanism for epilepsy?. Physical review letters, 91(26),
       268101. DOI: https://doi.org/10.1103/PhysRevLett.91.268101

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Import all necessary modules for simulation and plotting.

.. GENERATED FROM PYTHON SOURCE LINES 74-78

.. code-block:: Python


    import matplotlib.pyplot as plt
    import nest


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Set parameters for the simulation.

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.. code-block:: Python


    # simulation time
    sim_time = 60000
    # Poisson input for the presynaptic neuron
    poisson_rate_neuro = 1500.0
    # neuron parameters
    params_neuro = {"tau_syn_ex": 2.0}
    # astrocyte parameters
    params_astro = {"IP3_0": 0.16}
    # weights of connections
    w_pre2astro = 1.0
    w_pre2post = 1.0
    w_astro2post = 1.0


.. GENERATED FROM PYTHON SOURCE LINES 95-96

Create and connect the astrocyte and its devices.

.. GENERATED FROM PYTHON SOURCE LINES 96-101

.. code-block:: Python


    astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
    nest.Connect(mm_astro, astrocyte)


.. GENERATED FROM PYTHON SOURCE LINES 102-103

Create and connect the neurons and their devices.

.. GENERATED FROM PYTHON SOURCE LINES 103-113

.. code-block:: Python


    pre_neuron = nest.Create("aeif_cond_alpha_astro", params=params_neuro)
    post_neuron = nest.Create("aeif_cond_alpha_astro", params=params_neuro)
    ps_pre = nest.Create("poisson_generator", params={"rate": poisson_rate_neuro})
    mm_pre = nest.Create("multimeter", params={"record_from": ["V_m"]})
    mm_post = nest.Create("multimeter", params={"record_from": ["I_SIC"]})
    nest.Connect(ps_pre, pre_neuron)
    nest.Connect(mm_pre, pre_neuron)
    nest.Connect(mm_post, post_neuron)


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Create tripartite connectivity.

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.. code-block:: Python


    nest.Connect(pre_neuron, post_neuron, syn_spec={"weight": w_pre2post})
    nest.Connect(pre_neuron, astrocyte, syn_spec={"weight": w_pre2astro})
    nest.Connect(astrocyte, post_neuron, syn_spec={"synapse_model": "sic_connection", "weight": w_astro2post})


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Run simulation and get results.

.. GENERATED FROM PYTHON SOURCE LINES 122-128

.. code-block:: Python


    nest.Simulate(sim_time)
    data_pre = mm_pre.events
    data_post = mm_post.events
    data_astro = mm_astro.events


.. GENERATED FROM PYTHON SOURCE LINES 129-130

Create and show plots.

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.. code-block:: Python


    fig, ax = plt.subplots(2, 2, sharex=True, figsize=(6.4, 4.8), dpi=100)
    axes = ax.flat
    axes[0].plot(data_pre["times"], data_pre["V_m"])
    axes[1].plot(data_astro["times"], data_astro["IP3"])
    axes[2].plot(data_post["times"], data_post["I_SIC"])
    axes[3].plot(data_astro["times"], data_astro["Ca_astro"])
    axes[0].set_title(f"Presynaptic neuron\n(Poisson rate = {poisson_rate_neuro} Hz)")
    axes[0].set_ylabel("Membrane potential (mV)")
    axes[2].set_title("Postsynaptic neuron")
    axes[2].set_ylabel("Slow inward current (pA)")
    axes[2].set_xlabel("Time (ms)")
    axes[1].set_title("Astrocyte")
    axes[1].set_ylabel(r"[IP$_{3}$] ($\mu$M)")
    axes[3].set_ylabel(r"[Ca$^{2+}$] ($\mu$M)")
    axes[3].set_xlabel("Time (ms)")
    plt.tight_layout()
    plt.show()
    plt.close()


.. _sphx_glr_download_auto_examples_astrocytes_astrocyte_interaction.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: astrocyte_interaction.ipynb <astrocyte_interaction.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: astrocyte_interaction.py <astrocyte_interaction.py>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_