Shuler lab to NWB

NWB conversion scripts for the Shuler Lab data to the Neurodata Without Borders data format.

Installation

Clone this repository and set up a conda environment:

# Clone this repository
git clone https://github.com/catalystneuro/shuler-lab-to-nwb

# Set up a conda environment
conda env create --name env_shuler python=3.8 pip
conda activate env_shuler

# Install package
cd shuler-lab-to-nwb
pip install -e .

NWB Conversion

To convert experimental data to NWB you'll need to provide:

• spikeglx_file_path, the path to the SpikeGLX recodings file
• trials_file_path, the path to a CSV file containing behavioral events data
• reference_timestamps_file_path, the path to the reference timestamps file for synchronization
• subject_metadata_file_path, the path to the JSON file containing Subject metadata
• output_nwb_file, the path for the resulting NWB file

Example:

from shuler_lab_to_nwb import conversion

conversion.run_conversion(
    spikeglx_file_path="/path_to/ES029_2022-09-14_bot72_0_g0_t0.imec0.ap.bin",
    trials_file_path="/path_to/data_2022-09-14_12-13-31.csv",
    reference_timestamps_file_path="/path_to/ES029_2022-09-14_bot72_0_g0_tcat.imec0.ap.SY_384_6_0.txt",
    subject_metadata_file_path="/path_to/ES029_2022-09-14_bot72_0_g0/subject_metadata.json",
    output_nwb_file="output_file.nwb"
)

The trials file data_2022-09-14_12-13-31.csv is a CSV file containing formatted data from data_2022-09-14_12-13-31.txt.

The subject metadata file is a simple JSON file, containing metadata following the pynwb standard as described here, example:

{
    "subject_id": "ES029",
    "description": "ES029",
    "genotype": "wildtype",
    "sex": "M",
    "species": "black 6",
    "weight": 0.0254,
    "date_of_birth": "10-27-2021"
}

You can run this example conversion and visualize the resulting NWB file with the notebook in examples folder.

Spike sorting in the cloud

The infrasctructure documentation, Python scripts and Dockerfile for performing spike sorting in the Cloud are available in the cloud folder.