.. _sphx_glr_auto_examples_howto:

How to
------

These are short examples that show how to use HNN-core API to accomplish specific
tasks.



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    <div class="sphx-glr-thumbnails">

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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to inspect the firing pattern of cells in the HNN model.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_firing_pattern_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_howto_plot_firing_pattern.py`

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      <div class="sphx-glr-thumbnail-title">01. Plot firing pattern</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The main output of HNN simulations is the &#x27;dipole&#x27; waveform, i.e., the net intracellular current flowing in pyramidal cell apical dendrites. At the large distances between cells and M/EEG sensors, this &#x27;primary&#x27; current is the main contributor to the measured fields. Close to the cells, the local field potential (LFP) is the result of intracellular current leaking into the extracellular medium through active and passive membrane channels. Under some simplifying assumptions, we may approximate the LFP at virtual electrodes placed in and around the HNN network model.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_record_extracellular_potentials_thumb.png
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  :ref:`sphx_glr_auto_examples_howto_plot_record_extracellular_potentials.py`

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      <div class="sphx-glr-thumbnail-title">02. Record extracellular potentials</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to modify the network connectivity.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_connectivity_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_howto_plot_connectivity.py`

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      <div class="sphx-glr-thumbnail-title">03. Modifying local connectivity</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use the MPI backend for simulating dipoles using HNN-core.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_simulate_mpi_backend_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_howto_plot_simulate_mpi_backend.py`

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      <div class="sphx-glr-thumbnail-title">04. Use MPI backend for parallelization</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to optimize the parameters of the model simulation to match an experimental dipole waveform.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_optimize_evoked_thumb.png
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  :ref:`sphx_glr_auto_examples_howto_optimize_evoked.py`

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      <div class="sphx-glr-thumbnail-title">05. Optimize simulated evoked response parameters</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to animate HNN simulations">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_hnn_animation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_howto_plot_hnn_animation.py`

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      <div class="sphx-glr-thumbnail-title">06. Animating HNN simulations</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to do batch simulations in HNN-core, allowing users to efficiently run multiple simulations with different parameters for comprehensive analysis.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_plot_batch_simulate_thumb.png
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  :ref:`sphx_glr_auto_examples_howto_plot_batch_simulate.py`

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      <div class="sphx-glr-thumbnail-title">07. Batch Simulation</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to optimize the power spectral density (PSD) of a current dipole signal with significant alpha and beta spectral components.">

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  .. image:: /auto_examples/howto/images/thumb/sphx_glr_optimize_rhythmic_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_howto_optimize_rhythmic.py`

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      <div class="sphx-glr-thumbnail-title">08. Optimize simulated rhythmic responses</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /auto_examples/howto/plot_firing_pattern
   /auto_examples/howto/plot_record_extracellular_potentials
   /auto_examples/howto/plot_connectivity
   /auto_examples/howto/plot_simulate_mpi_backend
   /auto_examples/howto/optimize_evoked
   /auto_examples/howto/plot_hnn_animation
   /auto_examples/howto/plot_batch_simulate
   /auto_examples/howto/optimize_rhythmic