diff --git a/docs/gallery/domain/ecephys.py b/docs/gallery/domain/ecephys.py index 7abcff550..ee2d69a16 100644 --- a/docs/gallery/domain/ecephys.py +++ b/docs/gallery/domain/ecephys.py @@ -324,18 +324,38 @@ description="shank0", ) - -spike_events = SpikeEventSeries(name='SpikeEvents_Shank0', - description="events detected with 100uV threshold", - data=spike_snippets, - timestamps=np.arange(20), - electrodes=shank0) +spike_events = SpikeEventSeries( + name='SpikeEvents_Shank0', + description="events detected with 100uV threshold", + data=spike_snippets, + timestamps=np.arange(20), + electrodes=shank0, +) nwbfile.add_acquisition(spike_events) +############################################ +# If you need to store the complete, continuous raw voltage traces, along with unsorted spike times, you should store +# the traces with :py:class:`~pynwb.ecephys.ElectricalSeries` objects as :ref:`acquisition ` data, +# and use the :py:class:`~pynwb.ecephys.EventDetection` class to identify the spike events in your raw traces. + +from pynwb.ecephys import EventDetection + +event_detection = EventDetection( + name="threshold_events", + detection_method="thresholding, 1.5 * std", + source_electricalseries=raw_electrical_series, + source_idx=[1000, 2000, 3000], + times=[.033, .066, .099], +) + +ecephys_module.add(event_detection) + ####################### +# # If you do not want to store the raw voltage traces and only the waveform 'snippets' surrounding spike events, +# # you should use :py:class:`~pynwb.ecephys.SpikeEventSeries` objects. +# # Designating electrophysiology data # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -# # As mentioned above, :py:class:`~pynwb.ecephys.ElectricalSeries` objects # are meant for storing specific types of extracellular recordings. In addition to this # :py:class:`~pynwb.base.TimeSeries` class, NWB provides some :ref:`modules_overview` @@ -343,13 +363,6 @@ # :py:mod:`API documentation ` and :ref:`basics` for more details on # using these objects. # -# For storing unsorted spiking data, there are two options. Which one you choose depends on what data you -# have available. If you need to store the complete, continuous raw voltage traces, you should store the traces with -# :py:class:`~pynwb.ecephys.ElectricalSeries` objects as :ref:`acquisition ` data, and use -# the :py:class:`~pynwb.ecephys.EventDetection` class for identifying the spike events in your raw traces. -# If you do not want to store the raw voltage traces and only the waveform 'snippets' surrounding spike events, -# you should use :py:class:`~pynwb.ecephys.SpikeEventSeries` objects. -# # The results of spike sorting (or clustering) should be stored in the top-level :py:class:`~pynwb.misc.Units` table. # The :py:class:`~pynwb.misc.Units` table can contain simply the spike times of sorted units, or you can also include # individual and mean waveform information in some of the optional, predefined :py:class:`~pynwb.misc.Units` table