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
Upgrading from phy 1 to phy 2
- Never install phy 1 and phy 2 in the same conda environment.
- It is recommended to delete
Minimal installation instructions (to be completed):
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+https://github.com/cortex-lab/phy.git@dev pip install git+https://github.com/cortex-lab/phylib.git
- 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