README.md

ndx-labmetadata-example Extension for NWB

This is an example extension to illustrate how to extend the LabMetaData type from NWB to add lab-specific metadata. This extension is NOT intended for use in practice but is intended only as an example to illustrate how to generate an NWB extension using the LabMetaData type.

Installation

pip install .

Usage

from pynwb.file import NWBFile, Subject
from ndx_labmetadata_example import LabMetaDataExtensionExample
from pynwb import NWBHDF5IO
from uuid import uuid4
from datetime import datetime

# create an example NWBFile
nwbfile = NWBFile(
    session_description="test session description",
    identifier=str(uuid4()),
    session_start_time=datetime(1970, 1, 1),
    subject=Subject(
        age="P50D",
        description="example mouse",
        sex="F",
        subject_id="test_id")
)

# create our custom lab metadata
lab_meta_data = LabMetaDataExtensionExample(tissue_preparation="Example tissue preparation")

# Add the test LabMetaDataExtensionExample to the NWBFile
nwbfile.add_lab_meta_data(lab_meta_data=lab_meta_data)

# Write the file to disk
filename = 'testfile.nwb'
with NWBHDF5IO(path=filename, mode='a') as io:
    io.write(nwbfile)

# Read the file from disk
with NWBHDF5IO(path=filename, mode='r') as io:
    in_nwbfile = io.read()
    in_lab_meta_data = in_nwbfile.get_lab_meta_data(lab_meta_data.name)
    assert lab_meta_data.tissue_preparation == in_lab_meta_data.tissue_preparation

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This extension was created using ndx-template.