Welcome to SpikeInterface's documentation!
==========================================


SpikeInterface is a Python module to analyze extracellular electrophysiology data.

With a few lines of code, SpikeInterface enables you to load and pre-process the recording, run several
state-of-the-art spike sorters, post-process and curate the output, compute quality metrics, and visualize the results.


Overview of SpikeInterface modules
----------------------------------

.. image:: images/overview.png
  :align: center


SpikeInterface is made of several modules to deal with different aspects of the analysis pipeline:

- read/write many extracellular file formats.
- pre-process extracellular recordings.
- run many popular, semi-automatic spike sorters (kilosort1-4, mountainsort4-5, spykingcircus,
  tridesclous, ironclust, herdingspikes, yass, waveclus)
- run sorters developed in house (lupin, spkykingcicus2, tridesclous2, simple) that compete with
  kilosort4
- run theses polar sorters without installation using containers (Docker/Singularity).
- post-process sorted datasets using th SortingAnalyzer
- compare and benchmark spike sorting outputs.
- compute quality metrics to validate and curate spike sorting outputs.
- visualize recordings and spike sorting outputs in several ways (matplotlib, sortingview, jupyter, ephyviewer)
- export a report and/or export to phy
- curate your sorting with several strategies (ml-based, metrics based, manual, ...)
- offer a powerful Qt-based or we-based viewer in a separate package `spikeinterface-gui <https://github.com/SpikeInterface/spikeinterface-gui>`_ for manual curation that replace phy.
- have powerful sorting components to build your own sorter.
- have a full motion/drift correction framework (See :ref:`motion_correction`)



.. toctree::
    :maxdepth: 1
    :caption: Contents:

    overview
    get_started/index
    tutorials_custom_index
    how_to/index
    modules/index
    api
    development/development
    whatisnew
    authors
    references


Other resources
---------------

To get started with SpikeInterface, you can take a look at the following additional resources:

- | `spiketutorials <https://github.com/SpikeInterface/spiketutorials>`_ is a collection of basic and advanced
  | tutorials. It includes links to videos to dive into the SpikeInterface framework.

- | `SpikeInterface Reports <https://spikeinterface.github.io/>`_ contains several notebooks to reproduce analysis
  | figures of SpikeInterface-based papers and to showcase the latest features of SpikeInterface.

- | The `2020 eLife paper <https://elifesciences.org/articles/61834>`_ introduces the concept and motivation and
  | performs an in-depth comparison of multiple sorters (spoiler alert: they strongly disagree with each other!).
  | **Note**: the code-base and implementation have changed a lot since the "paper" version published in 2020.
  | For detailed documentation we therefore suggest more recent resources, like this documentation and :code:`spiketutorials`.


.. Indices and tables
.. ==================
..
.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`