neuro-py

Analysis of neuroelectrophysiology data in Python.

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Overview

neuro_py is a Python package for analysis of neuroelectrophysiology data. It is built on top of the nelpy package, which provides core data objects. neuro_py provides a set of functions for analysis of freely moving electrophysiology, including behavior tracking utilities, neural ensemble detection, peri-event analyses, robust batch analysis tools, and more.

Tutorials are here and more will be added.

Installation

git clone
cd neuro_py
pip install -e .

To sync the nelpy dependency to latest version, use following instead,

pip install -e . --force-reinstall --no-cache-dir

Usage

import neuro_py as npy

Dependencies

For ease of use, this package uses nelpy core data objects. See nelpy

Testing

python tools/run_pytest.py

To run a narrow target, pass the usual pytest arguments through:

python tools/run_pytest.py tests/detectors/test_sharp_wave_ripple.py -q

This wrapper sets a few local defaults that make editable nelpy installs more reliable in development environments:

• NUMBA_DISABLE_JIT=1
• PYTEST_DISABLE_PLUGIN_AUTOLOAD=1
• MPLBACKEND=Agg

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

Authors

• @ryanharvey1
• @lolaBerkowitz
• @kushaangupta