Version 2.10.0-alpha May 12, 2026

1. Format Overview

1.1. Namespace – NWB core

• Description: NWB namespace

• Name: core

• Full Name: NWB core

• Version: 2.10.0-alpha

• Authors:

  • Andrew Tritt

  • Oliver Ruebel

  • Ryan Ly

  • Ben Dichter

  • Keith Godfrey

  • Jeff Teeters

• Contacts:

  • ajtritt@lbl.gov

  • oruebel@lbl.gov

  • rly@lbl.gov

  • bdichter@lbl.gov

  • keithg@alleninstitute.org

  • jteeters@berkeley.edu

• Schema:

  • namespace: hdmf-common

  • doc: This source module contains base data types used throughout the NWB 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 event data.

  • source: nwb.event.yaml

  • title: Events

  • doc: This source module contains neurodata_types for image data.

  • source: nwb.image.yaml

  • title: Image data

  • doc: Main NWB file specification.

  • source: nwb.file.yaml

  • title: NWB 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

1.2. Type Hierarchy

• Container

  • CSRMatrix

  • DynamicTable

    • AlignedDynamicTable

      • IntracellularRecordingsTable

    • ElectrodesTable

    • EventsTable

    • ExperimentalConditionsTable

    • FrequencyBandsTable

    • IntracellularElectrodesTable

    • IntracellularResponsesTable

    • IntracellularStimuliTable

    • MeaningsTable

    • PlaneSegmentation

    • RepetitionsTable

    • SequentialRecordingsTable

    • SimultaneousRecordingsTable

    • SweepTable

    • TimeIntervals

    • Units

  • HERD

  • NWBContainer

    • Device

    • DeviceModel

    • ElectrodeGroup

    • ImagingPlane

    • IntracellularElectrode

    • LabMetaData

    • NWBDataInterface

      • BehavioralEpochs

      • BehavioralEvents

      • BehavioralTimeSeries

      • ClusterWaveforms

      • Clustering

      • CompassDirection

      • CorrectedImageStack

      • DfOverF

      • EventDetection

      • EventWaveform

      • EyeTracking

      • FeatureExtraction

      • FilteredEphys

      • Fluorescence

      • ImageSegmentation

      • Images

      • ImagingRetinotopy

      • LFP

      • MotionCorrection

      • Position

      • PupilTracking

      • TimeSeries

        • AbstractFeatureSeries

        • AnnotationSeries

        • DecompositionSeries

        • ElectricalSeries

          • SpikeEventSeries

        • ImageSeries

          • ImageMaskSeries

          • OnePhotonSeries

          • OpticalSeries

          • TwoPhotonSeries

        • IndexSeries

        • IntervalSeries

        • OptogeneticSeries

        • PatchClampSeries

          • CurrentClampSeries

            • IZeroClampSeries

          • CurrentClampStimulusSeries

          • VoltageClampSeries

          • VoltageClampStimulusSeries

        • RoiResponseSeries

        • SpatialSeries

    • NWBFile

    • OpticalChannel

    • OptogeneticStimulusSite

    • ProcessingModule

    • Subject

  • SimpleMultiContainer

• Data

  • ElementIdentifiers

  • NWBData

    • BaseImage

      • ExternalImage

      • Image

        • GrayscaleImage

        • RGBAImage

        • RGBImage

    • ImageReferences

    • ScratchData

  • VectorData

    • DurationVectorData

    • DynamicTableRegion

    • TimeSeriesReferenceVectorData

    • TimestampVectorData

    • VectorIndex

2. Type Specifications

2.1. Base data types

This source module contains base data types used throughout the NWB data format.

2.1.1. NWBData

Overview: An abstract data type for a dataset.

NWBData extends Data and includes all elements of Data with the following additions or changes.

• Extends: Data

• Primitive Type: Dataset

• Inherits from: Data

• Subtypes: ImageReferences, RGBAImage, ScratchData, GrayscaleImage, RGBImage, Image, BaseImage, ExternalImage

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.1

2.1.2. TimeSeriesReferenceVectorData

Overview: 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.

TimeSeriesReferenceVectorData extends VectorData and includes all elements of VectorData with the following additions or changes.

• Extends: VectorData

• Primitive Type: Dataset

• Data Type: Compound data type with the following elements:

  • idx_start: Start index into the TimeSeries ‘data’ and ‘timestamp’ datasets of the referenced TimeSeries. The first dimension of those arrays is always time. (dtype= int32 )

  • count: Number of data samples available in this time series, during this epoch (dtype= int32 )

  • timeseries: The TimeSeries that this index applies to (dtype= object reference to TimeSeries )

• Default Name: timeseries

• Inherits from: VectorData, Data

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.2

2.1.3. BaseImage

Overview: An abstract base type for image data. Parent type for Image and ExternalImage types.

BaseImage extends NWBData and includes all elements of NWBData with the following additions or changes.

• Extends: NWBData

• Primitive Type: Dataset

• Inherits from: NWBData, Data

• Subtypes: RGBAImage, GrayscaleImage, RGBImage, Image, ExternalImage

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.3

Table 2.2 Datasets, Links, and Attributes contained in <BaseImage>

Id	Type	Description
<BaseImage>	Dataset	Top level Dataset for <BaseImage> Neurodata Type: BaseImage Extends: NWBData
—description	Attribute	Description of the image. Data Type: text Required: False Name: description

2.1.4. Image

Overview: A type for storing image data directly. 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)).

Image extends BaseImage and includes all elements of BaseImage with the following additions or changes.

• Extends: BaseImage

• Primitive Type: Dataset

• Data Type: numeric

• Dimensions: [[‘x’, ‘y’], [‘x’, ‘y’, ‘r, g, b’], [‘x’, ‘y’, ‘r, g, b, a’]]

• Shape: [[None, None], [None, None, 3], [None, None, 4]]

• Inherits from: BaseImage, NWBData, Data

• Subtypes: RGBAImage, GrayscaleImage, RGBImage

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.4

Table 2.3 Datasets, Links, and Attributes contained in <Image>

Id	Type	Description
<Image>	Dataset	Top level Dataset for <Image> Neurodata Type: Image Extends: BaseImage Data Type: numeric Dimensions: [[‘x’, ‘y’], [‘x’, ‘y’, ‘r, g, b’], [‘x’, ‘y’, ‘r, g, b, a’]] Shape: [[None, None], [None, None, 3], [None, None, 4]]
—resolution	Attribute	Pixel resolution of the image, in pixels per centimeter. Data Type: float32 Required: False Name: resolution

2.1.5. ExternalImage

Overview: A type for referencing an external image file. The single file path or URI to the external image file should be stored in the dataset. This type should NOT be used if the image is stored in another NWB file and that file is linked to this file.

