Estimate Spike Detection Parameters

Estimate spike detection parameters

Out:

/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/docs/gallery/spikes_examples/estimate_params.py:28: VisibleDeprecationWarning: Function create_ephys_data_set is deprecated. Instead of using ipfx.data_set_utils.create_data_set, use ipfx.dataset.create.create_ephys_data_set
  data_set = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/v1.0.0.1/lib/python3.7/site-packages/hdmf/spec/namespace.py:470: UserWarning: ignoring namespace 'hdmf-common' because it already exists
  warn("ignoring namespace '%s' because it already exists" % ns['name'])
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/envs/v1.0.0.1/lib/python3.7/site-packages/hdmf/spec/namespace.py:470: UserWarning: ignoring namespace 'core' because it already exists
  warn("ignoring namespace '%s' because it already exists" % ns['name'])
/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/ipfx/dataset/create.py:124: VisibleDeprecationWarning: Class EphysDataSet is deprecated. Import EphysDataSet from ipfx.dataset.ephys_dataset rather than ipfx.ephys_dataset
  data=nwb_data,

from ipfx.data_set_utils import create_data_set
from ipfx.spike_features import estimate_adjusted_detection_parameters
from ipfx.feature_extractor import SpikeFeatureExtractor

from allensdk.api.queries.cell_types_api import CellTypesApi

import os
import matplotlib.pyplot as plt

# Download and access the experimental data
ct = CellTypesApi()
nwb_file = os.path.join(
    os.path.dirname(os.getcwd()),
    "data",
    "nwb2_H17.03.008.11.03.05.nwb"
)
specimen_id = 595570553
sweep_info = ct.get_ephys_sweeps(specimen_id)

# build a data set and find the short squares
data_set = create_data_set(sweep_info=sweep_info, nwb_file=nwb_file)
ssq_table = data_set.filtered_sweep_table(stimuli=["Short Square"])
ssq_set = data_set.sweep_set(ssq_table.sweep_number)

# estimate the dv cutoff and threshold fraction
dv_cutoff, thresh_frac = estimate_adjusted_detection_parameters(
    ssq_set.v, ssq_set.t, 1.02, 1.021
)

# detect spikes
sweep_number = 16
sweep = data_set.sweep(sweep_number)
ext = SpikeFeatureExtractor(dv_cutoff=dv_cutoff, thresh_frac=thresh_frac)
spikes = ext.process(t=sweep.t, v=sweep.v, i=sweep.i)

# and plot them
plt.plot(sweep.t, sweep.v)
plt.plot(spikes["peak_t"], spikes["peak_v"], 'r.')
plt.plot(spikes["threshold_t"], spikes["threshold_v"], 'k.')
plt.xlim(1.018, 1.028)
plt.xlabel('Time (s)')
plt.ylabel('Membrane potential (mV)')
plt.show()