Optogenetics

This tutorial will demonstrate how to write optogenetics data.

Creating an NWBFile object

When creating a NWB file, the first step is to create the NWBFile object.

from datetime import datetime
from uuid import uuid4

from dateutil.tz import tzlocal

from pynwb import NWBFile

nwbfile = NWBFile(
    session_description="my first synthetic recording",
    identifier=str(uuid4()),
    session_start_time=datetime.now(tzlocal()),
    experimenter="Baggins, Bilbo",
    lab="Bag End Laboratory",
    institution="University of Middle Earth at the Shire",
    experiment_description="I went on an adventure to reclaim vast treasures.",
    session_id="LONELYMTN",
)

Adding optogenetic data

The ogen module contains two data types that you will need to write optogenetics data, OptogeneticStimulusSite, which contains metadata about the stimulus site, and OptogeneticSeries, which contains the power applied by the laser over time, in watts.

First, you need to create a Device object linked to the NWBFile:

device = nwbfile.create_device(
    name="device",
    description="description of device",
    manufacturer="optional but recommended",
)

Now, you can create an OptogeneticStimulusSite. The easiest way to do this is to use the create_ogen_site method.

ogen_site = nwbfile.create_ogen_site(
    name="OptogeneticStimulusSite",
    device=device,
    description="This is an example optogenetic site.",
    excitation_lambda=600.0,  # nm
    location="VISrl",
)

Another equivalent approach would be to create a OptogeneticStimulusSite and then add it to the NWBFile:

from pynwb.ogen import OptogeneticStimulusSite

ogen_stim_site = OptogeneticStimulusSite(
    name="OptogeneticStimulusSite2",
    device=device,
    description="This is an example optogenetic site.",
    excitation_lambda=600.0,  # nm
    location="VISrl",
)

nwbfile.add_ogen_site(ogen_stim_site)

The second approach is necessary if you have an extension of OptogeneticStimulusSite.

With the OptogeneticStimulusSite added, you can now create a OptogeneticSeries. Here, we will generate some random data using numpy and specify the timing using rate. By default, the starting time of the time series is the session start time, specified in NWBFile. If you have samples at irregular intervals, you should use timestamps instead.

import numpy as np

from pynwb.ogen import OptogeneticSeries

ogen_series = OptogeneticSeries(
    name="OptogeneticSeries",
    data=np.random.randn(20),  # watts
    site=ogen_site,
    rate=30.0,  # Hz
)

nwbfile.add_stimulus(ogen_series)