phy works better on computers with sufficient RAM, a recent graphics card, and an SSD to store data files.


Main dependencies are NumPy, SciPy, PyQt5, pyopengl, joblib. The full list of dependencies is available in the environment.yml file.

Upgrading from phy 1 to phy 2

  • Never install phy 1 and phy 2 in the same conda environment.
  • It is recommended to delete ~/.phy/TemplateGUI/state.json when upgrading.


Minimal installation instructions (to be completed):

  1. Install Anaconda.

  2. Open a terminal and type:

conda create -n phy2 python pip numpy matplotlib scipy h5py pyqt cython -y
conda activate phy2
pip install colorcet pyopengl qtconsole requests traitlets tqdm joblib click mkdocs
pip install git+
pip install git+
  1. 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