phy 2.0b1

Interactive visualization and manual spike sorting of large-scale ephys data

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).

What's new

• [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. Install the latest version of Anaconda 64-bit with Python 3.

2. 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 --upgrade
   

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
   

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 ~/.phy/*GUI/state.json when upgrading.

Developer instructions

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 .

Troubleshooting

• Raise a GitHub issue.

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