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add schema files and update default version
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| Original file line number | Diff line number | Diff line change |
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| datasets: | ||
| - neurodata_type_def: NWBData | ||
| neurodata_type_inc: Data | ||
| doc: An abstract data type for a dataset. | ||
|
|
||
| - neurodata_type_def: TimeSeriesReferenceVectorData | ||
| neurodata_type_inc: VectorData | ||
| default_name: timeseries | ||
| dtype: | ||
| - name: idx_start | ||
| dtype: int32 | ||
| doc: Start index into the TimeSeries 'data' and 'timestamp' datasets of the referenced | ||
| TimeSeries. The first dimension of those arrays is always time. | ||
| - name: count | ||
| dtype: int32 | ||
| doc: Number of data samples available in this time series, during this epoch | ||
| - name: timeseries | ||
| dtype: | ||
| target_type: TimeSeries | ||
| reftype: object | ||
| doc: The TimeSeries that this index applies to | ||
| doc: Column storing references to a TimeSeries (rows). For each TimeSeries this | ||
| VectorData column stores the start_index and count to indicate the range in time | ||
| to be selected as well as an object reference to the TimeSeries. | ||
|
|
||
| - neurodata_type_def: Image | ||
| neurodata_type_inc: NWBData | ||
| dtype: numeric | ||
| dims: | ||
| - - x | ||
| - y | ||
| - - x | ||
| - y | ||
| - r, g, b | ||
| - - x | ||
| - y | ||
| - r, g, b, a | ||
| shape: | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - 3 | ||
| - - null | ||
| - null | ||
| - 4 | ||
| doc: An abstract data type for an image. Shape can be 2-D (x, y), or 3-D where the | ||
| third dimension can have three or four elements, e.g. (x, y, (r, g, b)) or | ||
| (x, y, (r, g, b, a)). | ||
| attributes: | ||
| - name: resolution | ||
| dtype: float32 | ||
| doc: Pixel resolution of the image, in pixels per centimeter. | ||
| required: false | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of the image. | ||
| required: false | ||
|
|
||
| - neurodata_type_def: ImageReferences | ||
| neurodata_type_inc: NWBData | ||
| dtype: | ||
| target_type: Image | ||
| reftype: object | ||
| dims: | ||
| - num_images | ||
| shape: | ||
| - null | ||
| doc: Ordered dataset of references to Image objects. | ||
|
|
||
| groups: | ||
| - neurodata_type_def: NWBContainer | ||
| neurodata_type_inc: Container | ||
| doc: An abstract data type for a generic container storing collections of data and | ||
| metadata. Base type for all data and metadata containers. | ||
|
|
||
| - neurodata_type_def: NWBDataInterface | ||
| neurodata_type_inc: NWBContainer | ||
| doc: An abstract data type for a generic container storing collections of data, | ||
| as opposed to metadata. | ||
|
|
||
| - neurodata_type_def: TimeSeries | ||
| neurodata_type_inc: NWBDataInterface | ||
| doc: General purpose time series. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| default_value: no description | ||
| doc: Description of the time series. | ||
| required: false | ||
| - name: comments | ||
| dtype: text | ||
| default_value: no comments | ||
| doc: Human-readable comments about the TimeSeries. This second descriptive field | ||
| can be used to store additional information, or descriptive information if the | ||
| primary description field is populated with a computer-readable string. | ||
| required: false | ||
| datasets: | ||
| - name: data | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - num_DIM2 | ||
| - - num_times | ||
| - num_DIM2 | ||
| - num_DIM3 | ||
| - - num_times | ||
| - num_DIM2 | ||
| - num_DIM3 | ||
| - num_DIM4 | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - null | ||
| doc: Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension | ||
| should always represent time. This can also be used to store binary data | ||
| (e.g., image frames). This can also be a link to data stored in an external file. | ||
| attributes: | ||
| - name: conversion | ||
| dtype: float32 | ||
| default_value: 1.0 | ||
| doc: Scalar to multiply each element in data to convert it to the specified 'unit'. | ||
| If the data are stored in acquisition system units or other units | ||
| that require a conversion to be interpretable, multiply the data by 'conversion' | ||
| to convert the data to the specified 'unit'. e.g. if the data acquisition system | ||
| stores values in this object as signed 16-bit integers (int16 range | ||
| -32,768 to 32,767) that correspond to a 5V range (-2.5V to 2.5V), and the data | ||
| acquisition system gain is 8000X, then the 'conversion' multiplier to get from | ||
| raw data acquisition values to recorded volts is 2.5/32768/8000 = 9.5367e-9. | ||
| required: false | ||
| - name: offset | ||
| dtype: float32 | ||
| default_value: 0.0 | ||
| doc: Scalar to add to the data after scaling by 'conversion' to finalize its coercion | ||
| to the specified 'unit'. Two common examples of this include (a) data stored in an | ||
| unsigned type that requires a shift after scaling to re-center the data, | ||
| and (b) specialized recording devices that naturally cause a scalar offset with | ||
| respect to the true units. | ||
| required: false | ||
| - name: resolution | ||
| dtype: float32 | ||
| default_value: -1.0 | ||
| doc: Smallest meaningful difference between values in data, stored in the specified | ||
| by unit, e.g., the change in value of the least significant bit, or a larger | ||
| number if signal noise is known to be present. If unknown, use -1.0. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| doc: Base unit of measurement for working with the data. Actual stored values are | ||
| not necessarily stored in these units. To access the data in these units, | ||
| multiply 'data' by 'conversion' and add 'offset'. | ||
| - name: continuity | ||
| dtype: text | ||
| doc: Optionally describe the continuity of the data. Can be "continuous", "instantaneous", or | ||
| "step". For example, a voltage trace would be "continuous", because samples | ||
| are recorded from a continuous process. An array of lick times would be "instantaneous", | ||
| because the data represents distinct moments in time. Times of image presentations would be | ||
| "step" because the picture remains the same until the next timepoint. This field is optional, | ||
| but is useful in providing information about the underlying data. It may inform the way this | ||
| data is interpreted, the way it is visualized, and what analysis methods are applicable. | ||
| required: false | ||
| - name: starting_time | ||
| dtype: float64 | ||
| doc: Timestamp of the first sample in seconds. When timestamps are uniformly | ||
| spaced, the timestamp of the first sample can be specified and all subsequent | ||
| ones calculated from the sampling rate attribute. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: rate | ||
| dtype: float32 | ||
| doc: Sampling rate, in Hz. | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for time, which is fixed to 'seconds'. | ||
| - name: timestamps | ||
| dtype: float64 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Timestamps for samples stored in data, in seconds, relative to the | ||
| common experiment master-clock stored in NWBFile.timestamps_reference_time. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: interval | ||
| dtype: int32 | ||
| value: 1 | ||
| doc: Value is '1' | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for timestamps, which is fixed to 'seconds'. | ||
| - name: control | ||
| dtype: uint8 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Numerical labels that apply to each time point in data for the purpose of | ||
| querying and slicing data by these values. If present, the length of this | ||
| array should be the same size as the first dimension of data. | ||
| quantity: '?' | ||
| - name: control_description | ||
| dtype: text | ||
| dims: | ||
| - num_control_values | ||
| shape: | ||
| - null | ||
| doc: Description of each control value. Must be present if control is present. | ||
| If present, control_description[0] should describe time points where control == 0. | ||
| quantity: '?' | ||
| groups: | ||
| - name: sync | ||
| doc: Lab-specific time and sync information as provided directly from hardware | ||
| devices and that is necessary for aligning all acquired time information to | ||
| a common timebase. The timestamp array stores time in the common timebase. | ||
| This group will usually only be populated in TimeSeries that are | ||
| stored external to the NWB file, in files storing raw data. Once timestamp | ||
| data is calculated, the contents of 'sync' are mostly for archival purposes. | ||
| quantity: '?' | ||
|
|
||
| - neurodata_type_def: ProcessingModule | ||
| neurodata_type_inc: NWBContainer | ||
| doc: A collection of processed data. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of this collection of processed data. | ||
| groups: | ||
| - neurodata_type_inc: NWBDataInterface | ||
| doc: Data objects stored in this collection. | ||
| quantity: '*' | ||
| - neurodata_type_inc: DynamicTable | ||
| doc: Tables stored in this collection. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: Images | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Images | ||
| doc: A collection of images with an optional way to specify the order of the images | ||
| using the "order_of_images" dataset. An order must be specified if the images are | ||
| referenced by index, e.g., from an IndexSeries. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of this collection of images. | ||
| datasets: | ||
| - neurodata_type_inc: Image | ||
| doc: Images stored in this collection. | ||
| quantity: '+' | ||
| - name: order_of_images | ||
| neurodata_type_inc: ImageReferences | ||
| doc: Ordered dataset of references to Image objects stored in the parent group. | ||
| Each Image object in the Images group should be stored once and only once, so | ||
| the dataset should have the same length as the number of images. | ||
| quantity: '?' |
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| groups: | ||
| - neurodata_type_def: SpatialSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: "Direction, e.g., of gaze or travel, or position. The TimeSeries::data field\ | ||
| \ is a 2D array storing position or direction relative to some reference frame.\ | ||
| \ Array structure: [num measurements] [num dimensions]. Each SpatialSeries has\ | ||
| \ a text dataset reference_frame that indicates the zero-position, or the zero-axes\ | ||
| \ for direction. For example, if representing gaze direction, 'straight-ahead'\ | ||
| \ might be a specific pixel on the monitor, or some other point in space. For\ | ||
| \ position data, the 0,0 point might be the top-left corner of an enclosure, as\ | ||
| \ viewed from the tracking camera. The unit of data will indicate how to interpret\ | ||
| \ SpatialSeries values." | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - x | ||
| - - num_times | ||
| - x,y | ||
| - - num_times | ||
| - x,y,z | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - 1 | ||
| - - null | ||
| - 2 | ||
| - - null | ||
| - 3 | ||
| doc: 1-D or 2-D array storing position or direction relative to some reference frame. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: meters | ||
| doc: Base unit of measurement for working with the data. The default value | ||
| is 'meters'. Actual stored values are not necessarily stored in these units. | ||
| To access the data in these units, multiply 'data' by 'conversion' and add 'offset'. | ||
| required: false | ||
| - name: reference_frame | ||
| dtype: text | ||
| doc: Description defining what exactly 'straight-ahead' means. | ||
| quantity: '?' | ||
|
|
||
| - neurodata_type_def: BehavioralEpochs | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralEpochs | ||
| doc: TimeSeries for storing behavioral epochs. The objective of this and the other | ||
| two Behavioral interfaces (e.g. BehavioralEvents and BehavioralTimeSeries) is | ||
| to provide generic hooks for software tools/scripts. This allows a tool/script | ||
| to take the output one specific interface (e.g., UnitTimes) and plot that data | ||
| relative to another data modality (e.g., behavioral events) without having to | ||
| define all possible modalities in advance. Declaring one of these interfaces means | ||
| that one or more TimeSeries of the specified type is published. These TimeSeries | ||
| should reside in a group having the same name as the interface. For example, if | ||
| a BehavioralTimeSeries interface is declared, the module will have one or more | ||
| TimeSeries defined in the module sub-group 'BehavioralTimeSeries'. BehavioralEpochs | ||
| should use IntervalSeries. BehavioralEvents is used for irregular events. BehavioralTimeSeries | ||
| is for continuous data. | ||
| groups: | ||
| - neurodata_type_inc: IntervalSeries | ||
| doc: IntervalSeries object containing start and stop times of epochs. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: BehavioralEvents | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralEvents | ||
| doc: TimeSeries for storing behavioral events. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a> | ||
| for more details. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing behavioral events. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: BehavioralTimeSeries | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: BehavioralTimeSeries | ||
| doc: TimeSeries for storing Behavoioral time series data. See description of <a href="#BehavioralEpochs">BehavioralEpochs</a> | ||
| for more details. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing continuous behavioral data. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: PupilTracking | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: PupilTracking | ||
| doc: Eye-tracking data, representing pupil size. | ||
| groups: | ||
| - neurodata_type_inc: TimeSeries | ||
| doc: TimeSeries object containing time series data on pupil size. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: EyeTracking | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: EyeTracking | ||
| doc: Eye-tracking data, representing direction of gaze. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing data measuring direction of gaze. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: CompassDirection | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: CompassDirection | ||
| doc: With a CompassDirection interface, a module publishes a SpatialSeries object | ||
| representing a floating point value for theta. The SpatialSeries::reference_frame | ||
| field should indicate what direction corresponds to 0 and which is the direction | ||
| of rotation (this should be clockwise). The si_unit for the SpatialSeries should | ||
| be radians or degrees. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing direction of gaze travel. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: Position | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Position | ||
| doc: Position data, whether along the x, x/y or x/y/z axis. | ||
| groups: | ||
| - neurodata_type_inc: SpatialSeries | ||
| doc: SpatialSeries object containing position data. | ||
| quantity: '+' |
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| groups: | ||
| - neurodata_type_def: Device | ||
| neurodata_type_inc: NWBContainer | ||
| doc: Metadata about a data acquisition device, e.g., recording system, electrode, microscope. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of the device (e.g., model, firmware version, processing software version, etc.) | ||
| as free-form text. | ||
| required: false | ||
| - name: manufacturer | ||
| dtype: text | ||
| doc: The name of the manufacturer of the device. | ||
| required: false |
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| groups: | ||
| - neurodata_type_def: ElectricalSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: A time series of acquired voltage data from extracellular recordings. | ||
| The data field is an int or float array storing data in volts. The first | ||
| dimension should always represent time. The second dimension, if present, | ||
| should represent channels. | ||
| attributes: | ||
| - name: filtering | ||
| dtype: text | ||
| doc: Filtering applied to all channels of the data. For example, if this ElectricalSeries represents | ||
| high-pass-filtered data (also known as AP Band), then this value could be "High-pass 4-pole Bessel filter | ||
| at 500 Hz". If this ElectricalSeries represents low-pass-filtered LFP data and the type of filter is unknown, | ||
| then this value could be "Low-pass filter at 300 Hz". If a non-standard filter type is used, provide as much | ||
| detail about the filter properties as possible. | ||
| required: false | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - num_channels | ||
| - - num_times | ||
| - num_channels | ||
| - num_samples | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| doc: Recorded voltage data. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| value: volts | ||
| doc: Base unit of measurement for working with the data. This value is fixed to | ||
| 'volts'. Actual stored values are not necessarily stored in these units. To | ||
| access the data in these units, multiply 'data' by 'conversion', followed by | ||
| 'channel_conversion' (if present), and then add 'offset'. | ||
| - name: electrodes | ||
| neurodata_type_inc: DynamicTableRegion | ||
| doc: DynamicTableRegion pointer to the electrodes that this time series was generated from. | ||
| - name: channel_conversion | ||
| dtype: float32 | ||
| dims: | ||
| - num_channels | ||
| shape: | ||
| - null | ||
| doc: Channel-specific conversion factor. Multiply the data in the 'data' dataset by these | ||
| values along the channel axis (as indicated by axis attribute) AND by the global | ||
| conversion factor in the 'conversion' attribute of 'data' to get the data values in | ||
| Volts, i.e, data in Volts = data * data.conversion * channel_conversion. This | ||
| approach allows for both global and per-channel data conversion factors needed | ||
| to support the storage of electrical recordings as native values generated by data | ||
| acquisition systems. If this dataset is not present, then there is no channel-specific | ||
| conversion factor, i.e. it is 1 for all channels. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: axis | ||
| dtype: int32 | ||
| value: 1 | ||
| doc: The zero-indexed axis of the 'data' dataset that the channel-specific conversion | ||
| factor corresponds to. This value is fixed to 1. | ||
|
|
||
| - neurodata_type_def: SpikeEventSeries | ||
| neurodata_type_inc: ElectricalSeries | ||
| doc: "Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This | ||
| may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description | ||
| field should describe how events were detected. All SpikeEventSeries should | ||
| reside in a module (under EventWaveform interface) even if the spikes were reported | ||
| and stored by hardware. All events span the same recording channels and store | ||
| snapshots of equal duration. TimeSeries::data array structure: [num events] | ||
| [num channels] [num samples] (or [num events] [num samples] for single electrode)." | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_events | ||
| - num_samples | ||
| - - num_events | ||
| - num_channels | ||
| - num_samples | ||
| shape: | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| doc: Spike waveforms. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| value: volts | ||
| doc: Unit of measurement for waveforms, which is fixed to 'volts'. | ||
| - name: timestamps | ||
| dtype: float64 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Timestamps for samples stored in data, in seconds, relative to the | ||
| common experiment master-clock stored in NWBFile.timestamps_reference_time. | ||
| Timestamps are required for the events. Unlike for TimeSeries, timestamps are | ||
| required for SpikeEventSeries and are thus re-specified here. | ||
| attributes: | ||
| - name: interval | ||
| dtype: int32 | ||
| value: 1 | ||
| doc: Value is '1' | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for timestamps, which is fixed to 'seconds'. | ||
|
|
||
| - neurodata_type_def: FeatureExtraction | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: FeatureExtraction | ||
| doc: Features, such as PC1 and PC2, that are extracted from signals stored in a | ||
| SpikeEventSeries or other source. | ||
| datasets: | ||
| - name: description | ||
| dtype: text | ||
| dims: | ||
| - num_features | ||
| shape: | ||
| - null | ||
| doc: Description of features (eg, ''PC1'') for each of the extracted features. | ||
| - name: features | ||
| dtype: float32 | ||
| dims: | ||
| - num_events | ||
| - num_channels | ||
| - num_features | ||
| shape: | ||
| - null | ||
| - null | ||
| - null | ||
| doc: Multi-dimensional array of features extracted from each event. | ||
| - name: times | ||
| dtype: float64 | ||
| dims: | ||
| - num_events | ||
| shape: | ||
| - null | ||
| doc: Times of events that features correspond to (can be a link). | ||
| - name: electrodes | ||
| neurodata_type_inc: DynamicTableRegion | ||
| doc: DynamicTableRegion pointer to the electrodes that this time series was generated from. | ||
|
|
||
| - neurodata_type_def: EventDetection | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: EventDetection | ||
| doc: Detected spike events from voltage trace(s). | ||
| datasets: | ||
| - name: detection_method | ||
| dtype: text | ||
| doc: Description of how events were detected, such as voltage threshold, or dV/dT | ||
| threshold, as well as relevant values. | ||
| - name: source_idx | ||
| dtype: int32 | ||
| dims: | ||
| - num_events | ||
| shape: | ||
| - null | ||
| doc: Indices (zero-based) into source ElectricalSeries::data array corresponding | ||
| to time of event. ''description'' should define what is meant by time of | ||
| event (e.g., .25 ms before action potential peak, zero-crossing time, etc). | ||
| The index points to each event from the raw data. | ||
| - name: times | ||
| dtype: float64 | ||
| dims: | ||
| - num_events | ||
| shape: | ||
| - null | ||
| doc: Timestamps of events, in seconds. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| value: seconds | ||
| doc: Unit of measurement for event times, which is fixed to 'seconds'. | ||
| links: | ||
| - name: source_electricalseries | ||
| target_type: ElectricalSeries | ||
| doc: Link to the ElectricalSeries that this data was calculated from. Metadata | ||
| about electrodes and their position can be read from that ElectricalSeries so | ||
| it's not necessary to include that information here. | ||
|
|
||
| - neurodata_type_def: EventWaveform | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: EventWaveform | ||
| doc: Represents either the waveforms of detected events, as extracted from a raw | ||
| data trace in /acquisition, or the event waveforms that were stored during experiment | ||
| acquisition. | ||
| groups: | ||
| - neurodata_type_inc: SpikeEventSeries | ||
| doc: SpikeEventSeries object(s) containing detected spike event waveforms. | ||
| quantity: '*' | ||
|
|
||
| - neurodata_type_def: FilteredEphys | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: FilteredEphys | ||
| doc: Electrophysiology data from one or more channels that has been subjected to filtering. | ||
| Examples of filtered data include Theta and Gamma (LFP has its own interface). | ||
| FilteredEphys modules publish an ElectricalSeries for each filtered channel or | ||
| set of channels. The name of each ElectricalSeries is arbitrary but should be | ||
| informative. The source of the filtered data, whether this is from analysis of | ||
| another time series or as acquired by hardware, should be noted in each's TimeSeries::description | ||
| field. There is no assumed 1::1 correspondence between filtered ephys signals | ||
| and electrodes, as a single signal can apply to many nearby electrodes, and one | ||
| electrode may have different filtered (e.g., theta and/or gamma) signals represented. | ||
| Filter properties should be noted in the ElectricalSeries 'filtering' attribute. | ||
| groups: | ||
| - neurodata_type_inc: ElectricalSeries | ||
| doc: ElectricalSeries object(s) containing filtered electrophysiology data. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: LFP | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: LFP | ||
| doc: LFP data from one or more channels. The electrode map in each published ElectricalSeries | ||
| will identify which channels are providing LFP data. Filter properties should | ||
| be noted in the ElectricalSeries 'filtering' attribute. | ||
| groups: | ||
| - neurodata_type_inc: ElectricalSeries | ||
| doc: ElectricalSeries object(s) containing LFP data for one or more channels. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: ElectrodeGroup | ||
| neurodata_type_inc: NWBContainer | ||
| doc: A physical grouping of electrodes, e.g. a shank of an array. | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of this electrode group. | ||
| - name: location | ||
| dtype: text | ||
| doc: Location of electrode group. Specify the area, layer, comments on estimation | ||
| of area/layer, etc. Use standard atlas names for anatomical regions when possible. | ||
| datasets: | ||
| - name: position | ||
| dtype: | ||
| - name: x | ||
| dtype: float32 | ||
| doc: x coordinate | ||
| - name: y | ||
| dtype: float32 | ||
| doc: y coordinate | ||
| - name: z | ||
| dtype: float32 | ||
| doc: z coordinate | ||
| doc: stereotaxic or common framework coordinates | ||
| quantity: '?' | ||
| links: | ||
| - name: device | ||
| target_type: Device | ||
| doc: Link to the device that was used to record from this electrode group. | ||
|
|
||
| # The types below have been deprecated | ||
| - neurodata_type_def: ClusterWaveforms | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: ClusterWaveforms | ||
| doc: DEPRECATED The mean waveform shape, including standard deviation, of the different | ||
| clusters. Ideally, the waveform analysis should be performed on data that is only | ||
| high-pass filtered. This is a separate module because it is expected to require | ||
| updating. For example, IMEC probes may require different storage requirements | ||
| to store/display mean waveforms, requiring a new interface or an extension of | ||
| this one. | ||
| datasets: | ||
| - name: waveform_filtering | ||
| dtype: text | ||
| doc: Filtering applied to data before generating mean/sd | ||
| - name: waveform_mean | ||
| dtype: float32 | ||
| dims: | ||
| - num_clusters | ||
| - num_samples | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: The mean waveform for each cluster, using the same indices for each wave | ||
| as cluster numbers in the associated Clustering module (i.e, cluster 3 is in | ||
| array slot [3]). Waveforms corresponding to gaps in cluster sequence should | ||
| be empty (e.g., zero- filled) | ||
| - name: waveform_sd | ||
| dtype: float32 | ||
| dims: | ||
| - num_clusters | ||
| - num_samples | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Stdev of waveforms for each cluster, using the same indices as in mean | ||
| links: | ||
| - name: clustering_interface | ||
| target_type: Clustering | ||
| doc: Link to Clustering interface that was the source of the clustered data | ||
|
|
||
| - neurodata_type_def: Clustering | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Clustering | ||
| doc: DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., | ||
| klustakwik) or as a result of manual sorting. | ||
| datasets: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of clusters or clustering, (e.g. cluster 0 is noise, clusters | ||
| curated using Klusters, etc) | ||
| - name: num | ||
| dtype: int32 | ||
| dims: | ||
| - num_events | ||
| shape: | ||
| - null | ||
| doc: Cluster number of each event | ||
| - name: peak_over_rms | ||
| dtype: float32 | ||
| dims: | ||
| - num_clusters | ||
| shape: | ||
| - null | ||
| doc: Maximum ratio of waveform peak to RMS on any channel in the cluster (provides | ||
| a basic clustering metric). | ||
| - name: times | ||
| dtype: float64 | ||
| dims: | ||
| - num_events | ||
| shape: | ||
| - null | ||
| doc: Times of clustered events, in seconds. This may be a link to times field | ||
| in associated FeatureExtraction module. |
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| groups: | ||
| - neurodata_type_def: TimeIntervals | ||
| neurodata_type_inc: DynamicTable | ||
| doc: A container for aggregating epoch data and the TimeSeries that each epoch applies | ||
| to. | ||
| datasets: | ||
| - name: start_time | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| doc: Start time of epoch, in seconds. | ||
| - name: stop_time | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| doc: Stop time of epoch, in seconds. | ||
| - name: tags | ||
| neurodata_type_inc: VectorData | ||
| dtype: text | ||
| doc: User-defined tags that identify or categorize events. | ||
| quantity: '?' | ||
| - name: tags_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index for tags. | ||
| quantity: '?' | ||
| - name: timeseries | ||
| neurodata_type_inc: TimeSeriesReferenceVectorData | ||
| doc: An index into a TimeSeries object. | ||
| quantity: '?' | ||
| - name: timeseries_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index for timeseries. | ||
| quantity: '?' |
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| datasets: | ||
| - neurodata_type_def: GrayscaleImage | ||
| neurodata_type_inc: Image | ||
| dims: | ||
| - x | ||
| - y | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: A grayscale image. | ||
| dtype: numeric | ||
|
|
||
| - neurodata_type_def: RGBImage | ||
| neurodata_type_inc: Image | ||
| dims: | ||
| - x | ||
| - y | ||
| - r, g, b | ||
| shape: | ||
| - null | ||
| - null | ||
| - 3 | ||
| doc: A color image. | ||
| dtype: numeric | ||
|
|
||
| - neurodata_type_def: RGBAImage | ||
| neurodata_type_inc: Image | ||
| dims: | ||
| - x | ||
| - y | ||
| - r, g, b, a | ||
| shape: | ||
| - null | ||
| - null | ||
| - 4 | ||
| doc: A color image with transparency. | ||
| dtype: numeric | ||
|
|
||
| groups: | ||
