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).

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

• Documentation
• Mailing list

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 --pre --upgrade

3. 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

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

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 .

• See a list of common issues.
• Raise a GitHub issue.

In addition to launching phy from the terminal with the phy command, you can also launch it from a Python script or an IPython terminal. This may be useful when debugging or profiling. Here's a code example to copy-paste in a new launch.py text file within your data directory:

from phy.apps.template import template_gui
template_gui("params.py")

phy is developed and maintained by Cyrille Rossant.

• International Brain Laboratory
• Cortex Lab (UCL) (Kenneth Harris and Matteo Carandini).

Contributors to the repository are:

• Alessio Buccino
• Michael Economo
• Cedric Gestes
• Dan Goodman
• Max Hunter
• Shabnam Kadir
• Christopher Nolan
• Martin Spacek
• Nick Steinmetz