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...
Phy requires a recent GPU and an SSD for storing your data (the GUI may be slow if the data is on an HDD).
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Install the latest version of Anaconda 64-bit with Python 3.
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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
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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.jsonwhen 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 .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: