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sneakers-the-rat
4faaa8efe8
or at least all the semantics are present. it's not pretty by any stretch of the imagination
588 lines
22 KiB
YAML
588 lines
22 KiB
YAML
name: core.nwb.ecephys
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id: core.nwb.ecephys
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imports:
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- core.nwb.base
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- hdmf-common.table
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- nwb.language
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default_prefix: core.nwb.ecephys/
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classes:
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ElectricalSeries:
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name: ElectricalSeries
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description: A time series of acquired voltage data from extracellular recordings.
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The data field is an int or float array storing data in volts. The first dimension
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should always represent time. The second dimension, if present, should represent
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channels.
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is_a: TimeSeries
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attributes:
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filtering:
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name: filtering
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description: Filtering applied to all channels of the data. For example, if
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this ElectricalSeries represents high-pass-filtered data (also known as
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AP Band), then this value could be "High-pass 4-pole Bessel filter at 500
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Hz". If this ElectricalSeries represents low-pass-filtered LFP data and
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the type of filter is unknown, then this value could be "Low-pass filter
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at 300 Hz". If a non-standard filter type is used, provide as much detail
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about the filter properties as possible.
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range: text
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data:
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name: data
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description: Recorded voltage data.
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multivalued: false
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range: ElectricalSeries_data
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required: true
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electrodes:
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name: electrodes
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description: DynamicTableRegion pointer to the electrodes that this time series
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was generated from.
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multivalued: false
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range: ElectricalSeries_electrodes
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required: true
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channel_conversion:
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name: channel_conversion
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description: Channel-specific conversion factor. Multiply the data in the
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'data' dataset by these values along the channel axis (as indicated by axis
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attribute) AND by the global conversion factor in the 'conversion' attribute
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of 'data' to get the data values in Volts, i.e, data in Volts = data * data.conversion
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* channel_conversion. This approach allows for both global and per-channel
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data conversion factors needed to support the storage of electrical recordings
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as native values generated by data acquisition systems. If this dataset
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is not present, then there is no channel-specific conversion factor, i.e.
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it is 1 for all channels.
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multivalued: false
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range: ElectricalSeries_channel_conversion
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required: false
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ElectricalSeries_data:
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name: ElectricalSeries_data
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description: Recorded voltage data.
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attributes:
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unit:
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name: unit
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description: Base unit of measurement for working with the data. This value
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is fixed to 'volts'. Actual stored values are not necessarily stored in
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these units. To access the data in these units, multiply 'data' by 'conversion',
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followed by 'channel_conversion' (if present), and then add 'offset'.
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range: text
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array:
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name: array
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range: ElectricalSeries_data_Array
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ElectricalSeries_data_Array:
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name: ElectricalSeries_data_Array
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is_a: Arraylike
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attributes:
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num_times:
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name: num_times
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range: numeric
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required: true
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num_channels:
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name: num_channels
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range: numeric
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required: false
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num_samples:
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name: num_samples
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range: numeric
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required: false
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ElectricalSeries_electrodes:
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name: ElectricalSeries_electrodes
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description: DynamicTableRegion pointer to the electrodes that this time series
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was generated from.
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is_a: DynamicTableRegion
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ElectricalSeries_channel_conversion:
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name: ElectricalSeries_channel_conversion
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description: Channel-specific conversion factor. Multiply the data in the 'data'
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dataset by these values along the channel axis (as indicated by axis attribute)
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AND by the global conversion factor in the 'conversion' attribute of 'data'
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to get the data values in Volts, i.e, data in Volts = data * data.conversion
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* channel_conversion. This approach allows for both global and per-channel data
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conversion factors needed to support the storage of electrical recordings as
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native values generated by data acquisition systems. If this dataset is not
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present, then there is no channel-specific conversion factor, i.e. it is 1 for
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all channels.
