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:
- Extracellular electrophysiology (Intan -> NWB data conversion)
- See README-ephys.md for detailed information
- Widefield Imaging (Matlab & python)
- See README-widefield.md for detailed information
- 2-Photon Imaging (terminal)
- See README-2photon.md for detailed information
- Behavioral (Matlab or python)
- See README-behavior.md for detailed information
- fMRI (terminal)
- See README-mri.md for detailed information
1. Activate python virtual environment with required modules (nwb on my computer) *see requirements.txt for installed modules
2. Download and complete Excel sheet that most closely correponds to experiment
3. Run with 'python share.py' and add terminal arguments as needed
1. Activate python virtual environment with required modules (nwb on my computer) *see requirements.txt for installed modules
2. Download and complete Excel sheet that most closely correponds to experiment
3. Run with 'python prep.py' and add terminal arguments as needed
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
1. Install MatNWB as Matlab Add-On (Add-Ons button on top ribbon, search for 'nwb'; and click 'Add' button)
2. Install Image Processing toolbox Add-On (Add-Ons button on top ribbon, search for 'Image Processing Toolbox'; and click 'Add' button)
- Conversion for Intan format to NWB format (ePhys)
- Ability to add tif image stacks to NWB files (Widefield, Behavioral)
- Integration with back-end relational database (in progress), NoSQL 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/ActiveBrainAtlas2/nwb/issues)
[Source Code] (https://github.com/ActiveBrainAtlas2/nwb)
If you are having issues, please let me know. Duane Rinehart drinehart[at]ucsd.edu
The project is licensed under the MIT license.
Last update: 9-JUL-2024