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.

  • NOTE: v1.9.* seems to have an issue in mda file export (tested on Linux as of 10/4/2020). Install v1.8.2 instead.

  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

   cd rec_to_nwb/rec_to_nwb
   conda env create -f environment.yml
   

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

   jupyter notebook
   

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

5. 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.

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.