ExternalImage extends BaseImage and includes all elements of BaseImage with the following additions or changes.

• Extends: BaseImage

• Primitive Type: Dataset

• Data Type: text

• Inherits from: BaseImage, NWBData, Data

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.5

Table 2.4 Datasets, Links, and Attributes contained in <ExternalImage>

Id	Type	Description
<ExternalImage>	Dataset	Top level Dataset for <ExternalImage> Neurodata Type: ExternalImage Extends: BaseImage Data Type: text
—image_mode	Attribute	Image mode (color mode) of the image, e.g., “RGB”, “RGBA”, “grayscale”, and “LA”. Data Type: text Required: False Name: image_mode
—image_format	Attribute	Common name of the image file format. Only widely readable, open file formats are allowed. Allowed values are “PNG”, “JPEG”, and “GIF”. Data Type: text Name: image_format

2.1.6. ImageReferences

Overview: Ordered dataset of references to BaseImage (e.g., Image or ExternalImage) objects.

ImageReferences extends NWBData and includes all elements of NWBData with the following additions or changes.

• Extends: NWBData

• Primitive Type: Dataset

• Data Type: object reference to BaseImage

• Dimensions: [‘num_images’]

• Shape: [None]

• Inherits from: NWBData, Data

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.6

2.1.7. NWBContainer

Overview: An abstract data type for a generic container storing collections of data and metadata. Base type for all data and metadata containers.

NWBContainer extends Container and includes all elements of Container with the following additions or changes.

• Extends: Container

• Primitive Type: Group

• Inherits from: Container

• Subtypes: IntervalSeries, BehavioralEvents, ImagingPlane, Images, AnnotationSeries, PatchClampSeries, Fluorescence, OptogeneticStimulusSite, FilteredEphys, LabMetaData, ElectricalSeries, SpikeEventSeries, LFP, RoiResponseSeries, EventWaveform, OpticalSeries, EyeTracking, ProcessingModule, CurrentClampStimulusSeries, EventDetection, OnePhotonSeries, Clustering, ImageSeries, FeatureExtraction, MotionCorrection, DfOverF, ImagingRetinotopy, TimeSeries, AbstractFeatureSeries, BehavioralTimeSeries, VoltageClampStimulusSeries, TwoPhotonSeries, CurrentClampSeries, CorrectedImageStack, SpatialSeries, VoltageClampSeries, PupilTracking, IntracellularElectrode, ImageSegmentation, IZeroClampSeries, OptogeneticSeries, DecompositionSeries, ImageMaskSeries, Device, Subject, IndexSeries, OpticalChannel, DeviceModel, CompassDirection, NWBFile, BehavioralEpochs, ClusterWaveforms, ElectrodeGroup, Position, NWBDataInterface

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.7

2.1.8. NWBDataInterface

Overview: An abstract data type for a generic container storing collections of data, as opposed to metadata.

NWBDataInterface extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Subtypes: IntervalSeries, BehavioralEvents, Images, AnnotationSeries, PatchClampSeries, Fluorescence, FilteredEphys, ElectricalSeries, SpikeEventSeries, LFP, RoiResponseSeries, EventWaveform, OpticalSeries, EyeTracking, CurrentClampStimulusSeries, EventDetection, OnePhotonSeries, Clustering, ImageSeries, FeatureExtraction, MotionCorrection, DfOverF, ImagingRetinotopy, TimeSeries, AbstractFeatureSeries, BehavioralTimeSeries, VoltageClampStimulusSeries, TwoPhotonSeries, CurrentClampSeries, CorrectedImageStack, SpatialSeries, VoltageClampSeries, PupilTracking, ImageSegmentation, IZeroClampSeries, OptogeneticSeries, DecompositionSeries, ImageMaskSeries, IndexSeries, CompassDirection, BehavioralEpochs, ClusterWaveforms, Position

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.8

2.1.9. TimeSeries

Overview: General purpose time series.

TimeSeries extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Inherits from: NWBDataInterface, NWBContainer, Container

• Subtypes: IntervalSeries, AnnotationSeries, PatchClampSeries, ElectricalSeries, SpikeEventSeries, RoiResponseSeries, OpticalSeries, CurrentClampStimulusSeries, OnePhotonSeries, ImageSeries, AbstractFeatureSeries, VoltageClampStimulusSeries, TwoPhotonSeries, CurrentClampSeries, SpatialSeries, VoltageClampSeries, IZeroClampSeries, OptogeneticSeries, DecompositionSeries, ImageMaskSeries, IndexSeries

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.9

Table 2.5 Datasets, Links, and Attributes contained in <TimeSeries>

Id	Type	Description
<TimeSeries>	Group	Top level Group for <TimeSeries> Neurodata Type: TimeSeries Extends: NWBDataInterface
—description	Attribute	Description of the time series. Data Type: text Required: False Default Value: no description Name: description
—comments	Attribute	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. Data Type: text Required: False Default Value: no comments Name: comments
—data	Dataset	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. Dimensions: [[‘num_times’], [‘num_times’, ‘num_DIM2’], [‘num_times’, ‘num_DIM2’, ‘num_DIM3’], [‘num_times’, ‘num_DIM2’, ‘num_DIM3’, ‘num_DIM4’]] Shape: [[None], [None, None], [None, None, None], [None, None, None, None]] Name: data
——conversion	Attribute	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. Data Type: float32 Required: False Default Value: 1.0 Name: conversion
——offset	Attribute	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. Data Type: float32 Required: False Default Value: 0.0 Name: offset
——resolution	Attribute	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. Data Type: float32 Required: False Default Value: -1.0 Name: resolution
——unit	Attribute	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’. Data Type: text Name: unit
——continuity	Attribute	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. For storing instantaneous event information, it is recommended to use an EventsTable instead of a TimeSeries with continuity set to “instantaneous”. Data Type: text Required: False Name: continuity
—starting_time	Dataset	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: 0 or 1 Data Type: float64 Name: starting_time
——rate	Attribute	Sampling rate, in Hz. Data Type: float32 Name: rate
——unit	Attribute	Unit of measurement for time, which is fixed to ‘seconds’. Data Type: text Value: seconds Name: unit
—timestamps	Dataset	Timestamps for samples stored in data, in seconds, relative to the common experiment master-clock stored in NWBFile.timestamps_reference_time. Quantity: 0 or 1 Data Type: float64 Dimensions: [‘num_times’] Shape: [None] Name: timestamps
——interval	Attribute	Value is ‘1’ Data Type: int32 Value: 1 Name: interval
——unit	Attribute	Unit of measurement for timestamps, which is fixed to ‘seconds’. Data Type: text Value: seconds Name: unit
—control	Dataset	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: 0 or 1 Data Type: uint8 Dimensions: [‘num_times’] Shape: [None] Name: control
—control_description	Dataset	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: 0 or 1 Data Type: text Dimensions: [‘num_control_values’] Shape: [None] Name: control_description

Table 2.6 Groups contained in <TimeSeries>

Id	Type	Description
<TimeSeries>	Group	Top level Group for <TimeSeries> Neurodata Type: TimeSeries Extends: NWBDataInterface
—sync	Group	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: 0 or 1 Name: sync

2.1.9.1. Groups: sync

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: 0 or 1

• Name: sync

2.1.10. ProcessingModule

Overview: A collection of processed data.

ProcessingModule extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.10

Table 2.7 Datasets, Links, and Attributes contained in <ProcessingModule>

Id	Type	Description
<ProcessingModule>	Group	Top level Group for <ProcessingModule> Neurodata Type: ProcessingModule Extends: NWBContainer
—description	Attribute	Description of this collection of processed data. Data Type: text Name: description

Table 2.8 Groups contained in <ProcessingModule>

Id	Type	Description
<ProcessingModule>	Group	Top level Group for <ProcessingModule> Neurodata Type: ProcessingModule Extends: NWBContainer
—<NWBDataInterface>	Group	Data objects stored in this collection. Extends: NWBDataInterface Quantity: 0 or more
—<DynamicTable>	Group	Tables stored in this collection. Extends: DynamicTable Quantity: 0 or more

2.1.10.1. Groups: <NWBDataInterface>

Data objects stored in this collection.

• Extends: NWBDataInterface

• Quantity: 0 or more

2.1.10.2. Groups: <DynamicTable>

Tables stored in this collection.

• Extends: DynamicTable

• Quantity: 0 or more

2.1.11. Images

Overview: 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.

Images extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: Images

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.base.yaml

• Source Specification: see Section 3.2.11

Table 2.9 Datasets, Links, and Attributes contained in <Images>

Id	Type	Description
<Images>	Group	Top level Group for <Images> Neurodata Type: Images Extends: NWBDataInterface Default Name: Images
—description	Attribute	Description of this collection of images. Data Type: text Name: description
—<BaseImage>	Dataset	Images stored in this collection. Extends: BaseImage Quantity: 1 or more
—order_of_images	Dataset	Ordered dataset of references to BaseImage objects stored in the parent group. Each 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. Extends: ImageReferences Quantity: 0 or 1 Name: order_of_images

2.2. Devices

This source module contains neurodata_types for device data.

2.2.1. Device

Overview: Metadata about a specific instance of a data acquisition device, e.g., recording system, electrode, microscope. Link to a DeviceModel.model to represent information about the model of the device.

Device extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.device.yaml

• Source Specification: see Section 3.3.1

Table 2.10 Datasets, Links, and Attributes contained in <Device>

Id	Type	Description
<Device>	Group	Top level Group for <Device> Neurodata Type: Device Extends: NWBContainer
—description	Attribute	Description of the device as free-form text. If there is any software/firmware associated with the device, the names and versions of those can be added to NWBFile.was_generated_by. Data Type: text Required: False Name: description
—manufacturer	Attribute	DEPRECATED. The name of the manufacturer of the device, e.g., Imec, Plexon, Thorlabs. Instead of using this field, store the value in DeviceModel.manufacturer and link to that DeviceModel from this Device. Data Type: text Required: False Name: manufacturer
—model_number	Attribute	DEPRECATED. The model number (or part/product number) of the device, e.g., PRB_1_4_0480_1, PLX-VP-32-15SE(75)-(260-80)(460-10)-300-(1)CON/32m-V, BERGAMO. Instead of using this field, store the value in DeviceModel.model_number and link to that DeviceModel from this Device. Data Type: text Required: False Name: model_number
—model_name	Attribute	DEPRECATED. The model name of the device, e.g., Neuropixels 1.0, V-Probe, Bergamo III. Instead of using this field, create and add a new DeviceModel named the model name and link to that DeviceModel from this Device. Data Type: text Required: False Name: model_name
—serial_number	Attribute	The serial number of the device. Data Type: text Required: False Name: serial_number
—model	Link	The model of the device. Target Type DeviceModel Name: model

Table 2.11 Groups contained in <Device>

Id	Type	Description
<Device>	Group	Top level Group for <Device> Neurodata Type: Device Extends: NWBContainer
—model	Link	The model of the device. Target Type DeviceModel Name: model

2.2.2. DeviceModel

Overview: Model properties of a data acquisition device, e.g., recording system, electrode, microscope. This should be extended for specific types of device models to include additional attributes specific to each type. The name of the DeviceModel should be the most common representation of the model name, e.g., Neuropixels 1.0, V-Probe, Bergamo III.

DeviceModel extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.device.yaml

• Source Specification: see Section 3.3.2

Table 2.12 Datasets, Links, and Attributes contained in <DeviceModel>

Id	Type	Description
<DeviceModel>	Group	Top level Group for <DeviceModel> Neurodata Type: DeviceModel Extends: NWBContainer
—manufacturer	Attribute	The name of the manufacturer of the device model, e.g., Imec, Plexon, Thorlabs. Data Type: text Name: manufacturer
—model_number	Attribute	The model number (or part/product number) of the device, e.g., PRB_1_4_0480_1, PLX-VP-32-15SE(75)-(260-80)(460-10)-300-(1)CON/32m-V, BERGAMO. Data Type: text Required: False Name: model_number
—description	Attribute	Description of the device model as free-form text. Data Type: text Required: False Name: description

2.3. Epochs

This source module contains neurodata_types for epoch data.

2.3.1. TimeIntervals

Overview: A column-based table to store information about time intervals, one interval per row. Use TimeIntervals when each row naturally has a start and stop time and represents a contiguous period of time, often encompassing an experimental condition. Rows can optionally reference TimeSeries data via the timeseries column. Examples include trials, epochs, behavioral states (e.g., “running”, “resting”), and invalid recording windows.

TimeIntervals extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.epoch.yaml

• Source Specification: see Section 3.4.1

Table 2.13 Datasets, Links, and Attributes contained in <TimeIntervals>

Id	Type	Description
<TimeIntervals>	Group	Top level Group for <TimeIntervals> Neurodata Type: TimeIntervals Extends: DynamicTable
—start_time	Dataset	Start time of epoch, in seconds. Extends: VectorData Data Type: float32 Name: start_time
—stop_time	Dataset	Stop time of epoch, in seconds. Extends: VectorData Data Type: float32 Name: stop_time
—tags	Dataset	User-defined tags that identify or categorize events. Extends: VectorData Quantity: 0 or 1 Data Type: text Name: tags
—tags_index	Dataset	Index for tags. Extends: VectorIndex Quantity: 0 or 1 Name: tags_index
—timeseries	Dataset	An index into a TimeSeries object. Extends: TimeSeriesReferenceVectorData Quantity: 0 or 1 Name: timeseries
—timeseries_index	Dataset	Index for timeseries. Extends: VectorIndex Quantity: 0 or 1 Name: timeseries_index

2.4. Events

This source module contains neurodata_types for event data.

2.4.1. TimestampVectorData

Overview: A 1-dimensional VectorData that stores timestamps in seconds from the session start time. Timestamp are not required to be sorted in time.

TimestampVectorData extends VectorData and includes all elements of VectorData with the following additions or changes.

• Extends: VectorData

• Primitive Type: Dataset

• Data Type: float

• Dimensions: [‘num_times’]

• Shape: [None]

• Inherits from: VectorData, Data

• Source filename: nwb.event.yaml

• Source Specification: see Section 3.5.1

Table 2.14 Datasets, Links, and Attributes contained in <TimestampVectorData>

Id	Type	Description
<TimestampVectorData>	Dataset	Top level Dataset for <TimestampVectorData> Neurodata Type: TimestampVectorData Extends: VectorData Data Type: float Dimensions: [‘num_times’] Shape: [None]
—unit	Attribute	The unit of measurement for the timestamps, fixed to ‘seconds’. Data Type: text Value: seconds Name: unit
—resolution	Attribute	The temporal resolution of the timestamps, in seconds. This is typically the sampling period (1 / sampling_rate), also known as the clock period, of the data acquisition system from which the timestamps were recorded or derived. Data Type: float Required: False Name: resolution

2.4.2. DurationVectorData

Overview: A 1-dimensional VectorData that stores durations in seconds.

DurationVectorData extends VectorData and includes all elements of VectorData with the following additions or changes.

• Extends: VectorData

• Primitive Type: Dataset

• Data Type: float

• Dimensions: [‘num_times’]

• Shape: [None]

• Inherits from: VectorData, Data

• Source filename: nwb.event.yaml

• Source Specification: see Section 3.5.2

Table 2.15 Datasets, Links, and Attributes contained in <DurationVectorData>

Id	Type	Description
<DurationVectorData>	Dataset	Top level Dataset for <DurationVectorData> Neurodata Type: DurationVectorData Extends: VectorData Data Type: float Dimensions: [‘num_times’] Shape: [None]
—unit	Attribute	The unit of measurement for the durations, fixed to ‘seconds’. Data Type: text Value: seconds Name: unit
—resolution	Attribute	The temporal resolution of the durations, in seconds. This is typically the sampling period (1 / sampling_rate), also known as the clock period, of the data acquisition system from which the durations were recorded or derived. Data Type: float Required: False Name: resolution

2.4.3. EventsTable

Overview: A column-based table to store information about events, one event per row. Use EventsTable when each row is anchored at a single timestamp and duration is absent, optional, or mixed across rows. Additional columns may be added to store metadata about each event, such as the duration of the event. Examples include TTL pulses, licks, rewards, stimulus onsets, and detected ripples.

EventsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.event.yaml

• Source Specification: see Section 3.5.3

Table 2.16 Datasets, Links, and Attributes contained in <EventsTable>

Id	Type	Description
<EventsTable>	Group	Top level Group for <EventsTable> Neurodata Type: EventsTable Extends: DynamicTable
—description	Attribute	A description of the events stored in the table, including information about how the event times were computed, especially if the times are the result of processing or filtering raw data. For example, if the experimenter is encoding different types of events using a strobed or N-bit encoding, then the description should describe which channels were used and how the event time is computed, e.g., as the rise time of the first bit. Data Type: text Name: description
—timestamp	Dataset	Column containing the time that each event occurred, in seconds, from the session start time. Extends: TimestampVectorData Name: timestamp
—duration	Dataset	Optional column containing the duration of each event, in seconds. A value of NaN can be used for events without a duration or with a duration that is not yet specified. Extends: DurationVectorData Quantity: 0 or 1 Name: duration
—annotation	Dataset	Column containing user annotations about events. Extends: VectorData Quantity: 0 or 1 Data Type: text Dimensions: [‘num_times’] Shape: [None] Name: annotation

2.5. Image data

This source module contains neurodata_types for image data.

2.5.1. GrayscaleImage

Overview: A grayscale image.

GrayscaleImage extends Image and includes all elements of Image with the following additions or changes.

• Extends: Image

• Primitive Type: Dataset

• Data Type: numeric

• Dimensions: [‘x’, ‘y’]

• Shape: [None, None]

• Inherits from: Image, BaseImage, NWBData, Data

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.1

2.5.2. RGBImage

Overview: A color image.

RGBImage extends Image and includes all elements of Image with the following additions or changes.

• Extends: Image

• Primitive Type: Dataset

• Data Type: numeric

• Dimensions: [‘x’, ‘y’, ‘r, g, b’]

• Shape: [None, None, 3]

• Inherits from: Image, BaseImage, NWBData, Data

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.2

2.5.3. RGBAImage

Overview: A color image with transparency.

RGBAImage extends Image and includes all elements of Image with the following additions or changes.

• Extends: Image

• Primitive Type: Dataset

• Data Type: numeric

• Dimensions: [‘x’, ‘y’, ‘r, g, b, a’]

• Shape: [None, None, 4]

• Inherits from: Image, BaseImage, NWBData, Data

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.3

2.5.4. ImageSeries

Overview: 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].

ImageSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Subtypes: TwoPhotonSeries, OnePhotonSeries, OpticalSeries, ImageMaskSeries

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.4

Table 2.17 Datasets, Links, and Attributes contained in <ImageSeries>

Id	Type	Description
<ImageSeries>	Group	Top level Group for <ImageSeries> Neurodata Type: ImageSeries Extends: TimeSeries
—data	Dataset	Binary data representing images across frames. If data are stored in an external file, this should be an empty 3D array. Data Type: numeric Dimensions: [[‘frame’, ‘x’, ‘y’], [‘frame’, ‘x’, ‘y’, ‘z’]] Shape: [[None, None, None], [None, None, None, None]] Name: data
—dimension	Dataset	Number of pixels on x, y, (and z) axes. Quantity: 0 or 1 Data Type: int32 Dimensions: [‘rank’] Shape: [None] Name: dimension
—external_file	Dataset	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: 0 or 1 Data Type: text Dimensions: [‘num_files’] Shape: [None] Name: external_file
——starting_frame	Attribute	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 facilitate 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]. Data Type: int32 Dimensions: [‘num_files’] Shape: [None] Name: starting_frame
—num_samples	Dataset	Total number of frames across all external files. This is required when format=’external’ and timing is described using starting_time and rate, since data is empty and its first dimension cannot be used to determine the number of frames. When timestamps is provided, len(timestamps) already serves this purpose. Quantity: 0 or 1 Data Type: uint32 Name: num_samples
—format	Dataset	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: 0 or 1 Data Type: text Name: format
—device	Link	Link to the Device object that was used to capture these images. Target Type Device Name: device

Table 2.18 Groups contained in <ImageSeries>

Id	Type	Description
<ImageSeries>	Group	Top level Group for <ImageSeries> Neurodata Type: ImageSeries Extends: TimeSeries
—device	Link	Link to the Device object that was used to capture these images. Target Type Device Name: device

2.5.5. ImageMaskSeries

Overview: DEPRECATED. 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.

ImageMaskSeries extends ImageSeries and includes all elements of ImageSeries with the following additions or changes.

• Extends: ImageSeries

• Primitive Type: Group

• Inherits from: ImageSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.5

Table 2.19 Datasets, Links, and Attributes contained in <ImageMaskSeries>

Id	Type	Description
<ImageMaskSeries>	Group	Top level Group for <ImageMaskSeries> Neurodata Type: ImageMaskSeries Extends: ImageSeries
—masked_imageseries	Link	Link to ImageSeries object that this image mask is applied to. Target Type ImageSeries Name: masked_imageseries

Table 2.20 Groups contained in <ImageMaskSeries>

Id	Type	Description
<ImageMaskSeries>	Group	Top level Group for <ImageMaskSeries> Neurodata Type: ImageMaskSeries Extends: ImageSeries
—masked_imageseries	Link	Link to ImageSeries object that this image mask is applied to. Target Type ImageSeries Name: masked_imageseries

2.5.6. OpticalSeries

Overview: 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.

OpticalSeries extends ImageSeries and includes all elements of ImageSeries with the following additions or changes.

• Extends: ImageSeries

• Primitive Type: Group

• Inherits from: ImageSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.6

Table 2.21 Datasets, Links, and Attributes contained in <OpticalSeries>

Id	Type	Description
<OpticalSeries>	Group	Top level Group for <OpticalSeries> Neurodata Type: OpticalSeries Extends: ImageSeries
—distance	Dataset	Distance from camera/monitor to target/eye. Quantity: 0 or 1 Data Type: float32 Name: distance
—field_of_view	Dataset	Width, height and depth of image, or imaged area, in meters. Quantity: 0 or 1 Data Type: float32 Dimensions: [[‘width, height’], [‘width, height, depth’]] Shape: [[2], [3]] Name: field_of_view
—data	Dataset	Images presented to subject, either grayscale or RGB Data Type: numeric Dimensions: [[‘frame’, ‘x’, ‘y’], [‘frame’, ‘x’, ‘y’, ‘r, g, b’]] Shape: [[None, None, None], [None, None, None, 3]] Name: data
—orientation	Dataset	Description of image relative to some reference frame (e.g., which way is up). Must also specify frame of reference. Quantity: 0 or 1 Data Type: text Name: orientation

2.5.7. IndexSeries

Overview: Stores indices that reference images defined in other containers. The primary purpose of the IndexSeries is to allow images stored in an Images container to be referenced in a specific sequence through the ‘indexed_images’ link. This approach avoids duplicating image data when the same image needs to be presented multiple times or when images need to be shown in a different order than they are stored. Since images in an Images container do not have an inherent order, the Images container needs to include an ‘order_of_images’ dataset (of type ImageReferences) when being referenced by an IndexSeries. This dataset establishes the ordered sequence that the indices in IndexSeries refer to. The ‘data’ field stores the index into this ordered sequence, and the ‘timestamps’ array indicates the precise presentation time of each indexed image during an experiment. This can be used for displaying individual images or creating movie segments by referencing a sequence of images with the appropriate timestamps. While IndexSeries can also reference frames from an ImageSeries through the ‘indexed_timeseries’ link, this usage is discouraged and will be deprecated in favor of using Images containers with ‘order_of_images’.

IndexSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.image.yaml

• Source Specification: see Section 3.6.7

Table 2.22 Datasets, Links, and Attributes contained in <IndexSeries>

Id	Type	Description
<IndexSeries>	Group	Top level Group for <IndexSeries> Neurodata Type: IndexSeries Extends: TimeSeries
—data	Dataset	Index of the image (using zero-indexing) in the linked Images object. Data Type: uint32 Dimensions: [‘num_times’] Shape: [None] Name: data
——conversion	Attribute	This field is unused by IndexSeries. Data Type: float32 Required: False Name: conversion
——resolution	Attribute	This field is unused by IndexSeries. Data Type: float32 Required: False Name: resolution
——offset	Attribute	This field is unused by IndexSeries. Data Type: float32 Required: False Name: offset
——unit	Attribute	This field is unused by IndexSeries and has the value N/A. Data Type: text Value: N/A Name: unit
—indexed_timeseries	Link	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. Target Type ImageSeries Name: indexed_timeseries
—indexed_images	Link	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. Target Type Images Name: indexed_images

Table 2.23 Groups contained in <IndexSeries>

Id	Type	Description
<IndexSeries>	Group	Top level Group for <IndexSeries> Neurodata Type: IndexSeries Extends: TimeSeries
—indexed_timeseries	Link	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. Target Type ImageSeries Name: indexed_timeseries
—indexed_images	Link	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. Target Type Images Name: indexed_images

2.6. NWB file

Main NWB file specification.

2.6.1. ScratchData

Overview: Any one-off datasets

ScratchData extends NWBData and includes all elements of NWBData with the following additions or changes.

• Extends: NWBData

• Primitive Type: Dataset

• Inherits from: NWBData, Data

• Source filename: nwb.file.yaml

• Source Specification: see Section 3.7.1

Table 2.24 Datasets, Links, and Attributes contained in <ScratchData>

Id	Type	Description
<ScratchData>	Dataset	Top level Dataset for <ScratchData> Neurodata Type: ScratchData Extends: NWBData
—notes	Attribute	Any notes the user has about the dataset being stored Data Type: text Name: notes

2.6.2. NWBFile

Overview: An NWB file storing cellular-based neurophysiology data from a single experimental session.

NWBFile extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Name: root

• Inherits from: NWBContainer, Container

• Source filename: nwb.file.yaml

• Source Specification: see Section 3.7.2

Table 2.25 Datasets, Links, and Attributes contained in <NWBFile>

Id	Type	Description
root	Group	Top level Group for root Neurodata Type: NWBFile Extends: NWBContainer Name: root
—nwb_version	Attribute	File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers. Data Type: text Value: 2.10.0-alpha Name: nwb_version
—file_create_date	Dataset	A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in “Z” with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array. Data Type: isodatetime Dimensions: [‘num_modifications’] Shape: [None] Name: file_create_date
—identifier	Dataset	A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files. Data Type: text Name: identifier
—session_description	Dataset	A description of the experimental session and data in the file. Data Type: text Name: session_description
—session_start_time	Dataset	Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in “Z” with no timezone offset. Date accuracy is up to milliseconds. Data Type: isodatetime Name: session_start_time
—timestamps_reference_time	Dataset	Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in “Z” with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero). Data Type: isodatetime Name: timestamps_reference_time

Table 2.26 Groups contained in <NWBFile>

Id	Type	Description
root	Group	Top level Group for root Neurodata Type: NWBFile Extends: NWBContainer Name: root
—acquisition	Group	Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. Name: acquisition
—analysis	Group	Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs. Name: analysis
—scratch	Group	A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. Quantity: 0 or 1 Name: scratch
—processing	Group	The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. ‘Processing’ refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. Name: processing
—stimulus	Group	Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be reused during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. Name: stimulus
—general	Group	Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under ‘general’. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. Name: general
—intervals	Group	Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data. Quantity: 0 or 1 Name: intervals
—events	Group	Primary experimental event tables for the session, stored as EventsTable instances. This location is intended for event data that are ready to be used in downstream analysis. It replaces the deprecated BehavioralEvents placement. Events emitted directly by the acquisition system (TTL edges, hardware event channels) belong in /acquisition/. Events derived by user processing (filtering, detection algorithms, annotation with experimental context) belong in a ProcessingModule under /processing/. For periods with required start and stop times, see /intervals/. For continuous acquired signals or stimulus templates from which events may have been derived, see /acquisition/ or /stimulus/. For more guidance on choosing between /events/, /acquisition/, /processing/, and /analysis/, see the schema docs FAQ. Quantity: 0 or 1 Name: events
—units	Group	Data about sorted spike units. Extends: Units Quantity: 0 or 1 Name: units

2.6.2.1. Groups: /acquisition

Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis.

• Name: acquisition

Table 2.27 Groups contained in <acquisition>

Id	Type	Description
acquisition	Group	Top level Group for acquisition Name: acquisition
—<NWBDataInterface>	Group	Acquired, raw data. Extends: NWBDataInterface Quantity: 0 or more
—<DynamicTable>	Group	Tabular data that is relevant to acquisition Extends: DynamicTable Quantity: 0 or more

2.6.2.2. Groups: /acquisition/<NWBDataInterface>

Acquired, raw data.

• Extends: NWBDataInterface

• Quantity: 0 or more

2.6.2.3. Groups: /acquisition/<DynamicTable>

Tabular data that is relevant to acquisition

• Extends: DynamicTable

• Quantity: 0 or more

2.6.2.4. Groups: /analysis

Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs.

• Name: analysis

Table 2.28 Groups contained in <analysis>

Id	Type	Description
analysis	Group	Top level Group for analysis Name: analysis
—<NWBContainer>	Group	Custom analysis results. Extends: NWBContainer Quantity: 0 or more
—<DynamicTable>	Group	Tabular data that is relevant to data stored in analysis Extends: DynamicTable Quantity: 0 or more

2.6.2.5. Groups: /analysis/<NWBContainer>

Custom analysis results.

• Extends: NWBContainer

• Quantity: 0 or more

2.6.2.6. Groups: /analysis/<DynamicTable>

Tabular data that is relevant to data stored in analysis

• Extends: DynamicTable

• Quantity: 0 or more

2.6.2.7. Groups: /scratch

A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard.

• Quantity: 0 or 1

• Name: scratch

Table 2.29 Datasets, Links, and Attributes contained in /scratch

Id	Type	Description
scratch	Group	Top level Group for scratch Quantity: 0 or 1 Name: scratch
—<ScratchData>	Dataset	Any one-off datasets Extends: ScratchData Quantity: 0 or more

Table 2.30 Groups contained in <scratch>

Id	Type	Description
scratch	Group	Top level Group for scratch Quantity: 0 or 1 Name: scratch
—<NWBContainer>	Group	Any one-off containers Extends: NWBContainer Quantity: 0 or more
—<DynamicTable>	Group	Any one-off tables Extends: DynamicTable Quantity: 0 or more

2.6.2.8. Groups: /scratch/<NWBContainer>

Any one-off containers

• Extends: NWBContainer

• Quantity: 0 or more

2.6.2.9. Groups: /scratch/<DynamicTable>

Any one-off tables

• Extends: DynamicTable

• Quantity: 0 or more

2.6.2.10. Groups: /processing

The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. ‘Processing’ refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis.

• Name: processing

Table 2.31 Groups contained in <processing>

Id	Type	Description
processing	Group	Top level Group for processing Name: processing
—<ProcessingModule>	Group	Intermediate analysis of acquired data. Extends: ProcessingModule Quantity: 0 or more

2.6.2.11. Groups: /processing/<ProcessingModule>

Intermediate analysis of acquired data.

• Extends: ProcessingModule

• Quantity: 0 or more

2.6.2.12. Groups: /stimulus

Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be reused during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file.

• Name: stimulus

Table 2.32 Groups contained in <stimulus>

Id	Type	Description
stimulus	Group	Top level Group for stimulus Name: stimulus
—presentation	Group	Stimuli presented during the experiment. Name: presentation
—templates	Group	Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame. Name: templates

2.6.2.13. Groups: /stimulus/presentation

Stimuli presented during the experiment.

• Name: presentation

Table 2.33 Groups contained in <presentation>

Id	Type	Description
presentation	Group	Top level Group for presentation Name: presentation
—<TimeSeries>	Group	TimeSeries objects containing data of presented stimuli. Extends: TimeSeries Quantity: 0 or more
—<NWBDataInterface>	Group	Generic NWB data interfaces, usually from an extension, containing data of presented stimuli. Extends: NWBDataInterface Quantity: 0 or more
—<DynamicTable>	Group	DynamicTable objects containing data of presented stimuli. Extends: DynamicTable Quantity: 0 or more

2.6.2.14. Groups: /stimulus/presentation/<TimeSeries>

TimeSeries objects containing data of presented stimuli.

• Extends: TimeSeries

• Quantity: 0 or more

2.6.2.15. Groups: /stimulus/presentation/<NWBDataInterface>

Generic NWB data interfaces, usually from an extension, containing data of presented stimuli.

• Extends: NWBDataInterface

• Quantity: 0 or more

2.6.2.16. Groups: /stimulus/presentation/<DynamicTable>

DynamicTable objects containing data of presented stimuli.

• Extends: DynamicTable

• Quantity: 0 or more

2.6.2.17. Groups: /stimulus/templates

Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame.

• Name: templates

Table 2.34 Groups contained in <templates>

Id	Type	Description
templates	Group	Top level Group for templates Name: templates
—<TimeSeries>	Group	TimeSeries objects containing template data of presented stimuli. Extends: TimeSeries Quantity: 0 or more
—<Images>	Group	Images objects containing images of presented stimuli. Extends: Images Quantity: 0 or more

2.6.2.18. Groups: /stimulus/templates/<TimeSeries>

TimeSeries objects containing template data of presented stimuli.

• Extends: TimeSeries

• Quantity: 0 or more

2.6.2.19. Groups: /stimulus/templates/<Images>

Images objects containing images of presented stimuli.

• Extends: Images

• Quantity: 0 or more

2.6.2.20. Groups: /general

Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under ‘general’. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them.

• Name: general

Table 2.35 Datasets, Links, and Attributes contained in /general

Id	Type	Description
general	Group	Top level Group for general Name: general
—data_collection	Dataset	Notes about data collection and analysis. Quantity: 0 or 1 Data Type: text Name: data_collection
—experiment_description	Dataset	General description of the experiment. Quantity: 0 or 1 Data Type: text Name: experiment_description
—experimenter	Dataset	Name of person(s) who performed the experiment. Can also specify roles of different people involved. Quantity: 0 or 1 Data Type: text Dimensions: [‘num_experimenters’] Shape: [None] Name: experimenter
—institution	Dataset	Institution(s) where experiment was performed. Quantity: 0 or 1 Data Type: text Name: institution
—keywords	Dataset	Terms to search over. Quantity: 0 or 1 Data Type: text Dimensions: [‘num_keywords’] Shape: [None] Name: keywords
—lab	Dataset	Laboratory where experiment was performed. Quantity: 0 or 1 Data Type: text Name: lab
—notes	Dataset	Notes about the experiment. Quantity: 0 or 1 Data Type: text Name: notes
—pharmacology	Dataset	Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. Quantity: 0 or 1 Data Type: text Name: pharmacology
—protocol	Dataset	Experimental protocol, if applicable. e.g., include IACUC protocol number. Quantity: 0 or 1 Data Type: text Name: protocol
—related_publications	Dataset	Publication information. PMID, DOI, URL, etc. Quantity: 0 or 1 Data Type: text Dimensions: [‘num_publications’] Shape: [None] Name: related_publications
—session_id	Dataset	Lab-specific ID for the session. Quantity: 0 or 1 Data Type: text Name: session_id
—slices	Dataset	Description of slices, including information about preparation thickness, orientation, temperature, and bath solution. Quantity: 0 or 1 Data Type: text Name: slices
—source_script	Dataset	Script file or link to public source code used to create this NWB file. Quantity: 0 or 1 Data Type: text Name: source_script
——file_name	Attribute	Name of script file. Data Type: text Name: file_name
—was_generated_by	Dataset	Name and version of software package(s) used to generate data contained in this NWB File. For each software package or library, include the name of the software as the first value and the version as the second value. Quantity: 0 or 1 Data Type: text Dimensions: [‘num_sources’, ‘name, version’] Shape: [None, 2] Name: was_generated_by
—stimulus	Dataset	Notes about stimuli, such as how and where they were presented. Quantity: 0 or 1 Data Type: text Name: stimulus
—surgery	Dataset	Narrative description about surgery/surgeries, including date(s) and who performed surgery. Quantity: 0 or 1 Data Type: text Name: surgery
—virus	Dataset	Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. Quantity: 0 or 1 Data Type: text Name: virus