| - neurodata_type_def: ImageSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: General image data that is common between acquisition and stimulus time series. | ||
| Sometimes the image data is stored in the file in a raw format while other | ||
| times it will be stored as a series of external image files in the host file system. | ||
| The data field will either be binary data, if the data is stored in the NWB file, or | ||
| empty, if the data is stored in an external image stack. [frame][x][y] or [frame][x][y][z]. | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - frame | ||
| - x | ||
| - y | ||
| - - frame | ||
| - x | ||
| - y | ||
| - z | ||
| shape: | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - null | ||
| doc: Binary data representing images across frames. If data are stored in an external | ||
| file, this should be an empty 3D array. | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - rank | ||
| shape: | ||
| - null | ||
| doc: Number of pixels on x, y, (and z) axes. | ||
| quantity: '?' | ||
| - name: external_file | ||
| dtype: text | ||
| dims: | ||
| - num_files | ||
| shape: | ||
| - null | ||
| doc: Paths to one or more external file(s). The field is only present if format='external'. | ||
| This is only relevant if the image series is stored in the file system as one | ||
| or more image file(s). This field should NOT be used if the image is stored | ||
| in another NWB file and that file is linked to this file. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: starting_frame | ||
| dtype: int32 | ||
| dims: | ||
| - num_files | ||
| shape: | ||
| - null | ||
| doc: Each external image may contain one or more consecutive frames of the full | ||
| ImageSeries. This attribute serves as an index to indicate which frames each file | ||
| contains, to faciliate random access. The 'starting_frame' attribute, hence, | ||
| contains a list of frame numbers within the full ImageSeries of the first frame | ||
| of each file listed in the parent 'external_file' dataset. Zero-based indexing is | ||
| used (hence, the first element will always be zero). For example, if the | ||
| 'external_file' dataset has three paths to files and the first file has 5 frames, | ||
| the second file has 10 frames, and the third file has 20 frames, then this | ||
| attribute will have values [0, 5, 15]. If there is a single external file that | ||
| holds all of the frames of the ImageSeries (and so there is a single element in | ||
| the 'external_file' dataset), then this attribute should have value [0]. | ||
| - name: format | ||
| dtype: text | ||
| default_value: raw | ||
| doc: Format of image. If this is 'external', then the attribute 'external_file' | ||
| contains the path information to the image files. If this is 'raw', then the raw | ||
| (single-channel) binary data is stored in the 'data' dataset. If this attribute | ||
| is not present, then the default format='raw' case is assumed. | ||
| quantity: '?' | ||
| links: | ||
| - name: device | ||
| target_type: Device | ||
| doc: Link to the Device object that was used to capture these images. | ||
| quantity: '?' | ||
|
|
||
| - neurodata_type_def: ImageMaskSeries | ||
| neurodata_type_inc: ImageSeries | ||
| doc: An alpha mask that is applied to a presented visual stimulus. The 'data' array | ||
| contains an array of mask values that are applied to the displayed image. Mask | ||
| values are stored as RGBA. Mask can vary with time. The timestamps array indicates | ||
| the starting time of a mask, and that mask pattern continues until it's explicitly | ||
| changed. | ||
| links: | ||
| - name: masked_imageseries | ||
| target_type: ImageSeries | ||
| doc: Link to ImageSeries object that this image mask is applied to. | ||
|
|
||
| - neurodata_type_def: OpticalSeries | ||
| neurodata_type_inc: ImageSeries | ||
| doc: Image data that is presented or recorded. A stimulus template movie will be | ||
| stored only as an image. When the image is presented as stimulus, additional data | ||
| is required, such as field of view (e.g., how much of the visual field the image | ||
| covers, or how what is the area of the target being imaged). If the OpticalSeries | ||
| represents acquired imaging data, orientation is also important. | ||
| datasets: | ||
| - name: distance | ||
| dtype: float32 | ||
| doc: Distance from camera/monitor to target/eye. | ||
| quantity: '?' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - - width, height | ||
| - - width, height, depth | ||
| shape: | ||
| - - 2 | ||
| - - 3 | ||
| doc: Width, height and depth of image, or imaged area, in meters. | ||
| quantity: '?' | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - frame | ||
| - x | ||
| - y | ||
| - - frame | ||
| - x | ||
| - y | ||
| - r, g, b | ||
| shape: | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - 3 | ||
| doc: Images presented to subject, either grayscale or RGB | ||
| - name: orientation | ||
| dtype: text | ||
| doc: Description of image relative to some reference frame (e.g., which way is | ||
| up). Must also specify frame of reference. | ||
| quantity: '?' | ||
|
|
||
| - neurodata_type_def: IndexSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: Stores indices to image frames stored in an ImageSeries. The purpose of the | ||
| IndexSeries is to allow a static image stack to be stored in an Images | ||
| object, and the images in the stack to be referenced out-of-order. This can be for | ||
| the display of individual images, or of movie segments (as a movie is simply a | ||
| series of images). The data field stores the index of the frame in the referenced | ||
| Images object, and the timestamps array indicates when that image | ||
| was displayed. | ||
| datasets: | ||
| - name: data | ||
| dtype: uint32 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Index of the image (using zero-indexing) in the linked Images object. | ||
| attributes: | ||
| - name: conversion | ||
| dtype: float32 | ||
| doc: This field is unused by IndexSeries. | ||
| required: false | ||
| - name: resolution | ||
| dtype: float32 | ||
| doc: This field is unused by IndexSeries. | ||
| required: false | ||
| - name: offset | ||
| dtype: float32 | ||
| doc: This field is unused by IndexSeries. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| value: N/A | ||
| doc: This field is unused by IndexSeries and has the value N/A. | ||
| links: | ||
| - name: indexed_timeseries | ||
| target_type: ImageSeries | ||
| doc: Link to ImageSeries object containing images that are indexed. Use of this link | ||
| is discouraged and will be deprecated. Link to an Images type instead. | ||
| quantity: '?' | ||
| - name: indexed_images | ||
| target_type: Images | ||
| doc: Link to Images object containing an ordered set of images that are indexed. The Images object | ||
| must contain a 'ordered_images' dataset specifying the order of the images in the Images type. | ||
| quantity: '?' |
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| groups: | ||
| - neurodata_type_def: AbstractFeatureSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: 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. | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - num_features | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| doc: Values of each feature at each time. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: see 'feature_units' | ||
| doc: Since there can be different units for different features, store the units | ||
| in 'feature_units'. The default value for this attribute is "see 'feature_units'". | ||
| required: false | ||
| - name: feature_units | ||
| dtype: text | ||
| dims: | ||
| - num_features | ||
| shape: | ||
| - null | ||
| doc: Units of each feature. | ||
| quantity: '?' | ||
| - name: features | ||
| dtype: text | ||
| dims: | ||
| - num_features | ||
| shape: | ||
| - null | ||
| doc: Description of the features represented in TimeSeries::data. | ||
|
|
||
| - neurodata_type_def: AnnotationSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: 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. | ||
| datasets: | ||
| - name: data | ||
| dtype: text | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Annotations made during an experiment. | ||
| attributes: | ||
| - name: resolution | ||
| dtype: float32 | ||
| value: -1.0 | ||
| doc: Smallest meaningful difference between values in data. Annotations have | ||
| no units, so the value is fixed to -1.0. | ||
| - name: unit | ||
| dtype: text | ||
| value: n/a | ||
| doc: Base unit of measurement for working with the data. Annotations have | ||
| no units, so the value is fixed to 'n/a'. | ||
|
|
||
| - neurodata_type_def: IntervalSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: 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. | ||
| datasets: | ||
| - name: data | ||
| dtype: int8 | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Use values >0 if interval started, <0 if interval ended. | ||
| attributes: | ||
| - name: resolution | ||
| dtype: float32 | ||
| value: -1.0 | ||
| doc: Smallest meaningful difference between values in data. Annotations have | ||
| no units, so the value is fixed to -1.0. | ||
| - name: unit | ||
| dtype: text | ||
| value: n/a | ||
| doc: Base unit of measurement for working with the data. Annotations have | ||
| no units, so the value is fixed to 'n/a'. | ||
|
|
||
| - neurodata_type_def: DecompositionSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: Spectral analysis of a time series, e.g. of an LFP or a speech signal. | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - num_times | ||
| - num_channels | ||
| - num_bands | ||
| shape: | ||
| - null | ||
| - null | ||
| - null | ||
| doc: Data decomposed into frequency bands. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: no unit | ||
| doc: Base unit of measurement for working with the data. Actual stored values are | ||
| not necessarily stored in these units. To access the data in these units, | ||
| multiply 'data' by 'conversion'. | ||
| - name: metric | ||
| dtype: text | ||
| doc: The metric used, e.g. phase, amplitude, power. | ||
| - name: source_channels | ||
