Scripts are useful in converting data from prorpritary formats into NWB format. Scripts are expected to be used as back-end to U19 data sharing portals: usarhythms.ucsd.edu, highandlow.dk.ucsd.edu
Currently supported experimental data is:
- Widefield Imaging (meta-data only)
- Extracellular electrophysiology (Intan -> NWB data conversion)
- See README-ephys.md for detailed information
- Calcium imaging (WIP)
1. Activate python virtual environment with required modules (nwb on my computer) *see requirements.txt for installed modules
2. Open jupyter notebook corresponding to experiment type
3. Edit constants (file paths at top file) and run
Note: You will need input.xlsx for electrophysiology experiments (sample coming) for inclusion of raw data
- Conversion for Intan format to NWB format
- Integration with back-end relational database (in progress)
- Ability to aggregate NWB containers (for uploading to NIH-approved respositories)
- create virtual environment in home directory (e.g. 'C:/Users/Duane/')
python -m venv nwb - Activate virtual environment
C:/Users/Duane/nwb/Scripts/activate.ps1 - Install required modules
pip install -r requirements.txt
[Issue Tracker] (https://github.com/drinehart1/nwb/issues)
[Source Code] (https://github.com/drinehart1/nwb)
If you are having issues, please let me know. Duane Rinehart drinehart[at]ucsd.edu
The project is licensed under the MIT license.