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

Project description

phy: interactive visualization and manual spike sorting of large-scale ephys data

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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 2.0b1 screenshot

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

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

Credits

phy is developed and maintained by Cyrille Rossant.

Contributors to the repository are:

Project details


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Files for phy, version 2.0b1
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Filename, size phy-2.0b1-py2.py3-none-any.whl (593.8 kB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size phy-2.0b1.tar.gz (524.1 kB) File type Source Python version None Upload date Hashes View

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