| neurodata_type_inc: DynamicTableRegion | ||
| doc: DynamicTableRegion pointer to the channels that this decomposition series was generated from. | ||
| quantity: '?' | ||
| groups: | ||
| - name: bands | ||
| neurodata_type_inc: DynamicTable | ||
| doc: Table for describing the bands that this series was generated from. There | ||
| should be one row in this table for each band. | ||
| datasets: | ||
| - name: band_name | ||
| neurodata_type_inc: VectorData | ||
| dtype: text | ||
| doc: Name of the band, e.g. theta. | ||
| - name: band_limits | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| dims: | ||
| - num_bands | ||
| - low, high | ||
| shape: | ||
| - null | ||
| - 2 | ||
| doc: Low and high limit of each band in Hz. If it is a Gaussian filter, use | ||
| 2 SD on either side of the center. | ||
| - name: band_mean | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| dims: | ||
| - num_bands | ||
| shape: | ||
| - null | ||
| doc: The mean Gaussian filters, in Hz. | ||
| - name: band_stdev | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| dims: | ||
| - num_bands | ||
| shape: | ||
| - null | ||
| doc: The standard deviation of Gaussian filters, in Hz. | ||
| links: | ||
| - name: source_timeseries | ||
| target_type: TimeSeries | ||
| doc: Link to TimeSeries object that this data was calculated from. Metadata about | ||
| electrodes and their position can be read from that ElectricalSeries so it is | ||
| not necessary to store that information here. | ||
| quantity: '?' | ||
|
|
||
| - neurodata_type_def: Units | ||
| neurodata_type_inc: DynamicTable | ||
| default_name: Units | ||
| doc: Data about spiking units. Event times of observed units (e.g. cell, synapse, | ||
| etc.) should be concatenated and stored in spike_times. | ||
| datasets: | ||
| - name: spike_times_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into the spike_times dataset. | ||
| quantity: '?' | ||
| - name: spike_times | ||
| neurodata_type_inc: VectorData | ||
| dtype: float64 | ||
| doc: Spike times for each unit in seconds. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: resolution | ||
| dtype: float64 | ||
| doc: The smallest possible difference between two spike times. Usually 1 divided by the acquisition sampling rate | ||
| from which spike times were extracted, but could be larger if the acquisition time series was downsampled or | ||
| smaller if the acquisition time series was smoothed/interpolated and it is possible for the spike time to be | ||
| between samples. | ||
| required: false | ||
| - name: obs_intervals_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into the obs_intervals dataset. | ||
| quantity: '?' | ||
| - name: obs_intervals | ||
| neurodata_type_inc: VectorData | ||
| dtype: float64 | ||
| dims: | ||
| - num_intervals | ||
| - start|end | ||
| shape: | ||
| - null | ||
| - 2 | ||
| doc: Observation intervals for each unit. | ||
| quantity: '?' | ||
| - name: electrodes_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into electrodes. | ||
| quantity: '?' | ||
| - name: electrodes | ||
| neurodata_type_inc: DynamicTableRegion | ||
| doc: Electrode that each spike unit came from, specified using a DynamicTableRegion. | ||
| quantity: '?' | ||
| - name: electrode_group | ||
| neurodata_type_inc: VectorData | ||
| dtype: | ||
| target_type: ElectrodeGroup | ||
| reftype: object | ||
| doc: Electrode group that each spike unit came from. | ||
| quantity: '?' | ||
| - name: waveform_mean | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| dims: | ||
| - - num_units | ||
| - num_samples | ||
| - - num_units | ||
| - num_samples | ||
| - num_electrodes | ||
| shape: | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| doc: Spike waveform mean for each spike unit. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: sampling_rate | ||
| dtype: float32 | ||
| doc: Sampling rate, in hertz. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| value: volts | ||
| doc: Unit of measurement. This value is fixed to 'volts'. | ||
| required: false | ||
| - name: waveform_sd | ||
| neurodata_type_inc: VectorData | ||
| dtype: float32 | ||
| dims: | ||
| - - num_units | ||
| - num_samples | ||
| - - num_units | ||
| - num_samples | ||
| - num_electrodes | ||
| shape: | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| doc: Spike waveform standard deviation for each spike unit. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: sampling_rate | ||
| dtype: float32 | ||
| doc: Sampling rate, in hertz. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| value: volts | ||
| doc: Unit of measurement. This value is fixed to 'volts'. | ||
| required: false | ||
| - name: waveforms | ||
| neurodata_type_inc: VectorData | ||
| dtype: numeric | ||
| dims: | ||
| - num_waveforms | ||
| - num_samples | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: "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." | ||
| quantity: '?' | ||
| attributes: | ||
| - name: sampling_rate | ||
| dtype: float32 | ||
| doc: Sampling rate, in hertz. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| value: volts | ||
| doc: Unit of measurement. This value is fixed to 'volts'. | ||
| required: false | ||
| - name: waveforms_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into the waveforms dataset. One value for every spike event. See 'waveforms' for more detail. | ||
| quantity: '?' | ||
| - name: waveforms_index_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into the waveforms_index dataset. One value for every unit (row in the table). See 'waveforms' for more | ||
| detail. | ||
| quantity: '?' |
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| namespaces: | ||
| - name: core | ||
| doc: NWB namespace | ||
| author: | ||
| - Andrew Tritt | ||
| - Oliver Ruebel | ||
| - Ryan Ly | ||
| - Ben Dichter | ||
| - Keith Godfrey | ||
| - Jeff Teeters | ||
| contact: | ||
| - ajtritt@lbl.gov | ||
| - oruebel@lbl.gov | ||
| - rly@lbl.gov | ||
| - bdichter@lbl.gov | ||
| - keithg@alleninstitute.org | ||
| - jteeters@berkeley.edu | ||
| full_name: NWB core | ||
| schema: | ||
| - namespace: hdmf-common | ||
| - doc: This source module contains base data types used throughout the NWB:N data | ||
| format. | ||
| source: nwb.base.yaml | ||
| title: Base data types | ||
| - doc: This source module contains neurodata_types for device data. | ||
| source: nwb.device.yaml | ||
| title: Devices | ||
| - doc: This source module contains neurodata_types for epoch data. | ||
| source: nwb.epoch.yaml | ||
| title: Epochs | ||
| - doc: This source module contains neurodata_types for image data. | ||
| source: nwb.image.yaml | ||
| title: Image data | ||
| - doc: Main NWB:N file specification. | ||
| source: nwb.file.yaml | ||
| title: NWB:N file | ||
| - doc: Miscellaneous types. | ||
| source: nwb.misc.yaml | ||
| title: Miscellaneous neurodata_types. | ||
| - doc: This source module contains neurodata_types for behavior data. | ||
| source: nwb.behavior.yaml | ||
| title: Behavior | ||
| - doc: This source module contains neurodata_types for extracellular electrophysiology | ||
| data. | ||
| source: nwb.ecephys.yaml | ||
| title: Extracellular electrophysiology | ||
| - doc: This source module contains neurodata_types for intracellular electrophysiology | ||
| data. | ||
| source: nwb.icephys.yaml | ||
| title: Intracellular electrophysiology | ||
| - doc: This source module contains neurodata_types for opto-genetics data. | ||
| source: nwb.ogen.yaml | ||
| title: Optogenetics | ||
| - doc: This source module contains neurodata_types for optical physiology data. | ||
| source: nwb.ophys.yaml | ||
| title: Optical physiology | ||
| - doc: This source module contains neurodata_type for retinotopy data. | ||
| source: nwb.retinotopy.yaml | ||
| title: Retinotopy | ||
| version: "2.6.0-alpha" |
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| groups: | ||
| - neurodata_type_def: OptogeneticSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: An optogenetic stimulus. | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - num_times | ||
| shape: | ||
| - null | ||
| doc: Applied power for optogenetic stimulus, in watts. | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| value: watts | ||
| doc: Unit of measurement for data, which is fixed to 'watts'. | ||
| links: | ||
| - name: site | ||
| target_type: OptogeneticStimulusSite | ||
| doc: Link to OptogeneticStimulusSite object that describes the site to which this | ||
| stimulus was applied. | ||
|
|
||
| - neurodata_type_def: OptogeneticStimulusSite | ||
| neurodata_type_inc: NWBContainer | ||
| doc: A site of optogenetic stimulation. | ||
| datasets: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of stimulation site. | ||
| - name: excitation_lambda | ||
| dtype: float32 | ||
| doc: Excitation wavelength, in nm. | ||
| - name: location | ||
| dtype: text | ||
| doc: Location of the stimulation site. Specify the area, layer, comments on estimation | ||
| of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas | ||
| names for anatomical regions when possible. | ||
| links: | ||
| - name: device | ||
| target_type: Device | ||
| doc: Device that generated the stimulus. |
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| groups: | ||
| - neurodata_type_def: OnePhotonSeries | ||
| neurodata_type_inc: ImageSeries | ||
| doc: Image stack recorded over time from 1-photon microscope. | ||
| attributes: | ||
| - name: pmt_gain | ||
| dtype: float32 | ||
| doc: Photomultiplier gain. | ||
| required: false | ||
| - name: scan_line_rate | ||
| dtype: float32 | ||
| doc: Lines imaged per second. This is also stored in /general/optophysiology but | ||
| is kept here as it is useful information for analysis, and so good to be stored | ||
| w/ the actual data. | ||
| required: false | ||
| - name: exposure_time | ||
| dtype: float32 | ||
| doc: Exposure time of the sample; often the inverse of the frequency. | ||
| required: false | ||
| - name: binning | ||
| dtype: uint8 | ||
| doc: Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc. | ||
| required: false | ||
| - name: power | ||
