esi-oephys2nwb
Export Open Ephys binary data to NWB 2.0
Science Score: 44.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
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○DOI references
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary
Repository
Export Open Ephys binary data to NWB 2.0
Basic Info
Statistics
- Stars: 3
- Watchers: 2
- Forks: 2
- Open Issues: 2
- Releases: 2
Metadata Files
README.md
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
shell
pip install esi-oephys2nwb
To get the latest development version, simply clone our GitHub repository and (optionally) create a dedicated conda development environment:
shell
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.
shell
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
shell
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
shell
conda activate oephys2nwb-env
python -m oephys2nwb -i /path/to/recordingDir -o /path/to/outputFile.nwb
Calling oephys2nwb without arguments prints the function help
shell
python -m oephys2nwb
Python Code
Alternatively, the package can be used like any other Python module
```python 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.
Owner
- Name: Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society
- Login: esi-neuroscience
- Kind: organization
- Location: Frankfurt, Germany
- Website: http://www.esi-frankfurt.de
- Repositories: 9
- Profile: https://github.com/esi-neuroscience
Citation (CITATION.cff)
authors:
- affiliation: "Ernst Str\xFCngmann Institute for Neuroscience in Cooperation with\
\ Max Planck Society"
family-names: Fuertinger
given-names: Stefan
orcid: https://orcid.org/0000-0002-8118-036X
- affiliation: "Ernst Str\xFCngmann Institute for Neuroscience in Cooperation with\
\ Max Planck Society"
family-names: Shapcott
given-names: Katharine
orcid: https://orcid.org/0000-0001-8618-5779
cff-version: 1.1.0
date-released: '2023-10-20'
keywords:
- neurodata without borders
- open ephys
- nwb 2.0
license: BSD-3-Clause
message: If you use this software, please cite it based on metadata found in this
file. The package oephys2nwb provides functionality to export Open Ephys binary
data to NWB 2.x format.
repository-code: https://github.com/esi-neuroscience/oephys2nwb.git
title: oephys2nwb
version: 2022.5rc1.dev11
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 9
- Total pull requests: 8
- Average time to close issues: 5 months
- Average time to close pull requests: 5 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 2.44
- Average comments per pull request: 1.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- KatharineShapcott (7)
- pantaray (1)
- MKVarun (1)
Pull Request Authors
- KatharineShapcott (6)
- pantaray (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 9 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: esi-oephys2nwb
Export binary Open Ephys data to NWB 2.x
- Homepage: https://github.com/esi-neuroscience/oephys2nwb
- Documentation: https://esi-oephys2nwb.readthedocs.io/en/latest/
- License: BSD-3
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Latest release: 0.5
published over 2 years ago