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attributes:
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axis:
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name: axis
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description: The zero-indexed axis of the 'data' dataset that the channel-specific
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conversion factor corresponds to. This value is fixed to 1.
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range: int32
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array:
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name: array
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range: ElectricalSeries_channel_conversion_Array
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ElectricalSeries_channel_conversion_Array:
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name: ElectricalSeries_channel_conversion_Array
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is_a: Arraylike
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attributes:
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num_channels:
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name: num_channels
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range: float32
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required: true
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SpikeEventSeries:
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name: SpikeEventSeries
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description: 'Stores snapshots/snippets of recorded spike events (i.e., threshold
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crossings). This may also be raw data, as reported by ephys hardware. If so,
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the TimeSeries::description field should describe how events were detected.
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All SpikeEventSeries should reside in a module (under EventWaveform interface)
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even if the spikes were reported and stored by hardware. All events span the
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same recording channels and store snapshots of equal duration. TimeSeries::data
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array structure: [num events] [num channels] [num samples] (or [num events]
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[num samples] for single electrode).'
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is_a: ElectricalSeries
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attributes:
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data:
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name: data
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description: Spike waveforms.
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multivalued: false
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range: SpikeEventSeries_data
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required: true
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timestamps:
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name: timestamps
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description: Timestamps for samples stored in data, in seconds, relative to
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the common experiment master-clock stored in NWBFile.timestamps_reference_time.
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Timestamps are required for the events. Unlike for TimeSeries, timestamps
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are required for SpikeEventSeries and are thus re-specified here.
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multivalued: false
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range: SpikeEventSeries_timestamps
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required: true
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SpikeEventSeries_data:
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name: SpikeEventSeries_data
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description: Spike waveforms.
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attributes:
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unit:
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name: unit
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description: Unit of measurement for waveforms, which is fixed to 'volts'.
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range: text
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array:
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name: array
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range: SpikeEventSeries_data_Array
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SpikeEventSeries_data_Array:
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name: SpikeEventSeries_data_Array
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is_a: Arraylike
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attributes:
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num_events:
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name: num_events
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range: numeric
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required: true
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num_samples:
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name: num_samples
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range: numeric
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required: true
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num_channels:
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name: num_channels
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range: numeric
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required: false
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SpikeEventSeries_timestamps:
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name: SpikeEventSeries_timestamps
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description: Timestamps for samples stored in data, in seconds, relative to the
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common experiment master-clock stored in NWBFile.timestamps_reference_time.
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Timestamps are required for the events. Unlike for TimeSeries, timestamps are
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required for SpikeEventSeries and are thus re-specified here.
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attributes:
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interval:
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name: interval
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description: Value is '1'
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range: int32
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unit:
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name: unit
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description: Unit of measurement for timestamps, which is fixed to 'seconds'.
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range: text
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array:
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name: array
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range: SpikeEventSeries_timestamps_Array
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SpikeEventSeries_timestamps_Array:
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name: SpikeEventSeries_timestamps_Array
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is_a: Arraylike
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attributes:
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num_times:
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name: num_times
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range: float64
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required: true
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FeatureExtraction:
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name: FeatureExtraction
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description: Features, such as PC1 and PC2, that are extracted from signals stored
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in a SpikeEventSeries or other source.
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is_a: NWBDataInterface
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attributes:
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description:
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name: description
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description: Description of features (eg, ''PC1'') for each of the extracted
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features.
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multivalued: false
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range: FeatureExtraction_description
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required: true
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features:
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name: features
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description: Multi-dimensional array of features extracted from each event.
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multivalued: false
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range: FeatureExtraction_features
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required: true
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times:
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name: times
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description: Times of events that features correspond to (can be a link).
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multivalued: false
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range: FeatureExtraction_times
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required: true
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electrodes:
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name: electrodes
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description: DynamicTableRegion pointer to the electrodes that this time series
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was generated from.