| dtype: float32 | ||
| doc: Power of the excitation in mW, if known. | ||
| required: false | ||
| - name: intensity | ||
| dtype: float32 | ||
| doc: Intensity of the excitation in mW/mm^2, if known. | ||
| required: false | ||
| links: | ||
| - name: imaging_plane | ||
| target_type: ImagingPlane | ||
| doc: Link to ImagingPlane object from which this TimeSeries data was generated. | ||
|
|
||
| - neurodata_type_def: TwoPhotonSeries | ||
| neurodata_type_inc: ImageSeries | ||
| doc: Image stack recorded over time from 2-photon microscope. | ||
| attributes: | ||
| - name: pmt_gain | ||
| dtype: float32 | ||
| doc: Photomultiplier gain. | ||
| required: false | ||
| - name: scan_line_rate | ||
| dtype: float32 | ||
| doc: Lines imaged per second. This is also stored in /general/optophysiology but | ||
| is kept here as it is useful information for analysis, and so good to be stored | ||
| w/ the actual data. | ||
| required: false | ||
| datasets: | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - - width|height | ||
| - - width|height|depth | ||
| shape: | ||
| - - 2 | ||
| - - 3 | ||
| doc: Width, height and depth of image, or imaged area, in meters. | ||
| quantity: '?' | ||
| links: | ||
| - name: imaging_plane | ||
| target_type: ImagingPlane | ||
| doc: Link to ImagingPlane object from which this TimeSeries data was generated. | ||
|
|
||
| - neurodata_type_def: RoiResponseSeries | ||
| neurodata_type_inc: TimeSeries | ||
| doc: ROI responses over an imaging plane. The first dimension represents time. | ||
| The second dimension, if present, represents ROIs. | ||
| datasets: | ||
| - name: data | ||
| dtype: numeric | ||
| dims: | ||
| - - num_times | ||
| - - num_times | ||
| - num_ROIs | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| doc: Signals from ROIs. | ||
| - name: rois | ||
| neurodata_type_inc: DynamicTableRegion | ||
| doc: DynamicTableRegion referencing into an ROITable containing information on the ROIs | ||
| stored in this timeseries. | ||
|
|
||
| - neurodata_type_def: DfOverF | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: DfOverF | ||
| doc: dF/F information about a region of interest (ROI). Storage hierarchy of dF/F | ||
| should be the same as for segmentation (i.e., same names for ROIs and for image | ||
| planes). | ||
| groups: | ||
| - neurodata_type_inc: RoiResponseSeries | ||
| doc: RoiResponseSeries object(s) containing dF/F for a ROI. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: Fluorescence | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: Fluorescence | ||
| doc: Fluorescence information about a region of interest (ROI). Storage hierarchy | ||
| of fluorescence should be the same as for segmentation (ie, same names for ROIs | ||
| and for image planes). | ||
| groups: | ||
| - neurodata_type_inc: RoiResponseSeries | ||
| doc: RoiResponseSeries object(s) containing fluorescence data for a ROI. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: ImageSegmentation | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: ImageSegmentation | ||
| doc: Stores pixels in an image that represent different regions of interest (ROIs) | ||
| or masks. All segmentation for a given imaging plane is stored together, with | ||
| storage for multiple imaging planes (masks) supported. Each ROI is stored in its | ||
| own subgroup, with the ROI group containing both a 2D mask and a list of pixels | ||
| that make up this mask. Segments can also be used for masking neuropil. If segmentation | ||
| is allowed to change with time, a new imaging plane (or module) is required and | ||
| ROI names should remain consistent between them. | ||
| groups: | ||
| - neurodata_type_inc: PlaneSegmentation | ||
| doc: Results from image segmentation of a specific imaging plane. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: PlaneSegmentation | ||
| neurodata_type_inc: DynamicTable | ||
| doc: Results from image segmentation of a specific imaging plane. | ||
| datasets: | ||
| - name: image_mask | ||
| neurodata_type_inc: VectorData | ||
| dims: | ||
| - - num_roi | ||
| - num_x | ||
| - num_y | ||
| - - num_roi | ||
| - num_x | ||
| - num_y | ||
| - num_z | ||
| shape: | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - null | ||
| doc: ROI masks for each ROI. Each image mask is the size of the original imaging | ||
| plane (or volume) and members of the ROI are finite non-zero. | ||
| quantity: '?' | ||
| - name: pixel_mask_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into pixel_mask. | ||
| quantity: '?' | ||
| - name: pixel_mask | ||
| neurodata_type_inc: VectorData | ||
| dtype: | ||
| - name: x | ||
| dtype: uint32 | ||
| doc: Pixel x-coordinate. | ||
| - name: y | ||
| dtype: uint32 | ||
| doc: Pixel y-coordinate. | ||
| - name: weight | ||
| dtype: float32 | ||
| doc: Weight of the pixel. | ||
| doc: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel | ||
| masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' | ||
| quantity: '?' | ||
| - name: voxel_mask_index | ||
| neurodata_type_inc: VectorIndex | ||
| doc: Index into voxel_mask. | ||
| quantity: '?' | ||
| - name: voxel_mask | ||
| neurodata_type_inc: VectorData | ||
| dtype: | ||
| - name: x | ||
| dtype: uint32 | ||
| doc: Voxel x-coordinate. | ||
| - name: y | ||
| dtype: uint32 | ||
| doc: Voxel y-coordinate. | ||
| - name: z | ||
| dtype: uint32 | ||
| doc: Voxel z-coordinate. | ||
| - name: weight | ||
| dtype: float32 | ||
| doc: Weight of the voxel. | ||
| doc: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel | ||
| masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation' | ||
| quantity: '?' | ||
| groups: | ||
| - name: reference_images | ||
| doc: Image stacks that the segmentation masks apply to. | ||
| groups: | ||
| - neurodata_type_inc: ImageSeries | ||
| doc: One or more image stacks that the masks apply to (can be one-element | ||
| stack). | ||
| quantity: '*' | ||
| links: | ||
| - name: imaging_plane | ||
| target_type: ImagingPlane | ||
| doc: Link to ImagingPlane object from which this data was generated. | ||
|
|
||
| - neurodata_type_def: ImagingPlane | ||
| neurodata_type_inc: NWBContainer | ||
| doc: An imaging plane and its metadata. | ||
| datasets: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of the imaging plane. | ||
| quantity: '?' | ||
| - name: excitation_lambda | ||
| dtype: float32 | ||
| doc: Excitation wavelength, in nm. | ||
| - name: imaging_rate | ||
| dtype: float32 | ||
| doc: Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored | ||
| there instead. | ||
| quantity: '?' | ||
| - name: indicator | ||
| dtype: text | ||
| doc: Calcium indicator. | ||
| - name: location | ||
| dtype: text | ||
| doc: Location of the imaging plane. Specify the area, layer, comments on estimation | ||
| of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas | ||
| names for anatomical regions when possible. | ||
| - name: manifold | ||
| dtype: float32 | ||
| dims: | ||
| - - height | ||
| - width | ||
| - x, y, z | ||
| - - height | ||
| - width | ||
| - depth | ||
| - x, y, z | ||
| shape: | ||
| - - null | ||
| - null | ||
| - 3 | ||
| - - null | ||
| - null | ||
| - null | ||
| - 3 | ||
| doc: "DEPRECATED Physical position of each pixel. 'xyz' represents the position\ | ||
| \ of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing." | ||
| quantity: '?' | ||
| attributes: | ||
| - name: conversion | ||
| dtype: float32 | ||
| default_value: 1.0 | ||
| doc: Scalar to multiply each element in data to convert it to the specified 'unit'. | ||
| If the data are stored in acquisition system units or other units | ||
| that require a conversion to be interpretable, multiply the data by 'conversion' | ||
| to convert the data to the specified 'unit'. e.g. if the data acquisition system | ||
| stores values in this object as pixels from x = -500 to 499, y = -500 to 499 | ||
| that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get | ||
| from raw data acquisition pixel units to meters is 2/1000. | ||
| required: false | ||
| - name: unit | ||
| dtype: text | ||
| default_value: meters | ||
| doc: Base unit of measurement for working with the data. The default value is 'meters'. | ||
| required: false | ||
| - name: origin_coords | ||
| dtype: float32 | ||
| dims: | ||
| - - x, y | ||
| - - x, y, z | ||
| shape: | ||
| - - 2 | ||
| - - 3 | ||
| doc: Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data. | ||
| See also reference_frame for what the physical location is relative to (e.g., bregma). | ||
| quantity: '?' | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: meters | ||
| doc: Measurement units for origin_coords. The default value is 'meters'. | ||
| - name: grid_spacing | ||
| dtype: float32 | ||
| dims: | ||
| - - x, y | ||
| - - x, y, z | ||
| shape: | ||
| - - 2 | ||
| - - 3 | ||
| doc: Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit. | ||
| Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: unit | ||
| dtype: text | ||
| default_value: meters | ||
| doc: Measurement units for grid_spacing. The default value is 'meters'. | ||
| - name: reference_frame | ||
| dtype: text | ||
| doc: Describes reference frame of origin_coords and grid_spacing. | ||
| For example, this can be a text description of the anatomical location and orientation of the grid | ||
| defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to | ||
| a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing. | ||
| If origin_coords and grid_spacing are not present, then this field is not required. | ||
| For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix | ||
| (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in | ||
| x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more | ||
| rightward, and larger numbers in z means more ventral, then enter the following -- | ||
| origin_coords = (-1.2, -0.6, -2) | ||
| grid_spacing = (0.2, 0.2, 0.5) | ||
| reference_frame = "Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior | ||
| axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more | ||
| rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral)." | ||
| quantity: '?' | ||
| groups: | ||
| - neurodata_type_inc: OpticalChannel | ||
| doc: An optical channel used to record from an imaging plane. | ||
| quantity: '+' | ||
| links: | ||
| - name: device | ||
| target_type: Device | ||
| doc: Link to the Device object that was used to record from this electrode. | ||
|
|
||
| - neurodata_type_def: OpticalChannel | ||
| neurodata_type_inc: NWBContainer | ||
| doc: An optical channel used to record from an imaging plane. | ||
| datasets: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description or other notes about the channel. | ||
| - name: emission_lambda | ||
| dtype: float32 | ||
| doc: Emission wavelength for channel, in nm. | ||
|
|
||
| - neurodata_type_def: MotionCorrection | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: MotionCorrection | ||
| doc: 'An image stack where all frames are shifted (registered) to a common coordinate | ||
| system, to account for movement and drift between frames. Note: each frame at | ||
| each point in time is assumed to be 2-D (has only x & y dimensions).' | ||
| groups: | ||
| - neurodata_type_inc: CorrectedImageStack | ||
| doc: Reuslts from motion correction of an image stack. | ||
| quantity: '+' | ||
|
|
||
| - neurodata_type_def: CorrectedImageStack | ||
| neurodata_type_inc: NWBDataInterface | ||
| doc: Reuslts from motion correction of an image stack. | ||
| groups: | ||
| - name: corrected | ||
| neurodata_type_inc: ImageSeries | ||
| doc: Image stack with frames shifted to the common coordinates. | ||
| - name: xy_translation | ||
| neurodata_type_inc: TimeSeries | ||
| doc: Stores the x,y delta necessary to align each frame to the common coordinates, | ||
| for example, to align each frame to a reference image. | ||
| links: | ||
| - name: original | ||
| target_type: ImageSeries | ||
| doc: Link to ImageSeries object that is being registered. |
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| groups: | ||
| - neurodata_type_def: ImagingRetinotopy | ||
| neurodata_type_inc: NWBDataInterface | ||
| default_name: ImagingRetinotopy | ||
| doc: 'Intrinsic signal optical imaging or widefield imaging for measuring retinotopy. | ||
| Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of responses to | ||
| specific stimuli and a combined polarity map from which to identify visual areas. | ||
| This group does not store the raw responses imaged during retinotopic mapping or the | ||
| stimuli presented, but rather the resulting phase and power maps after applying a Fourier | ||
| transform on the averaged responses. | ||
| Note: for data consistency, all images and arrays are stored in the format [row][column] | ||
| and [row, col], which equates to [y][x]. Field of view and dimension arrays may | ||
| appear backward (i.e., y before x).' | ||
| datasets: | ||
| - name: axis_1_phase_map | ||
| dtype: float32 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Phase response to stimulus on the first measured axis. | ||
| attributes: | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: unit | ||
| dtype: text | ||
| doc: Unit that axis data is stored in (e.g., degrees). | ||
| - name: axis_1_power_map | ||
| dtype: float32 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Power response on the first measured axis. Response is scaled so 0.0 is no | ||
| power in the response and 1.0 is maximum relative power. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: unit | ||
| dtype: text | ||
| doc: Unit that axis data is stored in (e.g., degrees). | ||
| - name: axis_2_phase_map | ||
| dtype: float32 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Phase response to stimulus on the second measured axis. | ||
| attributes: | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: unit | ||
| dtype: text | ||
| doc: Unit that axis data is stored in (e.g., degrees). | ||
| - name: axis_2_power_map | ||
| dtype: float32 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Power response on the second measured axis. Response is scaled so 0.0 is | ||
| no power in the response and 1.0 is maximum relative power. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: unit | ||
| dtype: text | ||
| doc: Unit that axis data is stored in (e.g., degrees). | ||
| - name: axis_descriptions | ||
| dtype: text | ||
| dims: | ||
| - axis_1, axis_2 | ||
| shape: | ||
| - 2 | ||
| doc: Two-element array describing the contents of the two response axis fields. | ||
| Description should be something like ['altitude', 'azimuth'] or '['radius', | ||
| 'theta']. | ||
| - name: focal_depth_image | ||
| dtype: uint16 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: 'Gray-scale image taken with same settings/parameters (e.g., focal depth, | ||
| wavelength) as data collection. Array format: [rows][columns].' | ||
| quantity: '?' | ||
| attributes: | ||
| - name: bits_per_pixel | ||
| dtype: int32 | ||
| doc: Number of bits used to represent each value. This is necessary to determine | ||
| maximum (white) pixel value. | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: focal_depth | ||
| dtype: float32 | ||
| doc: Focal depth offset, in meters. | ||
| - name: format | ||
| dtype: text | ||
| doc: Format of image. Right now only 'raw' is supported. | ||
| - name: sign_map | ||
| dtype: float32 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: Sine of the angle between the direction of the gradient in axis_1 and axis_2. | ||
| quantity: '?' | ||
| attributes: | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: vasculature_image | ||
| dtype: uint16 | ||
| dims: | ||
| - num_rows | ||
| - num_cols | ||
| shape: | ||
| - null | ||
| - null | ||
| doc: 'Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]' | ||
| attributes: | ||
| - name: bits_per_pixel | ||
| dtype: int32 | ||
| doc: Number of bits used to represent each value. This is necessary to determine | ||
| maximum (white) pixel value | ||
| - name: dimension | ||
| dtype: int32 | ||
| dims: | ||
| - num_rows, num_cols | ||
| shape: | ||
| - 2 | ||
| doc: 'Number of rows and columns in the image. NOTE: row, column representation | ||
| is equivalent to height, width.' | ||
| - name: field_of_view | ||
| dtype: float32 | ||
| dims: | ||
| - height, width | ||
| shape: | ||
| - 2 | ||
| doc: Size of viewing area, in meters. | ||
| - name: format | ||
| dtype: text | ||
| doc: Format of image. Right now only 'raw' is supported. |
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| # hdmf-schema-language=2.0.2 | ||
| datasets: | ||
| - data_type_def: Data | ||
| doc: An abstract data type for a dataset. | ||
|
|
||
| groups: | ||
| - data_type_def: Container | ||
| doc: An abstract data type for a group storing collections of data and | ||
| metadata. Base type for all data and metadata containers. | ||
|
|
||
| - data_type_def: SimpleMultiContainer | ||
| data_type_inc: Container | ||
| doc: A simple Container for holding onto multiple containers. | ||
| datasets: | ||
| - data_type_inc: Data | ||
| quantity: '*' | ||
| doc: Data objects held within this SimpleMultiContainer. | ||
| groups: | ||
| - data_type_inc: Container | ||
| quantity: '*' | ||
| doc: Container objects held within this SimpleMultiContainer. |
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nwb-schema/2.6.0/hdmf-common-schema/common/experimental.yaml
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| groups: [] | ||
| datasets: | ||
| - data_type_def: EnumData | ||
| data_type_inc: VectorData | ||
| dtype: uint8 | ||
| doc: Data that come from a fixed set of values. A data value of i corresponds | ||
| to the i-th value in the VectorData referenced by the 'elements' attribute. | ||
| attributes: | ||
| - name: elements | ||
| dtype: | ||
| target_type: VectorData | ||
| reftype: object | ||
| doc: Reference to the VectorData object that contains the enumerable elements | ||
|
|
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| # hdmf-schema-language=2.0.2 | ||
| namespaces: | ||
| - name: hdmf-common | ||
| doc: Common data structures provided by HDMF | ||
| author: | ||
| - Andrew Tritt | ||
| - Oliver Ruebel | ||
| - Ryan Ly | ||
| - Ben Dichter | ||
| contact: | ||
| - ajtritt@lbl.gov | ||
| - oruebel@lbl.gov | ||
| - rly@lbl.gov | ||
| - bdichter@lbl.gov | ||
| full_name: HDMF Common | ||
| schema: | ||
| - doc: base data types | ||
| source: base.yaml | ||
| title: Base data types | ||
| - doc: data types for a column-based table | ||
| source: table.yaml | ||
| title: Table data types | ||
| - doc: data types for different types of sparse matrices | ||
| source: sparse.yaml | ||
| title: Sparse data types | ||
| version: 1.5.0 | ||
|
|
||
| - name: hdmf-experimental | ||
| doc: Experimental data structures provided by HDMF. These are not guaranteed to be available in the future | ||
| author: | ||
| - Andrew Tritt | ||
| - Oliver Ruebel | ||
| - Ryan Ly | ||
| - Ben Dichter | ||
| contact: | ||
| - ajtritt@lbl.gov | ||
| - oruebel@lbl.gov | ||
| - rly@lbl.gov | ||
| - bdichter@lbl.gov | ||
| full_name: HDMF Experimental | ||
| schema: | ||
| - namespace: hdmf-common | ||
| - doc: Experimental data types | ||
| source: experimental.yaml | ||
| title: Experimental data types | ||
| - doc: data types for storing references to web accessible resources | ||
| source: resources.yaml | ||
| title: Resource reference data types | ||
| version: 0.1.0 |
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| # hdmf-schema-language=2.0.2 | ||
| groups: | ||
| - data_type_def: ExternalResources | ||
| data_type_inc: Container | ||
| doc: "A set of four tables for tracking external resource references in a file. NOTE: this data type is in beta | ||
| testing and is subject to change in a later version." | ||
| datasets: | ||
| - data_type_inc: Data | ||
| name: keys | ||
| doc: A table for storing user terms that are used to refer to external resources. | ||
| dtype: | ||
| - name: key | ||
| dtype: text | ||
| doc: The user term that maps to one or more resources in the 'resources' table. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
|
|
||
| - data_type_inc: Data | ||
| name: entities | ||
| doc: A table for mapping user terms (i.e., keys) to resource entities. | ||
