spiketools

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

WARNING: This module is in early development, and may change at any time.

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

In terms of scope, note that spiketools is currently organized around analyses of single cell activity, and is not focused on 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 work through each sub-module
• Examples: demonstrating example applications and workflows
• 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 >= 3.6 to run.

It has the following required dependencies:

• numpy
• pandas
• scipy
• matplotlib

There are also optional dependencies, that offer extra functionality:

• pytest is needed to run the test suite locally

We recommend using the Anaconda distribution to manage these requirements.

Installation

This module is currently in development, with no stable release version yet.

Development Version

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

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

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

$ pip install .

Editable Version

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

$ pip install -e .

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.