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
Hardware requirements
It is recommanded to store the data on a SSD for performance reasons.
There are no specific GPU requirements as long as relatively recent graphics and OpenGL drivers are installed on the system.
Installation instructions
Run the following commands in a terminal:
-
Create a new conda environment with the conda dependencies:
conda create -n phy2 -y cython dask h5py joblib matplotlib numpy pillow pip pyopengl pyqt pyqtwebengine pytest python qtconsole requests responses scikit-learn scipy traitlets -
Activate the new conda environment with
conda activate phy2 -
Install the development version of phy:
pip install git+https://github.com/cortex-lab/phy.git -
[OPTIONAL] If you plan to use the Kwik GUI, type
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.pyDealing 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 Python environment.
- It is recommended to delete
~/.phy/*GUI/state.jsonwhen 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 . --upgradeTroubleshooting
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.
Contributors to the repository are: