diff --git a/CHANGELOG.md b/CHANGELOG.md index fc360b840..4fcdcb4ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ - Deprecated `ImageMaskSeries` neurodata type. @rly [#1941](https://github.com/NeurodataWithoutBorders/pynwb/pull/1941) - Removed python 3.8 support, added python 3.13 support. @stephprince [#2007](https://github.com/NeurodataWithoutBorders/pynwb/pull/2007) +### Documentation and tutorial enhancements +- Updated `SpikeEventSeries`, `DecompositionSeries`, and `FilteredEphys` examples. @stephprince [#2012](https://github.com/NeurodataWithoutBorders/pynwb/pull/2012) + ## PyNWB 2.8.3 (November 19, 2024) ### Enhancements and minor changes diff --git a/docs/gallery/domain/ecephys.py b/docs/gallery/domain/ecephys.py index b66698044..11e39b44a 100644 --- a/docs/gallery/domain/ecephys.py +++ b/docs/gallery/domain/ecephys.py @@ -208,6 +208,7 @@ name="ElectricalSeries", description="LFP data", data=lfp_data, + filtering='Low-pass filter at 300 Hz', electrodes=all_table_region, starting_time=0.0, rate=200.0, @@ -237,8 +238,8 @@ lfp = LFP(electrical_series=lfp_electrical_series) #################### -# Unlike the raw data, which we put into the acquisition group of the :py:class:`~pynwb.file.NWBFile`, -# LFP data is typically considered processed data because the raw data was filtered and downsampled to generate the LFP. +# LFP refers to data that has been low-pass filtered, typically below 300 Hz. This data may also be downsampled. +# Because it is filtered and potentially resampled, it is categorized as processed data. # # Create a processing module named ``"ecephys"`` and add the :py:class:`~pynwb.ecephys.LFP` object to it. # This is analogous to how we can store the :py:class:`~pynwb.behavior.Position` object in a processing module @@ -250,9 +251,9 @@ ecephys_module.add(lfp) ####################### -# If the derived data is filtered but not downsampled, you can store the data in an -# :py:class:`~pynwb.ecephys.ElectricalSeries` object in a :py:class:`~pynwb.ecephys.FilteredEphys` object -# instead of a :py:class:`~pynwb.ecephys.LFP` object. +# If your data is filtered for frequency ranges other than LFP — such as Gamma or Theta — you should store it in an +# :py:class:`~pynwb.ecephys.ElectricalSeries` and encapsulate it within a +# :py:class:`~pynwb.ecephys.FilteredEphys` object. from pynwb.ecephys import FilteredEphys @@ -261,6 +262,7 @@ name="FilteredElectricalSeries", description="Filtered data", data=filtered_data, + filtering='Band-pass filtered between 4 and 8 Hz', electrodes=all_table_region, starting_time=0.0, rate=200.0, @@ -300,8 +302,6 @@ decomp_series.add_band( band_name=band_name, band_limits=band_limits, - band_mean=np.nan, - band_stdev=np.nan, ) ecephys_module.add(decomp_series) @@ -355,7 +355,7 @@ # unsorted spiking activity (e.g., multi-unit activity detected via threshold crossings during data acquisition). # This information can be stored using :py:class:`~pynwb.ecephys.SpikeEventSeries` objects. -spike_snippets = np.random.rand(20, 3, 40) # 20 events, 3 channels, 40 samples per event +spike_snippets = np.random.rand(40, 3, 30) # 40 events, 3 channels, 30 samples per event shank0 = nwbfile.create_electrode_table_region( region=[0, 1, 2], description="shank0", @@ -365,7 +365,7 @@ name='SpikeEvents_Shank0', description="events detected with 100uV threshold", data=spike_snippets, - timestamps=np.arange(20), + timestamps=np.arange(40).astype(float), electrodes=shank0, ) nwbfile.add_acquisition(spike_events)