spiketools

spiketools: a Python package for analyzing single-unit neural activity - Published in JOSS (2023)

https://github.com/spiketools/spiketools

Keywords

Scientific Fields

Repository

Tools for analyzing spiking data from single-neuron recodings.

README.rst

spiketools
==========

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``spiketools`` is a collection of tools and utilities for analyzing spiking data.

Overview
--------

``spiketools`` is an open-source module for processing and analyzing single-unit activity from neuro-electrophysiological recordings.

Available sub-modules in ``spiketools`` include:

- ``measures`` : measures and conversions that can be applied to spiking data
- ``objects`` : objects that can be used to manage spiking data
- ``spatial`` : space related functionality and measures
- ``stats`` : statistical measures for analyzing spiking data
- ``sim`` : simulations of spiking activity and related functionality
- ``plts`` : plotting functions for visualizing spike data and related measures
- ``utils`` : additional utilities for working with spiking data

Scope
-----

``spiketools`` is currently organized around analyses of single cell activity.

The current scope does not include population measures, though this may be extended in the future.

Note that ``spiketools`` does *not* cover spike sorting.
Check out `spikeinterface `_ for spike sorting.

Documentation
-------------

Documentation for ``spiketools`` is available
`here `_.

The documentation includes:

- `Tutorials `_:
  which describe and provide examples for each sub-module
- `API List `_:
  which lists and describes everything available in the module
- `Glossary `_:
  which defines key terms used in the module

If you have a question about using ``spiketools`` that doesn't seem to be covered by the documentation, feel free to
open an `issue `_ and ask!

Dependencies
------------

``spiketools`` is written in Python, and requires Python >= 3.7 to run.

It has the following required dependencies:

- `numpy `_
- `pandas `_
- `scipy `_
- `matplotlib `_

There are also optional dependencies, that offer extra functionality:

- `statsmodels `_
  is needed for some statistical measures, for example ANOVAs
- `pytest `_
  is needed to run the test suite locally

Installation
------------

The current release version of `spiketools` is the 0.X.X series.

See the `changelog `_ for notes on major version releases.

**Stable Release Version**

To install the latest stable release, you can use pip:

.. code-block:: shell

    $ pip install spiketools

Optionally, to include dependencies required for the `stats` module:

.. code-block:: shell

    $ pip install spiketools[stats]

**Development Version**

To get the current development version, first clone this repository:

.. code-block:: shell

    $ git clone https://github.com/spiketools/spiketools

To install this cloned copy, move into the directory you just cloned, and run:

.. code-block:: shell

    $ pip install .

**Editable Version**

To install an editable version, download the development version as above, and run:

.. code-block:: shell

    $ pip install -e .

Reference
---------

If you use this code in your project, please cite:

.. code-block:: text

    Donoghue, T., Maesta-Pereira, S., Han C. Z., Qasim, S. E., & Jacobs, J. (2023)
    spiketools: A Python package for analyzing single-unit neural activity.
    Journal of Open Source Software, 8(91), 5268. DOI: 10.21105/joss.05268

Direct Link: https://doi.org/10.21105/joss.05268

For citation information, see also the
`citation file `_.

Contribute
----------

This project welcomes and encourages contributions from the community!

To file bug reports and/or ask questions about this project, please use the
`Github issue tracker `_.

To see and get involved in discussions about the module, check out:

- the `issues board `_
  for topics relating to code updates, bugs, and fixes
- the `development page `_
  for discussion of potential major updates to the module

When interacting with this project, please use the
`contribution guidelines `_
and follow the
`code of conduct `_.

Owner

JOSS Publication

spiketools: a Python package for analyzing single-unit neural activity

Published

November 14, 2023

DOI

10.21105/joss.05268

Volume 8, Issue 91, Page 5268

Authors

Thomas Donoghue
Department of Biomedical Engineering, Columbia University, New York, United States of America

Sandra Maesta-Pereira
Department of Biomedical Engineering, Columbia University, New York, United States of America

Claire Zhixian Han
Department of Biomedical Engineering, Columbia University, New York, United States of America

Salman Ehtesham Qasim
Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America

Joshua Jacobs
Department of Biomedical Engineering, Columbia University, New York, United States of America, Department of Neurological Surgery, Columbia University, New York, United States of America

Editor

Andrew Quinn

Tags

neuroscience electrophysiology single unit activity

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Citation (CITATION.cff)

cff-version: 1.2.0
message: >-
  If you use this software, please cite it using the metadata from this file.
type: software
title: 'spiketools'
authors:
- given-names: 'Thomas'
  family-names: 'Donoghue'
  orcid: 'https://orcid.org/0000-0001-5911-0472'
- given-names: 'Sandra'
  family-names: 'Maesta Pereira'
  orcid: 'https://orcid.org/0000-0001-6522-8311'
- given-names: 'Claire Z'
  family-names: 'Han'
  orcid: 'https://orcid.org/0000-0001-9710-8381'
- given-names: 'Salman E'
  family-names: 'Qasim'
  orcid: 'https://orcid.org/0000-0001-8739-5962'
- given-names: 'Joshua'
  family-names: 'Jacobs'
  orcid: 'https://orcid.org/0000-0003-1807-6882'
repository-code: 'https://github.com/spiketools/spiketools'
url: 'https://spiketools.github.io/'
license: Apache-2.0
preferred-citation:
  type: article
  title: 'spiketools: A Python package for analyzing single-unit neural activity'
  authors:
  - given-names: Thomas
    family-names: Donoghue
    orcid: 'https://orcid.org/0000-0001-5911-0472'
  - given-names: 'Sandra'
    family-names: 'Maesta Pereira'
    orcid: 'https://orcid.org/0000-0001-6522-8311'
  - given-names: 'Claire Z'
    family-names: 'Han'
    orcid: 'https://orcid.org/0000-0001-9710-8381'
  - given-names: 'Salman E'
    family-names: 'Qasim'
    orcid: 'https://orcid.org/0000-0001-8739-5962'
  - given-names: 'Joshua'
    family-names: 'Jacobs'
    orcid: 'https://orcid.org/0000-0003-1807-6882'
  journal: 'Journal of Open Source Software'
  doi: '10.21105/joss.05268'
  issue: 91
  volume: 8
  year: 2023
  start: 5268

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