README.md

NSDS-Lab-to-NWB

Python code package to convert NSDS lab data to NWB files.

Setup

Prerequisite

Make sure that you have conda (either anaconda or miniconda) installed.

Installing this package

Clone this repository and cd to the repository root:

cd [your_project_folder]
git clone [email protected]:BouchardLab/nsds_lab_to_nwb.git
cd nsds_lab_to_nwb

Create a conda environment (named nsds_nwb by default), and activate it:

conda env create -f environment.yml
conda activate nsds_nwb

Also install this package:

pip install -e .

Setting the default paths

It is recommended to set the default data, metadata and stimulus paths as the environment variables.

If you are running this on catscan, open your ~/.bashrc file in any text editor, and copy and paste the following lines into the ~/.bashrc file.

export NSDS_METADATA_PATH='/clusterfs/NSDS_data/NSDSLab-NWB-metadata/'
export NSDS_DATA_PATH='/clusterfs/NSDS_data/raw/'
export NSDS_STIMULI_PATH='/clusterfs/NSDS_data/stimuli/'

After you edit the ~/.bashrc file, run

source ~/.bashrc

for the change to take effect.

If you are not on catscan, you should make sure that the values of the three environment variables are set correctly, such that the software can find the data, metadata and stimulus files. You will need to clone the NSDSLab-NWB-metadata repository and make sure that NSDS_METADATA_PATH points to the repository.

Also see the Naming Conventions documentation for more information.