| dtype: | ||
| - name: keys_idx | ||
| dtype: uint | ||
| doc: The index to the key in the 'keys' table. | ||
| - name: resources_idx | ||
| dtype: uint | ||
| doc: The index into the 'resources' table | ||
| - name: entity_id | ||
| dtype: text | ||
| doc: The unique identifier entity. | ||
| - name: entity_uri | ||
| dtype: text | ||
| doc: The URI for the entity this reference applies to. This can be an empty string. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
|
|
||
| - data_type_inc: Data | ||
| name: resources | ||
| doc: A table for mapping user terms (i.e., keys) to resource entities. | ||
| dtype: | ||
| - name: resource | ||
| dtype: text | ||
| doc: The name of the resource. | ||
| - name: resource_uri | ||
| dtype: text | ||
| doc: The URI for the resource. This can be an empty string. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
|
|
||
| - data_type_inc: Data | ||
| name: objects | ||
| doc: A table for identifying which objects in a file contain references to external resources. | ||
| dtype: | ||
| - name: object_id | ||
| dtype: text | ||
| doc: The UUID for the object. | ||
| - name: field | ||
| dtype: text | ||
| doc: The field of the object. This can be an empty string if the object is a dataset and the field is the | ||
| dataset values. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
|
|
||
| - data_type_inc: Data | ||
| name: object_keys | ||
| doc: A table for identifying which objects use which keys. | ||
| dtype: | ||
| - name: objects_idx | ||
| dtype: uint | ||
| doc: The index to the 'objects' table for the object that holds the key. | ||
| - name: keys_idx | ||
| dtype: uint | ||
| doc: The index to the 'keys' table for the key. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null |
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| # hdmf-schema-language=2.0.2 | ||
| groups: | ||
| - data_type_def: CSRMatrix | ||
| data_type_inc: Container | ||
| doc: 'A compressed sparse row matrix. Data are stored in the standard CSR format, where column indices for row i are | ||
| stored in indices[indptr[i]:indptr[i+1]] and their corresponding values are stored in data[indptr[i]:indptr[i+1]].' | ||
| attributes: | ||
| - name: shape | ||
| dtype: uint | ||
| dims: | ||
| - number of rows, number of columns | ||
| shape: | ||
| - 2 | ||
| doc: The shape (number of rows, number of columns) of this sparse matrix. | ||
| datasets: | ||
| - name: indices | ||
| dtype: uint | ||
| dims: | ||
| - number of non-zero values | ||
| shape: | ||
| - null | ||
| doc: The column indices. | ||
| - name: indptr | ||
| dtype: uint | ||
| dims: | ||
| - number of rows in the matrix + 1 | ||
| shape: | ||
| - null | ||
| doc: The row index pointer. | ||
| - name: data | ||
| dims: | ||
| - number of non-zero values | ||
| shape: | ||
| - null | ||
| doc: The non-zero values in the matrix. |
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| # hdmf-schema-language=2.0.2 | ||
| datasets: | ||
|
|
||
| - data_type_def: VectorData | ||
| data_type_inc: Data | ||
| doc: An n-dimensional dataset representing a column of a DynamicTable. | ||
| If used without an accompanying VectorIndex, first dimension is | ||
| along the rows of the DynamicTable and each step along the first | ||
| dimension is a cell of the larger table. VectorData can also be | ||
| used to represent a ragged array if paired with a VectorIndex. | ||
| This allows for storing arrays of varying length in a single cell | ||
| of the DynamicTable by indexing into this VectorData. The first | ||
| vector is at VectorData[0:VectorIndex[0]]. The second vector is at | ||
| VectorData[VectorIndex[0]:VectorIndex[1]], and so on. | ||
| dims: | ||
| - - dim0 | ||
| - - dim0 | ||
| - dim1 | ||
| - - dim0 | ||
| - dim1 | ||
| - dim2 | ||
| - - dim0 | ||
| - dim1 | ||
| - dim2 | ||
| - dim3 | ||
| shape: | ||
| - - null | ||
| - - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - - null | ||
| - null | ||
| - null | ||
| - null | ||
| attributes: | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of what these vectors represent. | ||
|
|
||
| - data_type_def: VectorIndex | ||
| data_type_inc: VectorData | ||
| dtype: uint8 | ||
| doc: Used with VectorData to encode a ragged array. An array of indices | ||
| into the first dimension of the target VectorData, and forming a map | ||
| between the rows of a DynamicTable and the indices of the VectorData. | ||
| The name of the VectorIndex is expected to be the name of the target | ||
| VectorData object followed by "_index". | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
| attributes: | ||
| - name: target | ||
| dtype: | ||
| target_type: VectorData | ||
| reftype: object | ||
| doc: Reference to the target dataset that this index applies to. | ||
|
|
||
| - data_type_def: ElementIdentifiers | ||
| data_type_inc: Data | ||
| default_name: element_id | ||
| dtype: int | ||
| dims: | ||
| - num_elements | ||
| shape: | ||
| - null | ||
| doc: A list of unique identifiers for values within a dataset, e.g. rows of a DynamicTable. | ||
|
|
||
| - data_type_def: DynamicTableRegion | ||
| data_type_inc: VectorData | ||
| dtype: int | ||
| doc: DynamicTableRegion provides a link from one table to an index or region of another. The `table` attribute is a | ||
| link to another `DynamicTable`, indicating which table is referenced, and the data is int(s) indicating the row(s) | ||
| (0-indexed) of the target array. `DynamicTableRegion`s can be used to associate rows with repeated meta-data without | ||
| data duplication. They can also be used to create hierarchical relationships between multiple `DynamicTable`s. | ||
| `DynamicTableRegion` objects may be paired with a `VectorIndex` object to create ragged references, so a single cell | ||
| of a `DynamicTable` can reference many rows of another `DynamicTable`. | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
| attributes: | ||
| - name: table | ||
| dtype: | ||
| target_type: DynamicTable | ||
| reftype: object | ||
| doc: Reference to the DynamicTable object that this region applies to. | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of what this table region points to. | ||
|
|
||
| groups: | ||
|
|
||
| - data_type_def: DynamicTable | ||
| data_type_inc: Container | ||
| doc: A group containing multiple datasets that are aligned on the first dimension | ||
| (Currently, this requirement if left up to APIs to check and enforce). These datasets | ||
| represent different columns in the table. Apart from a column that contains unique | ||
| identifiers for each row, there are no other required datasets. Users are free to add | ||
| any number of custom VectorData objects (columns) here. DynamicTable also supports | ||
| ragged array columns, where each element can be of a different size. To add a ragged | ||
| array column, use a VectorIndex type to index the corresponding VectorData type. | ||
| See documentation for VectorData and VectorIndex for more details. | ||
| Unlike a compound data type, which is analogous to storing an | ||
| array-of-structs, a DynamicTable can be thought of as a struct-of-arrays. This provides | ||
| an alternative structure to choose from when optimizing storage for anticipated access | ||
| patterns. Additionally, this type provides a way of creating a table without having to | ||
| define a compound type up front. Although this convenience may be attractive, users | ||
| should think carefully about how data will be accessed. DynamicTable is more appropriate | ||
| for column-centric access, whereas a dataset with a compound type would be more | ||
| appropriate for row-centric access. Finally, data size should also be taken into account. | ||
| For small tables, performance loss may be an acceptable trade-off for the flexibility of | ||
| a DynamicTable. | ||
| attributes: | ||
| - name: colnames | ||
| dtype: text | ||
| dims: | ||
| - num_columns | ||
| shape: | ||
| - null | ||
| doc: The names of the columns in this table. This should be used to specify | ||
| an order to the columns. | ||
| - name: description | ||
| dtype: text | ||
| doc: Description of what is in this dynamic table. | ||
| datasets: | ||
| - name: id | ||
| data_type_inc: ElementIdentifiers | ||
| dtype: int | ||
| dims: | ||
| - num_rows | ||
| shape: | ||
| - null | ||
| doc: Array of unique identifiers for the rows of this dynamic table. | ||
| - data_type_inc: VectorData | ||
| doc: Vector columns, including index columns, of this dynamic table. | ||
| quantity: '*' | ||
|
|
||
| - data_type_def: AlignedDynamicTable | ||
| data_type_inc: DynamicTable | ||
| doc: DynamicTable container that supports storing a collection of sub-tables. Each | ||
| sub-table is a DynamicTable itself that is aligned with the main table by row | ||
| index. I.e., all DynamicTables stored in this group MUST have the same number | ||
| of rows. This type effectively defines a 2-level table in which the main data | ||
| is stored in the main table implemented by this type and additional columns of | ||
| the table are grouped into categories, with each category being represented by | ||
| a separate DynamicTable stored within the group. | ||
| attributes: | ||
| - name: categories | ||
| dtype: text | ||
| dims: | ||
| - num_categories | ||
| shape: | ||
| - null | ||
| doc: The names of the categories in this AlignedDynamicTable. Each category is | ||
| represented by one DynamicTable stored in the parent group. This attribute should | ||
| be used to specify an order of categories and the category names must match | ||
| the names of the corresponding DynamicTable in the group. | ||
| groups: | ||
| - data_type_inc: DynamicTable | ||
| doc: A DynamicTable representing a particular category for columns in the AlignedDynamicTable | ||
| parent container. The table MUST be aligned with (i.e., have the same number | ||
| of rows) as all other DynamicTables stored in the AlignedDynamicTable parent | ||
| container. The name of the category is given by the name of the DynamicTable | ||
| and its description by the description attribute of the DynamicTable. | ||
| quantity: '*' |