opeth

Online Peri-Event Histogram for Open Ephys ZMQ plugin


Licenses
GPL-3.0-only/GPL-3.0-or-later
Install
pip install opeth==0.1a1

Documentation

OPETH

More detailed documentation: https://opeth.readthedocs.io/

Online Peri-Event Time Histogram for Open Ephys.

Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.

Usage

  • Needs ZMQInterface plugin (e.g. in the Open Ephys plugin folder). For Windows a precompiled dll is present.
  • Set up Open Ephys with ZMQInterface plugin. Plugin is recommended to be put after bandpass filter and/or common average reference filter, but spike detector is not required.
  • Start with the opeth command if using the pip package or start with python opeth/gui.py if running from sources.

Installation

Install the opeth package for Python 2.7 or Python <=3.7 with pip:

pip install opeth

Python 3.8 support is partially broken as of February 2020.

Dependencies

Required non-default packages: pyzmq, pyqtgraph plus one of the qt versions for pyqtgraph, preferably PyQt5, and also their dependencies (e.g. numpy).

Running from sources

After cloning the git repository or extracting a source zip file, multiple methods could work.

Setting up python environment with conda

Conda builds are not available yet.

Using conda/miniconda, create an opeth environment issuing the following command in the root dir of opeth:

conda env create --file environment.yml

which will install all necessary prerequisites for Python 3.7.

Using python 3.8 is not recommended (Feb 2020) as some bugs are need to be addressed (most probably residing in pyqtgraph), but possible using the conda-forge version of pyqtgraph:

conda env create --file env38.yml

Activate the new environment with the command

conda activate opeth

and once activated you may start OPETH with

python opeth/gui.py

Setting up python environment with pip

Python 3.7 dependencies can be installed with the command

pip install -r requirements.txt

Contributors

Developed by Andras Szell (szell.andris@gmail.com) and other Hangyalab members (http://hangyalab.koki.hu/).

Open Ephys ZMQ plugin connection is based on sample python scripts created by Francesco Battaglia.

License

GNU General Public License v3.0 or later.

See LICENSE for the full text.