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multivalued: false
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range: FeatureExtraction_electrodes
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required: true
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FeatureExtraction_description:
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name: FeatureExtraction_description
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description: Description of features (eg, ''PC1'') for each of the extracted features.
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attributes:
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array:
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name: array
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range: FeatureExtraction_description_Array
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FeatureExtraction_description_Array:
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name: FeatureExtraction_description_Array
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is_a: Arraylike
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attributes:
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num_features:
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name: num_features
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range: text
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required: true
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FeatureExtraction_features:
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name: FeatureExtraction_features
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description: Multi-dimensional array of features extracted from each event.
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attributes:
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array:
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name: array
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range: FeatureExtraction_features_Array
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FeatureExtraction_features_Array:
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name: FeatureExtraction_features_Array
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is_a: Arraylike
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attributes:
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num_events:
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name: num_events
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range: float32
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required: false
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num_channels:
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name: num_channels
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range: float32
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required: false
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num_features:
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name: num_features
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range: float32
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required: false
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FeatureExtraction_times:
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name: FeatureExtraction_times
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description: Times of events that features correspond to (can be a link).
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attributes:
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array:
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name: array
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range: FeatureExtraction_times_Array
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FeatureExtraction_times_Array:
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name: FeatureExtraction_times_Array
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is_a: Arraylike
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attributes:
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num_events:
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name: num_events
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range: float64
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required: true
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FeatureExtraction_electrodes:
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name: FeatureExtraction_electrodes
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description: DynamicTableRegion pointer to the electrodes that this time series
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was generated from.
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is_a: DynamicTableRegion
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EventDetection:
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name: EventDetection
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description: Detected spike events from voltage trace(s).
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is_a: NWBDataInterface
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attributes:
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detection_method:
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name: detection_method
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description: Description of how events were detected, such as voltage threshold,
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or dV/dT threshold, as well as relevant values.
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multivalued: false
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range: EventDetection_detection_method
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required: true
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source_idx:
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name: source_idx
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description: Indices (zero-based) into source ElectricalSeries::data array
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corresponding to time of event. ''description'' should define what is meant
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by time of event (e.g., .25 ms before action potential peak, zero-crossing
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time, etc). The index points to each event from the raw data.
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multivalued: false
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range: EventDetection_source_idx
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required: true
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times:
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name: times
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description: Timestamps of events, in seconds.
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multivalued: false
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range: EventDetection_times
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required: true
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EventDetection_detection_method:
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name: EventDetection_detection_method
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description: Description of how events were detected, such as voltage threshold,
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or dV/dT threshold, as well as relevant values.
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EventDetection_source_idx:
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name: EventDetection_source_idx
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description: Indices (zero-based) into source ElectricalSeries::data array corresponding
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to time of event. ''description'' should define what is meant by time of event
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(e.g., .25 ms before action potential peak, zero-crossing time, etc). The index
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points to each event from the raw data.
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attributes:
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array:
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name: array
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range: EventDetection_source_idx_Array
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EventDetection_source_idx_Array:
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name: EventDetection_source_idx_Array
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is_a: Arraylike
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attributes:
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num_events:
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name: num_events
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range: int32
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required: true
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EventDetection_times:
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name: EventDetection_times
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description: Timestamps of events, in seconds.
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attributes:
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unit:
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name: unit
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description: Unit of measurement for event times, which is fixed to 'seconds'.
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range: text
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array:
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name: array
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range: EventDetection_times_Array
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EventDetection_times_Array:
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name: EventDetection_times_Array
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is_a: Arraylike
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attributes:
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num_events:
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name: num_events
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range: float64
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required: true
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EventWaveform:
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name: EventWaveform
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description: Represents either the waveforms of detected events, as extracted
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from a raw data trace in /acquisition, or the event waveforms that were stored
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during experiment acquisition.
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is_a: NWBDataInterface
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attributes:
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SpikeEventSeries:
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name: SpikeEventSeries
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description: SpikeEventSeries object(s) containing detected spike event waveforms.
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multivalued: true
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range: SpikeEventSeries
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required: false
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FilteredEphys:
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name: FilteredEphys
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description: Electrophysiology data from one or more channels that has been subjected
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to filtering. Examples of filtered data include Theta and Gamma (LFP has its
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own interface). FilteredEphys modules publish an ElectricalSeries for each filtered
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channel or set of channels. The name of each ElectricalSeries is arbitrary but
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should be informative. The source of the filtered data, whether this is from
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analysis of another time series or as acquired by hardware, should be noted
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in each's TimeSeries::description field. There is no assumed 1::1 correspondence
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between filtered ephys signals and electrodes, as a single signal can apply
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to many nearby electrodes, and one electrode may have different filtered (e.g.,
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theta and/or gamma) signals represented. Filter properties should be noted in
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the ElectricalSeries 'filtering' attribute.
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is_a: NWBDataInterface
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attributes:
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ElectricalSeries:
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name: ElectricalSeries
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description: ElectricalSeries object(s) containing filtered electrophysiology
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data.
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multivalued: true
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range: ElectricalSeries
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required: true
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LFP:
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name: LFP
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description: LFP data from one or more channels. The electrode map in each published
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ElectricalSeries will identify which channels are providing LFP data. Filter
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properties should be noted in the ElectricalSeries 'filtering' attribute.
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is_a: NWBDataInterface
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attributes:
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ElectricalSeries:
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name: ElectricalSeries
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description: ElectricalSeries object(s) containing LFP data for one or more
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channels.
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multivalued: true
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range: ElectricalSeries
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required: true
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ElectrodeGroup:
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name: ElectrodeGroup
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description: A physical grouping of electrodes, e.g. a shank of an array.
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is_a: NWBContainer
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attributes:
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description:
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name: description
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description: Description of this electrode group.
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range: text
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location:
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name: location
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description: Location of electrode group. Specify the area, layer, comments
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on estimation of area/layer, etc. Use standard atlas names for anatomical
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regions when possible.
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range: text
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position:
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name: position
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description: stereotaxic or common framework coordinates
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multivalued: false
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range: ElectrodeGroup_position
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required: false
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ElectrodeGroup_position:
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name: ElectrodeGroup_position
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description: stereotaxic or common framework coordinates
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ClusterWaveforms:
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name: ClusterWaveforms
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description: DEPRECATED The mean waveform shape, including standard deviation,
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of the different clusters. Ideally, the waveform analysis should be performed
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on data that is only high-pass filtered. This is a separate module because it
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is expected to require updating. For example, IMEC probes may require different
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storage requirements to store/display mean waveforms, requiring a new interface
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or an extension of this one.
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is_a: NWBDataInterface
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attributes:
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waveform_filtering:
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name: waveform_filtering
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description: Filtering applied to data before generating mean/sd
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multivalued: false
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range: ClusterWaveforms_waveform_filtering
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required: true
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waveform_mean:
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name: waveform_mean
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description: The mean waveform for each cluster, using the same indices for
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each wave as cluster numbers in the associated Clustering module (i.e, cluster
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3 is in array slot [3]). Waveforms corresponding to gaps in cluster sequence
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should be empty (e.g., zero- filled)
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multivalued: false
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range: ClusterWaveforms_waveform_mean
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required: true
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waveform_sd:
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name: waveform_sd
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description: Stdev of waveforms for each cluster, using the same indices as
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in mean
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multivalued: false
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range: ClusterWaveforms_waveform_sd
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required: true
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ClusterWaveforms_waveform_filtering:
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name: ClusterWaveforms_waveform_filtering
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description: Filtering applied to data before generating mean/sd
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ClusterWaveforms_waveform_mean:
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name: ClusterWaveforms_waveform_mean
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description: The mean waveform for each cluster, using the same indices for each
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wave as cluster numbers in the associated Clustering module (i.e, cluster 3
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is in array slot [3]). Waveforms corresponding to gaps in cluster sequence should
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be empty (e.g., zero- filled)
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attributes:
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array:
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name: array
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range: ClusterWaveforms_waveform_mean_Array
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ClusterWaveforms_waveform_mean_Array:
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name: ClusterWaveforms_waveform_mean_Array
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is_a: Arraylike
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attributes:
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num_clusters:
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name: num_clusters
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range: float32
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required: false
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num_samples:
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name: num_samples
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range: float32
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required: false
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ClusterWaveforms_waveform_sd:
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name: ClusterWaveforms_waveform_sd
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description: Stdev of waveforms for each cluster, using the same indices as in
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mean
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attributes:
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array:
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name: array
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range: ClusterWaveforms_waveform_sd_Array
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ClusterWaveforms_waveform_sd_Array:
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name: ClusterWaveforms_waveform_sd_Array
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is_a: Arraylike
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attributes:
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num_clusters:
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name: num_clusters
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range: float32
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required: false
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num_samples:
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name: num_samples
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range: float32
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required: false
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Clustering:
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name: Clustering
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description: DEPRECATED Clustered spike data, whether from automatic clustering
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tools (e.g., klustakwik) or as a result of manual sorting.
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is_a: NWBDataInterface
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attributes:
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description:
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name: description
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description: Description of clusters or clustering, (e.g. cluster 0 is noise,
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clusters curated using Klusters, etc)
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multivalued: false
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range: Clustering_description
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required: true
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num:
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name: num
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description: Cluster number of each event
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multivalued: false
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range: Clustering_num
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required: true
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peak_over_rms:
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name: peak_over_rms
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description: Maximum ratio of waveform peak to RMS on any channel in the cluster
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|
(provides a basic clustering metric).
|
|
multivalued: false
|
|
range: Clustering_peak_over_rms
|
|
required: true
|
|
times:
|
|
name: times
|
|
description: Times of clustered events, in seconds. This may be a link to
|
|
times field in associated FeatureExtraction module.
|
|
multivalued: false
|
|
range: Clustering_times
|
|
required: true
|
|
Clustering_description:
|
|
name: Clustering_description
|
|
description: Description of clusters or clustering, (e.g. cluster 0 is noise,
|
|
clusters curated using Klusters, etc)
|
|
Clustering_num:
|
|
name: Clustering_num
|
|
description: Cluster number of each event
|
|
attributes:
|
|
array:
|
|
name: array
|
|
range: Clustering_num_Array
|
|
Clustering_num_Array:
|
|
name: Clustering_num_Array
|
|
is_a: Arraylike
|
|
attributes:
|
|
num_events:
|
|
name: num_events
|
|
range: int32
|
|
required: true
|
|
Clustering_peak_over_rms:
|
|
name: Clustering_peak_over_rms
|
|
description: Maximum ratio of waveform peak to RMS on any channel in the cluster
|
|
(provides a basic clustering metric).
|
|
attributes:
|
|
array:
|
|
name: array
|
|
range: Clustering_peak_over_rms_Array
|
|
Clustering_peak_over_rms_Array:
|
|
name: Clustering_peak_over_rms_Array
|
|
is_a: Arraylike
|
|
attributes:
|
|
num_clusters:
|
|
name: num_clusters
|
|
range: float32
|
|
required: true
|
|
Clustering_times:
|
|
name: Clustering_times
|
|
description: Times of clustered events, in seconds. This may be a link to times
|
|
field in associated FeatureExtraction module.
|
|
attributes:
|
|
array:
|
|
name: array
|
|
range: Clustering_times_Array
|
|
Clustering_times_Array:
|
|
name: Clustering_times_Array
|
|
is_a: Arraylike
|
|
attributes:
|
|
num_events:
|
|
name: num_events
|
|
range: float64
|
|
required: true
|