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 (recommanded): for datasets sorted with KiloSort and Spyking Circus,
- Kwik GUI (legacy): for datasets sorted with klusta and klustakwik2.
- [7 Feb 2020] Release of phy 2.0 beta 1, with many new views, new features, various improvements and bug fixes...
Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).
Install the latest version of Anaconda 64-bit with Python 3.
Open a terminal and type:
conda create -n phy2 python=3.7 pip numpy matplotlib scipy scikit-learn h5py pyqt cython pillow -y conda activate phy2 pip install phy --pre --upgrade # Only if you plan to use the Kwik GUI: # pip install klusta klustakwik2
- 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
Dealing with the error
ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidget
In some environments, you might get an error message related to QtWebEngineWidget. Run the command
pip install PyQtWebEngine and try launching phy again. This command should not run if the error message doesn't appear, as it could break the PyQt5 installation.
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
To install the development version of phy in a fresh environment, do:
git clone email@example.com:cortex-lab/phy.git cd phy pip install -r requirements.txt pip install -r requirements-dev.txt pip install -e . cd .. git clone firstname.lastname@example.org:cortex-lab/phylib.git cd phylib pip install -e . --upgrade
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")
phy is developed and maintained by Cyrille Rossant.
Contributors to the repository are: