Getting started¶
Detailed user guide: Using OPETH
Online Peri-Event Time Histogram for Open Ephys.
OPETH visualizes Peri-Event Time Histograms (PETH) of spikes detected in raw Open Ephys data, broadcasted via ZeroMQ. PETH is aligned to triggers from Open Ephys.
Quickstart¶
- OPETH requires ZMQInterface plugin. It is part of Open Ephys from version 0.4.6 up.
- Set up Open Ephys with ZMQInterface plugin. The ZMQ plugin is recommended to be put after bandpass filter and/or common average reference filter in the Open Ephys signal chain, while spike detector filter is not required.
- Start with the
opethcommand when using the pip package or start withpython opeth/gui.pywhen running from sources (see below).
Installation¶
Simplest way is to install the opeth package for Python 2.7 or Python <=3.7 with pip:
pip install opeth
Then start with:
opeth
(Python 3.8 support is partially broken until the release of pyqtgraph 0.11.)
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.
Activate the new environment with the command
conda activate opeth
and once activated, you may start OPETH with
python opeth/gui.py
Using python 3.8 is not recommended (Feb 2020) as some bugs are to be addressed (most probably residing in pyqtgraph),
but it is possible with the conda-forge version of pyqtgraph (default environment name will be opeth_python38):
conda env create --file env38.yml
Setting up python environment with pip¶
Python 3.7 dependencies can be installed with the command
pip install -r requirements.txt