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NWB conversion scripts and tutorials.

Project description

jaeger-lab-data-to-nwb

Convert Jaeger lab data to NWB format.

Currently includes:

  • FRET optical imaging (rsd)
  • Intan electrophysiology (rhd)
  • Labview behavioral data (txt)
  • Optogenetics stimulation data (txt)
  • Treadmill behavior (csv)
  • Bpod behavioral data (mat)

Authors: Luiz Tauffer and Ben Dichter

Install

To clone the repository and set up a conda environment, do:

$ git clone https://github.com/ben-dichter-consulting/jaeger-lab-to-nwb.git
$ conda env create -f jaeger_lab_to_nwb/make_env.yml
$ source activate jaeger_nwb

Alternatively, to install directly in an existing environment:

$ pip install git+https://github.com/ben-dichter-consulting/jaeger-lab-to-nwb.git

Use

After activating the correct environment, the conversion function can be used in different forms:

1. Imported and run from a python script:
Here's an example: we'll grab the data from a specific experiment, with several electrophysiology and behavioral data files stored base_path, and save it to a single nwb file.

import pynwb
from jaeger_lab_to_nwb.conversion_module import conversion_function
from pathlib import Path
import yaml

base_path = Path(PATH_TO_FILES)

# Source files
source_paths = dict()
source_paths['dir_ecephys_rhd'] = {'type': 'dir', 'path': base_path}
source_paths['file_electrodes'] = {'type': 'file', 'path': base_path.joinpath('UD09_impedance_1.csv')}
source_paths['dir_behavior_treadmill'] = {'type': 'dir', 'path': base_path}

# Output .nwb file
f_nwb = 'my_experiment.nwb'

# Load metadata from YAML file
metafile = 'metafile.yml'
with open(metafile) as f:
    metadata = yaml.safe_load(f)

# Lab-specific kwargs
kwargs_fields = {
    'add_rhd': True,
    'add_treadmill': True
}

conversion_function(source_paths=source_paths,
                    f_nwb=f_nwb,
                    metadata=metadata,
                    **kwargs_fields)

# Read nwb file and check its content
with pynwb.NWBHDF5IO(f_nwb, 'r') as io:
    nwb = io.read()
    print(nwb)

2. Command line:
Similarly, the conversion function can be called from the command line in terminal:

$ python conversion_module.py [output_file] [metafile] [--file_behavior_bpod]
[--dir_behavior_treadmill] [--dir_ecephys_rhd] [--file_electrodes]
[--dir_behavior_labview] [--dir_cortical_imaging] [--add_bpod] [--add_rhd]
[--add_treadmill] [--add_labview] [--add_ophys]

For example, the same experiment converted above with a python script could be converted with this command line input:

$ python conversion_module.py my_experiment.nwb metafile.yml --add_rhd --add_treadmill
--dir_behavior_treadmill PATH_TO_FILES --dir_ecepys_rhd PATH_TO_FILES
--file_electrodes PATH_TO_FILES\UD09_impedance_1.csv

3. Graphical User Interface:
To use the GUI, just type in the terminal:

$ nwbn-gui-jaeger [--experiment_name]

The GUI eases the task of editing the metadata of the resulting nwb file, it is integrated with the conversion module (conversion on-click) and allows for quick visual exploration the data in the end file with nwb-jupyter-widgets.

Project details


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