batter-wang / ecephys

Python extracellular electrophysiology tools

ecephys

Python tools for extracellular electrophysiology at the Wisconsin Institute for Sleep and Consciousness.

Installation

Requirements:

Updated 1/22/2024 -- May be more recent than CSC-UW/ece-env.

I reccomend Python 3.11. pyfftw technically allows you to use Python >3.11, but only provides prebuilt wheels through 3.11, and if you are using mamba/conda and CPython (probable), pyfftw's build will probably fail for 3.12.

You need to use the CSC-UW fork of spikeinterface. The specific branch you need depends on your intent. For running spike sorting, use wisc/sorting. For everything else, use wisc/dev.

pip install "git+ssh://[email protected]/CSC-UW/spikeinterface.git@wisc/dev # For general use 
pip install "git+ssh://[email protected]/CSC-UW/spikeinterface.git@wisc/sorting # For spike sorting
# Example of an editable install
git clone https://github.com/CSC-UW/spikeinterface.git
cd spikeinterface
pip install -e .
git checkout wisc/sorting

If you are spike sorting, you probably also want pytorch for spikeinterface's drift correction. If you are using ephyviewer and Python 3.11, I reccomend PySide6 + Qt6:

pip install PySide6

Note that ibllib depends indirectly on Qt5 (PyQtWebEngine-Qt5 and PyQt5-Qt5). It probably doesn't really need these, but they're going to get installed anyways, and that should be fine. You'll never invoke them. If you need to, see below.

Other

Unfortuantely, this package cannot be published to PyPI so long as its dependencies include git URLs (e.g. kCSD-python, our spikeinterface fork, etc.)

From the past

If for some reason you need to use Qt5, this is what used to work and is now broken. We have no working solution for Qt5 currently.

conda install -c conda-forge pyqt qtpy qtconsole
pip install pyqt5 ephyviewer