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

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 provides two GUIs:

• Template GUI (recommended): for datasets sorted with KiloSort and Spyking Circus,
• Kwik GUI (legacy): for datasets sorted with klusta and klustakwik2.

What's new

• [7 Sep 2021] Release of phy 2.0 beta 5, with some install and bug fixes
• [7 Feb 2020] Release of phy 2.0 beta 1, with many new views, new features, various improvements and bug fixes...

Links

• Documentation
• Mailing list

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. You need a recent Python distribution.

2. Open a terminal and type:

pip install phy --pre --upgrade
# If you plan to use the Kwik GUI, type the following without the leading hash # character:
# pip install klusta klustakwik2

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

Dependencies

For your information, here are the Python dependencies of phy (as found in requirements.txt):

phylib
mtscomp
numpy
matplotlib
scipy
h5py
dask
cython
pillow
colorcet
pyopengl
requests
qtconsole
tqdm
joblib
click
mkdocs

Upgrading from phy 1 to phy 2

• Do not install phy 1 and phy 2 in the same Python 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 [email protected]:cortex-lab/phy.git
cd phy
pip install -r requirements.txt
pip install -r requirements-dev.txt
pip install -e .
cd ..
git clone [email protected]:cortex-lab/phylib.git
cd phylib
pip install -e . --upgrade

Troubleshooting

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

Running phy from a Python script

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")

Credits

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