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).
- [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 pip numpy matplotlib scipy h5py pyqt cython pillow -y conda activate phy2 pip install phy
- 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
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 https://github.com/cortex-lab/phy.git cd phy pip install -r requirements.txt pip install -r requirements-dev.txt pip install -e .
phy is developed and maintained by Cyrille Rossant.
Contributors to the repository are: