Spike sorting and ephys data analysis for 1000 channels and beyond


Keywords
phy, data, analysis, electrophysiology, neuroscience, data-analysis, python
License
BSD-3-Clause
Install
pip install phy==2.0b1

Documentation

phy: interactive visualization and manual spike sorting of large-scale ephys data

Build Status codecov.io Documentation Status GitHub release PyPI release

phy is an open-source Python library providing a graphical user interface for visualization and manual curation of large-scale electrophysiological data. It is optimized for high-density multielectrode arrays containing hundreds to thousands of recording sites (mostly Neuropixels probes).

phy 2.0b1 screenshot

What's new

  • [7 Feb 2020] Release of phy 2.0 beta 1, with many new views, new features, various improvements and bug fixes...

Links

Installation instructions

Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).

  1. Install the latest version of Anaconda 64-bit with Python 3.

  2. Open a terminal and type:

conda create -n phy2 python pip numpy matplotlib scipy h5py pyqt cython pillow -y
conda activate phy2
pip install phy
  1. Phy should now be installed. Open the GUI on a dataset as follows (the phy2 environment should still be activated):
cd path/to/my/spikesorting/output
phy template-gui params.py

Upgrading from phy 1 to phy 2

  • Do not install phy 1 and phy 2 in the same conda environment.
  • It is recommended to delete ~/.phy/*GUI/state.json when upgrading.

Developer instructions

To install the development version of phy in a fresh environment, do:

git clone https://github.com/cortex-lab/phy.git
cd phy
pip install -r requirements.txt
pip install -r requirements-dev.txt
pip install -e .

Troubleshooting

Credits

phy is developed and maintained by Cyrille Rossant.

Contributors to the repository are: