nwb-linkml/nwb_linkml/schema/core.nwb.misc.yaml

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name: core.nwb.misc
id: core.nwb.misc
imports:
- core.nwb.base
- hdmf-common.table
- core.nwb.ecephys
- nwb.language
- core.nwb.misc.include
- core.nwb.misc
default_prefix: core.nwb.misc/
classes:
AbstractFeatureSeries:
name: AbstractFeatureSeries
description: Abstract features, such as quantitative descriptions of sensory stimuli.
The TimeSeries::data field is a 2D array, storing those features (e.g., for
visual grating stimulus this might be orientation, spatial frequency and contrast).
Null stimuli (eg, uniform gray) can be marked as being an independent feature
(eg, 1.0 for gray, 0.0 for actual stimulus) or by storing NaNs for feature values,
or through use of the TimeSeries::control fields. A set of features is considered
to persist until the next set of features is defined. The final set of features
stored should be the null set. This is useful when storing the raw stimulus
is impractical.
is_a: TimeSeries
attributes:
name:
name: name
range: string
required: true
data:
name: data
description: Values of each feature at each time.
multivalued: false
range: AbstractFeatureSeries__data
required: true
feature_units:
name: feature_units
description: Units of each feature.
multivalued: true
range: text
required: false
features:
name: features
description: Description of the features represented in TimeSeries::data.
multivalued: true
range: text
required: true
tree_root: true
AnnotationSeries:
name: AnnotationSeries
description: Stores user annotations made during an experiment. The data[] field
stores a text array, and timestamps are stored for each annotation (ie, interval=1).
This is largely an alias to a standard TimeSeries storing a text array but that
is identifiable as storing annotations in a machine-readable way.
is_a: TimeSeries
attributes:
name:
name: name
range: string
required: true
data:
name: data
description: Annotations made during an experiment.
multivalued: true
range: text
required: true
tree_root: true
IntervalSeries:
name: IntervalSeries
description: Stores intervals of data. The timestamps field stores the beginning
and end of intervals. The data field stores whether the interval just started
(>0 value) or ended (<0 value). Different interval types can be represented
in the same series by using multiple key values (eg, 1 for feature A, 2 for
feature B, 3 for feature C, etc). The field data stores an 8-bit integer. This
is largely an alias of a standard TimeSeries but that is identifiable as representing
time intervals in a machine-readable way.
is_a: TimeSeries
attributes:
name:
name: name
range: string
required: true
data:
name: data
description: Use values >0 if interval started, <0 if interval ended.
multivalued: true
range: int8
required: true
tree_root: true
DecompositionSeries:
name: DecompositionSeries
description: Spectral analysis of a time series, e.g. of an LFP or a speech signal.
is_a: TimeSeries
attributes:
name:
name: name
range: string
required: true
data:
name: data
description: Data decomposed into frequency bands.
multivalued: false
range: DecompositionSeries__data
required: true
metric:
name: metric
description: The metric used, e.g. phase, amplitude, power.
multivalued: false
range: text
required: true
source_channels:
name: source_channels
description: DynamicTableRegion pointer to the channels that this decomposition
series was generated from.
multivalued: false
range: DecompositionSeries__source_channels
required: false
bands:
name: bands
description: Table for describing the bands that this series was generated
from. There should be one row in this table for each band.
multivalued: false
range: DynamicTable
required: true
tree_root: true
Units:
name: Units
description: Data about spiking units. Event times of observed units (e.g. cell,
synapse, etc.) should be concatenated and stored in spike_times.
is_a: DynamicTable
attributes:
name:
name: name
range: string
required: true
spike_times_index:
name: spike_times_index
description: Index into the spike_times dataset.
multivalued: false
range: Units__spike_times_index
required: false
spike_times:
name: spike_times
description: Spike times for each unit in seconds.
multivalued: false
range: Units__spike_times
required: false
obs_intervals_index:
name: obs_intervals_index
description: Index into the obs_intervals dataset.
multivalued: false
range: Units__obs_intervals_index
required: false
obs_intervals:
name: obs_intervals
description: Observation intervals for each unit.
multivalued: false
range: Units__obs_intervals
required: false
electrodes_index:
name: electrodes_index
description: Index into electrodes.
multivalued: false
range: Units__electrodes_index
required: false
electrodes:
name: electrodes
description: Electrode that each spike unit came from, specified using a DynamicTableRegion.
multivalued: false
range: Units__electrodes
required: false
electrode_group:
name: electrode_group
description: Electrode group that each spike unit came from.
multivalued: true
range: ElectrodeGroup
waveform_mean:
name: waveform_mean
description: Spike waveform mean for each spike unit.
multivalued: false
range: Units__waveform_mean
required: false
waveform_sd:
name: waveform_sd
description: Spike waveform standard deviation for each spike unit.
multivalued: false
range: Units__waveform_sd
required: false
waveforms:
name: waveforms
description: Individual waveforms for each spike on each electrode. This is
a doubly indexed column. The 'waveforms_index' column indexes which waveforms
in this column belong to the same spike event for a given unit, where each
waveform was recorded from a different electrode. The 'waveforms_index_index'
column indexes the 'waveforms_index' column to indicate which spike events
belong to a given unit. For example, if the 'waveforms_index_index' column
has values [2, 5, 6], then the first 2 elements of the 'waveforms_index'
column correspond to the 2 spike events of the first unit, the next 3 elements
of the 'waveforms_index' column correspond to the 3 spike events of the
second unit, and the next 1 element of the 'waveforms_index' column corresponds
to the 1 spike event of the third unit. If the 'waveforms_index' column
has values [3, 6, 8, 10, 12, 13], then the first 3 elements of the 'waveforms'
column contain the 3 spike waveforms that were recorded from 3 different
electrodes for the first spike time of the first unit. See https://nwb-schema.readthedocs.io/en/stable/format_description.html#doubly-ragged-arrays
for a graphical representation of this example. When there is only one electrode
for each unit (i.e., each spike time is associated with a single waveform),
then the 'waveforms_index' column will have values 1, 2, ..., N, where N
is the number of spike events. The number of electrodes for each spike event
should be the same within a given unit. The 'electrodes' column should be
used to indicate which electrodes are associated with each unit, and the
order of the waveforms within a given unit x spike event should be in the
same order as the electrodes referenced in the 'electrodes' column of this
table. The number of samples for each waveform must be the same.
multivalued: false
range: Units__waveforms
required: false
waveforms_index:
name: waveforms_index
description: Index into the waveforms dataset. One value for every spike event.
See 'waveforms' for more detail.
multivalued: false
range: Units__waveforms_index
required: false
waveforms_index_index:
name: waveforms_index_index
description: Index into the waveforms_index dataset. One value for every unit
(row in the table). See 'waveforms' for more detail.
multivalued: false
range: Units__waveforms_index_index
required: false
tree_root: true