Skip to content
forked from cortex-lab/phy

Phy (older version) stable for MEA recordings at the cost of lacking the latest features

License

Notifications You must be signed in to change notification settings

gollischlab/phy-MEA

 
 

Repository files navigation

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

Build Status codecov.io Documentation Status GitHub release PyPI release

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 --pre --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

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:

About

Phy (older version) stable for MEA recordings at the cost of lacking the latest features

Resources

License

Stars

Watchers

Forks

Languages

  • Python 96.0%
  • GLSL 3.7%
  • CSS 0.2%
  • Makefile 0.1%
  • HTML 0.0%
  • Shell 0.0%