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Tutorials
=========

Longer form tutorials about using spikeinterface. Many of these are downloadable as notebooks or python scripts so that you can "code along" to the tutorials.

If you're new to SpikeInterface, we recommend trying out the :ref:`get_started/quickstart:Quickstart tutorial` first.

Updating from legacy
--------------------

.. toctree::
   :maxdepth: 1

   waveform_extractor_to_sorting_analyzer



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Core tutorials
---------------

These tutorials focus on the :py:mod:`spikeinterface.core` module



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    <div class="sphx-glr-thumbcontainer" tooltip="The :py~spikeinterface.core.BaseRecording is the basic class for handling recorded data. Here is how it works.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_core_plot_1_recording_extractor.py`

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      <div class="sphx-glr-thumbnail-title">Recording objects</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The :py~spikeinterface.core.BaseSorting is the basic class for handling spike sorted data. Here is how it works.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
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  :ref:`sphx_glr_tutorials_core_plot_2_sorting_extractor.py`

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      <div class="sphx-glr-thumbnail-title">Sorting objects</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In order to properly spike sort, you may need to load information related to the probe you are using.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
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  :ref:`sphx_glr_tutorials_core_plot_3_handle_probe_info.py`

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      <div class="sphx-glr-thumbnail-title">Handling probe information</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="SpikeInterface provides an object to gather a Recording and a Sorting to perform various analyses and visualizations of the sorting : :py~spikeinterface.core.SortingAnalyzer.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
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  :ref:`sphx_glr_tutorials_core_plot_4_sorting_analyzer.py`

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      <div class="sphx-glr-thumbnail-title">SortingAnalyzer</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Sometimes a recording can be split into several subparts, for instance a baseline and an intervention.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
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  :ref:`sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py`

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      <div class="sphx-glr-thumbnail-title">Append and/or concatenate segments</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Extracellular electrophysiology commonly involves synchronization of events across many timestreams. For example, an experiment may involve displaying stimuli to an animal and recording the stimuli-evoked neuronal responses. Accurate timing representation is critical for proper synchronization during analysis.">

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  .. image:: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_ver2_thumb.png
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  :ref:`sphx_glr_tutorials_core_plot_6_handle_times_ver2.py`

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      <div class="sphx-glr-thumbnail-title">How SpikeInterface Handles Time</div>
    </div>


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.. toctree::
   :hidden:

   /tutorials/core/plot_1_recording_extractor
   /tutorials/core/plot_2_sorting_extractor
   /tutorials/core/plot_3_handle_probe_info
   /tutorials/core/plot_4_sorting_analyzer
   /tutorials/core/plot_5_append_concatenate_segments
   /tutorials/core/plot_6_handle_times_ver2

Extractors tutorials
--------------------

The :py:mod:`spikeinterface.extractors` module is designed to load and save recorded and sorted data and to handle
probe information.

- RecordingExtractors
- SortingExtractors
- Handling probe information



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    <div class="sphx-glr-thumbcontainer" tooltip="SpikeInterface can read various formats of &quot;recording&quot; (traces) and &quot;sorting&quot; (spike train) data.">

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  .. image:: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_extractors_plot_1_read_various_formats.py`

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      <div class="sphx-glr-thumbnail-title">Read various format into SpikeInterface</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Some file formats store data in convenient types that require offsetting and scaling in order to convert the traces to uV. This example shows how to work with unscaled and scaled traces in the :pyspikeinterface.extractors module.">

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  .. image:: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
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  :ref:`sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py`

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      <div class="sphx-glr-thumbnail-title">Working with unscaled traces</div>
    </div>


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.. toctree::
   :hidden:

   /tutorials/extractors/plot_1_read_various_formats
   /tutorials/extractors/plot_2_working_with_unscaled_traces

Quality metrics tutorial
------------------------

The :code:`spikeinterface.qualitymetrics` module allows users to compute various quality metrics to assess the
goodness of a spike sorting output.



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    <div class="sphx-glr-thumbcontainer" tooltip="After spike sorting, you might want to validate the &#x27;goodness&#x27; of the sorted units. This can be done using the qualitymetrics submodule, which computes several quality metrics of the sorted units.">

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  .. image:: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
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  :ref:`sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py`

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      <div class="sphx-glr-thumbnail-title">Quality Metrics Tutorial</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="After spike sorting and computing quality metrics, you can automatically curate the spike sorting output using the quality metrics that you have calculated.">

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  .. image:: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
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  :ref:`sphx_glr_tutorials_qualitymetrics_plot_4_curation.py`

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      <div class="sphx-glr-thumbnail-title">Curation Tutorial</div>
    </div>


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.. toctree::
   :hidden:

   /tutorials/qualitymetrics/plot_3_quality_mertics
   /tutorials/qualitymetrics/plot_4_curation

Comparison tutorial
-------------------

The :code:`spikeinterface.comparison` module allows to compare sorter output or benchmark to ground truth.



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    <div class="sphx-glr-thumbcontainer" tooltip="This generate a erroneous sorting to illustrate in some example">

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  .. image:: /tutorials/comparison/images/thumb/sphx_glr_generate_erroneous_sorting_thumb.png
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  :ref:`sphx_glr_tutorials_comparison_generate_erroneous_sorting.py`

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      <div class="sphx-glr-thumbnail-title">This generate a erroneous sorting to illustrate in some example</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Here a synthetic dataset will demonstrate some weaknesses.">

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  .. image:: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
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  :ref:`sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py`

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      <div class="sphx-glr-thumbnail-title">Explore sorters weaknesses with ground-truth comparison</div>
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.. toctree::
   :hidden:

   /tutorials/comparison/generate_erroneous_sorting
   /tutorials/comparison/plot_5_comparison_sorter_weaknesses

Widgets tutorials
-----------------

The :code:`widgets` module contains several plotting routines (widgets) for
visualizing recordings and sorting data, probe layout, and many more!



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    <div class="sphx-glr-thumbcontainer" tooltip="Here is a gallery of all the available widgets using RecordingExtractor objects.">

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  .. image:: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_widgets_plot_1_rec_gallery.py`

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      <div class="sphx-glr-thumbnail-title">RecordingExtractor Widgets Gallery</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Here is a gallery of all the available widgets using SortingExtractor objects.">

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  .. image:: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_widgets_plot_2_sort_gallery.py`

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      <div class="sphx-glr-thumbnail-title">SortingExtractor Widgets Gallery</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Here is a gallery of all the available widgets using a pair of RecordingExtractor-SortingExtractor objects.">

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  .. image:: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py`

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      <div class="sphx-glr-thumbnail-title">Waveforms Widgets Gallery</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Some widgets are useful before sorting and works with the &quot;peaks&quot; given by the detect_peaks() function.">

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  .. image:: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
    :alt:

  :ref:`sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py`

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      <div class="sphx-glr-thumbnail-title">Peaks Widgets Gallery</div>
    </div>


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.. toctree::
   :hidden:

   /tutorials/widgets/plot_1_rec_gallery
   /tutorials/widgets/plot_2_sort_gallery
   /tutorials/widgets/plot_3_waveforms_gallery
   /tutorials/widgets/plot_4_peaks_gallery


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  .. container:: sphx-glr-footer sphx-glr-footer-gallery

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

      :download:`Download all examples in Python source code: tutorials_python.zip </tutorials/tutorials_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: tutorials_jupyter.zip </tutorials/tutorials_jupyter.zip>`


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