README.md

franklabnwb

Example notebook and related code to create NWB files from trodes .rec and associated files assuming franklab compatible naming system

Instructions for initial setup and testing:

Prerequisites

• Download and install Trodes export code, and add the installed directory to path.

  For more detailed instructions, see Installing SpikeGadgets.

Setting up a python environment

1. Clone this repository to your code source directory:

   cd your_source_directory
   git clone https://github.com/LorenFrankLab/franklabnwb.git
   git clone https://github.com/LorenFrankLab/rec_to_nwb.git
   

2. Create the conda environment required for the conversion and install the rec_to_nwb module

   cd rec_to_nwb
   conda env create -f environment.yml
   conda activate rec_to_nwb
   pip install -e .
   

3. Start the notebook server from a directory below the franklabnwb directory:

   jupyter notebook
   

4. Try from notebook: In the notebook, navigate to the franklabnwb/notebooks directory and open franklab_nwb_generation.ipynb.

   Edit the variables in that notebook as required for your data and run all cells. See below for more information on the animal metadata file.

5. Try from file: Edit 'create_nwb_example.py' to match your data and run that: python create_nwb_examply.py

Animal metadata file:

rec_to_nwb requires a metadata file for each day of recording. Details on the content of that file can be found in the documentation.

Alternatively, you can start with the franklabnwb/yaml/beans20190718_metadata.yml file as an example.