Intracellular Electrophysiology Data using SweepTable

The following tutorial describes storage of intracellular electrophysiology data in NWB using the SweepTable to manage recordings.

Warning

The use of SweepTable has been deprecated as of PyNWB >v2.0 in favor of the new hierarchical intracellular electrophysiology metadata tables to allow for a more complete description of intracellular electrophysiology experiments. See the Intracellular electrophysiology tutorial for details.

Creating and Writing NWB files

When creating a NWB file, the first step is to create the NWBFile. The first argument is is a brief description of the dataset.

from datetime import datetime
from uuid import uuid4

import numpy as np
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="LONELYMTN001",
)

Device metadata

Device metadata is represented by Device objects. To create a device, you can use the Device instance method create_device.

device = nwbfile.create_device(name="Heka ITC-1600")

Electrode metadata

Intracellular electrode metadata is represented by IntracellularElectrode objects. To create an electrode group, you can use the NWBFile instance method create_icephys_electrode.

elec = nwbfile.create_icephys_electrode(
    name="elec0", description="a mock intracellular electrode", device=device
)

Stimulus data

Intracellular stimulus and response data are represented with subclasses of PatchClampSeries. There are two classes for representing stimulus data

• VoltageClampStimulusSeries

• CurrentClampStimulusSeries

and three classes for representing response

• VoltageClampSeries

• CurrentClampSeries

• IZeroClampSeries

Here, we will use CurrentClampStimulusSeries to store current clamp stimulus data and then add it to our NWBFile as stimulus data using the NWBFile method add_stimulus.

from pynwb.icephys import CurrentClampStimulusSeries

ccss = CurrentClampStimulusSeries(
    name="ccss",
    data=[1, 2, 3, 4, 5],
    starting_time=123.6,
    rate=10e3,
    electrode=elec,
    gain=0.02,
    sweep_number=0,
)

nwbfile.add_stimulus(ccss, use_sweep_table=True)

We now add another stimulus series but from a different sweep. TimeSeries having the same starting time belong to the same sweep.

from pynwb.icephys import VoltageClampStimulusSeries

vcss = VoltageClampStimulusSeries(
    name="vcss",
    data=[2, 3, 4, 5, 6],
    starting_time=234.5,
    rate=10e3,
    electrode=elec,
    gain=0.03,
    sweep_number=1,
)

nwbfile.add_stimulus(vcss, use_sweep_table=True)

Here, we will use CurrentClampSeries to store current clamp data and then add it to our NWBFile as acquired data using the NWBFile method add_acquisition.

from pynwb.icephys import CurrentClampSeries

ccs = CurrentClampSeries(
    name="ccs",
    data=[0.1, 0.2, 0.3, 0.4, 0.5],
    conversion=1e-12,
    resolution=np.nan,
    starting_time=123.6,
    rate=20e3,
    electrode=elec,
    gain=0.02,
    bias_current=1e-12,
    bridge_balance=70e6,
    capacitance_compensation=1e-12,
    sweep_number=0,
)

nwbfile.add_acquisition(ccs, use_sweep_table=True)

And voltage clamp data from the second sweep using VoltageClampSeries.

from pynwb.icephys import VoltageClampSeries

vcs = VoltageClampSeries(
    name="vcs",
    data=[0.1, 0.2, 0.3, 0.4, 0.5],
    conversion=1e-12,
    resolution=np.nan,
    starting_time=234.5,
    rate=20e3,
    electrode=elec,
    gain=0.02,
    capacitance_slow=100e-12,
    resistance_comp_correction=70.0,
    sweep_number=1,
)

nwbfile.add_acquisition(vcs, use_sweep_table=True)

Once you have finished adding all of your data to the NWBFile, write the file with NWBHDF5IO.

from pynwb import NWBHDF5IO

with NWBHDF5IO("icephys_example.nwb", "w") as io:
    io.write(nwbfile)

For more details on NWBHDF5IO, see the basic tutorial.

Reading electrophysiology data

Now that you have written some intracellular electrophysiology data, you can read it back in.

io = NWBHDF5IO("icephys_example.nwb", "r")
nwbfile = io.read()

For details on retrieving data from an NWBFile, we refer the reader to the basic tutorial. For this tutorial, we will just get back our the CurrentClampStimulusSeries object we added above.

First, get the CurrentClampStimulusSeries we added as stimulus data.

ccss = nwbfile.get_stimulus("ccss")

Grabbing acquisition data can be done via get_acquisition

vcs = nwbfile.get_acquisition("vcs")

We can also get back the electrode we added.

elec = nwbfile.get_icephys_electrode("elec0")

Alternatively, we can also get this electrode from the CurrentClampStimulusSeries we retrieved above. This is exposed via the electrode attribute.

elec = ccss.electrode

And the device name via get_device

device = nwbfile.get_device("Heka ITC-1600")

If you have data from multiple electrodes and multiple sweeps, it can be tedious and expensive to search all PatchClampSeries for the TimeSeries with a given sweep.

Fortunately you don’t have to do that manually, instead you can just query the SweepTable which stores the mapping between the PatchClampSeries which belongs to a certain sweep number via get_series.

The following call will return the voltage clamp data of two timeseries consisting of acquisition and stimulus, from sweep 1.

series = nwbfile.sweep_table.get_series(1)

# close the file
io.close()