Neuro Digital Signal Processing Toolbox

A package of tools to simulat and analyze neural time series, focused on time and frequency domain analyses.

Documentation

Documentation for the NeuroDSP module is available here.

The documentation also includes a full set of tutorials covering the functionality of NeuroDSP.

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

Dependencies

NeuroDSP is written in Python, and requires Python >= 3.5 to run.

It has the following dependencies:

numpy
scipy
matplotlib
pandas
pytest (optional)

We recommend using the Anaconda distribution to manage these requirements.

Install

Stable Release Version

To install the latest release of neurodsp, you can install from pip:

$ pip install neurodsp

Development Version

To get the development version (updates that are not yet published to pip), you can clone this repo.

$ git clone https://github.com/neurodsp-tools/neurodsp

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

$ pip install .

Editable Version

If you want to install an editable version, for making contributions, download the development version as above, and run:

$ pip install -e .

Bug Reports

Please use the Github issue tracker to file bug reports and/or ask questions about this project.

Modules

Available modules in NeuroDSP include:

filt : Filter data with bandpass, highpass, lowpass, or notch filters
burst : Detect bursting oscillations in neural signals
rhythm : Find and analyze rhythmic and recurrent patterns in time series
spectral : Compute spectral domain features such as power spectra
timefrequency : Estimate instantaneous measures of oscillatory activity
sim : Simulate time series, including periodic and aperiodic signal components
plts : Plotting functions

Contribute

NeuroDSP welcomes and encourages contributions from the community!

If you have an idea of something to add to NeuroDSP, please start by opening an issue.

When writing code to add to NeuroDSP, please follow the Contribution Guidelines, and also make sure to follow our Code of Conduct.

Reference

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

Cole, S., Donoghue, T., Gao, R., & Voytek, B. (2019). NeuroDSP: A package for
neural digital signal processing. Journal of Open Source Software, 4(36), 1272.
https://doi.org/10.21105/joss.01272

Direct Link: https://doi.org/10.21105/joss.01272

Bibtex:

@article{cole_neurodsp:_2019,
	 title = {NeuroDSP: A package for neural digital signal processing},
	 author = {Cole, Scott and Donoghue, Thomas and Gao, Richard and Voytek, Bradley},
    	 journal = {Journal of Open Source Software},
	 year = {2019},
	 volume = {4},
    	 number = {36},
	 issn = {2475-9066},
	 url = {http://joss.theoj.org/papers/10.21105/joss.01272},
	 doi = {10.21105/joss.01272},
}

srcole/neurodsp