esi-oephys2nwb 2022.5rc0

Export binary Open Ephys data to NWB 2.x

oephys2nwb: Export Open Ephys binary data to NWB 2.x

Summary

This package can be used to export data saved in Open Ephys binary format (the default for the Open Ephys GUI) to the NWB 2.0 format. At the time of writing the NWBFormat plugin of Open Ephys only supports the deprecated NWB 1.0 format specification. The present package is developed and maintained at the Ernst Strüngmann Institute (ESI) gGmbH for Neuroscience in Cooperation with Max Planck Society and released free of charge under the BSD 3-Clause "New" or "Revised" License.

Installation

The package can be installed with pip

pip install git+https://github.com/open-ephys/open-ephys-python-tools
pip install esi-oephys2nwb

To get the latest development version, simply clone our GitHub repository and (optionally) create a dedicated conda development environment:

git clone https://github.com/esi-neuroscience/oephys2nwb.git
cd oephys2nwb/
python setup.py --version
conda env create -f oephys2nwb-dev.yml
conda activate oephys2nwb-dev
pip install -e .

Usage

We recommend setting up a dedicated conda environment for oephys2nwb. For general information about conda, please refer to the official documentation.

conda create -n oephys2nwb-env python=3.8 pip
conda activate oephys2nwb-env
pip install esi-oephys2nwb

Alternatively, we provide a conda environment file to automatically install all required dependencies

wget https://raw.githubusercontent.com/esi-neuroscience/oephys2nwb/main/oephys2nwb.yml
conda env create -f oephys2nwb.yml
conda activate oephys2nwb

Once the package is installed the exporter can be used either embedded in Python code or as a stand-alone command line utility.

Command Line

Activate the conda environment the package was installed in and invoke the exporter as follows

conda activate oephys2nwb-env
python -m oephys2nwb -i /path/to/recordingDir -o /path/to/outputFile.nwb

Calling oephys2nwb without arguments prints the function help

python -m oephys2nwb

Python Code

Alternatively, the package can be used like any other Python module

from oephys2nwb import export2nwb

input = "/path/to/recordingDir"
output = "/path/to/outputFile.nwb"

export2nwb(input, output)

Documentation and Contact

To report bugs or ask questions please use our GitHub issue tracker. More usage details and background information is available in our online documentation.