Table 2.36 Groups contained in <general>

Id	Type	Description
general	Group	Top level Group for general Name: general
—external_resources	Group	This is the HERD structure for this specific NWBFile, storing the mapped external resources. Extends: HERD Quantity: 0 or 1 Name: external_resources
—<LabMetaData>	Group	Place-holder than can be extended so that lab-specific meta-data can be placed in /general. Extends: LabMetaData Quantity: 0 or more
—devices	Group	Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. Quantity: 0 or 1 Name: devices
—subject	Group	Information about the animal or person from which the data was measured. Extends: Subject Quantity: 0 or 1 Name: subject
—extracellular_ephys	Group	Metadata related to extracellular electrophysiology. Quantity: 0 or 1 Name: extracellular_ephys
—intracellular_ephys	Group	Metadata related to intracellular electrophysiology. Quantity: 0 or 1 Name: intracellular_ephys
—optogenetics	Group	Metadata describing optogenetic stimuluation. Quantity: 0 or 1 Name: optogenetics
—optophysiology	Group	Metadata related to optophysiology. Quantity: 0 or 1 Name: optophysiology

2.6.2.21. Groups: /general/external_resources

This is the HERD structure for this specific NWBFile, storing the mapped external resources.

• Extends: HERD

• Quantity: 0 or 1

• Name: external_resources

2.6.2.22. Groups: /general/<LabMetaData>

Place-holder than can be extended so that lab-specific meta-data can be placed in /general.

• Extends: LabMetaData

• Quantity: 0 or more

2.6.2.23. Groups: /general/devices

Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc.

• Quantity: 0 or 1

• Name: devices

Table 2.37 Groups contained in <devices>

Id	Type	Description
devices	Group	Top level Group for devices Quantity: 0 or 1 Name: devices
—<Device>	Group	Data acquisition devices. Extends: Device Quantity: 0 or more
—models	Group	Collection of data acquisition device models. Quantity: 0 or 1 Name: models

2.6.2.24. Groups: /general/devices/<Device>

Data acquisition devices.

• Extends: Device

• Quantity: 0 or more

2.6.2.25. Groups: /general/devices/models

Collection of data acquisition device models.

• Quantity: 0 or 1

• Name: models

Table 2.38 Groups contained in <models>

Id	Type	Description
models	Group	Top level Group for models Quantity: 0 or 1 Name: models
—<DeviceModel>	Group	Data acquisition device models. Extends: DeviceModel Quantity: 0 or more

2.6.2.26. Groups: /general/devices/models/<DeviceModel>

Data acquisition device models.

• Extends: DeviceModel

• Quantity: 0 or more

2.6.2.27. Groups: /general/subject

Information about the animal or person from which the data was measured.

• Extends: Subject

• Quantity: 0 or 1

• Name: subject

2.6.2.28. Groups: /general/extracellular_ephys

Metadata related to extracellular electrophysiology.

• Quantity: 0 or 1

• Name: extracellular_ephys

Table 2.39 Groups contained in <extracellular_ephys>

Id	Type	Description
extracellular_ephys	Group	Top level Group for extracellular_ephys Quantity: 0 or 1 Name: extracellular_ephys
—<ElectrodeGroup>	Group	Physical group of electrodes. Extends: ElectrodeGroup Quantity: 0 or more
—electrodes	Group	A table of all electrodes (i.e. channels) used for recording. Changed in NWB 2.9.0 to use the newly added ElectrodesTable neurodata type instead of a DynamicTable with added columns. Extends: ElectrodesTable Quantity: 0 or 1 Name: electrodes

2.6.2.29. Groups: /general/extracellular_ephys/<ElectrodeGroup>

Physical group of electrodes.

• Extends: ElectrodeGroup

• Quantity: 0 or more

2.6.2.30. Groups: /general/extracellular_ephys/electrodes

A table of all electrodes (i.e. channels) used for recording. Changed in NWB 2.9.0 to use the newly added ElectrodesTable neurodata type instead of a DynamicTable with added columns.

• Extends: ElectrodesTable

• Quantity: 0 or 1

• Name: electrodes

2.6.2.31. Groups: /general/intracellular_ephys

Metadata related to intracellular electrophysiology.

• Quantity: 0 or 1

• Name: intracellular_ephys

Table 2.40 Datasets, Links, and Attributes contained in /general/intracellular_ephys

Id	Type	Description
intracellular_ephys	Group	Top level Group for intracellular_ephys Quantity: 0 or 1 Name: intracellular_ephys
—filtering	Dataset	[DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries. Quantity: 0 or 1 Data Type: text Name: filtering

Table 2.41 Groups contained in <intracellular_ephys>

Id	Type	Description
intracellular_ephys	Group	Top level Group for intracellular_ephys Quantity: 0 or 1 Name: intracellular_ephys
—<IntracellularElectrode>	Group	An intracellular electrode. Extends: IntracellularElectrode Quantity: 0 or more
—sweep_table	Group	[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata. Extends: SweepTable Quantity: 0 or 1 Name: sweep_table
—intracellular_recordings	Group	A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used. Extends: IntracellularRecordingsTable Quantity: 0 or 1 Name: intracellular_recordings
—simultaneous_recordings	Group	A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes Extends: SimultaneousRecordingsTable Quantity: 0 or 1 Name: simultaneous_recordings
—sequential_recordings	Group	A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence. Extends: SequentialRecordingsTable Quantity: 0 or 1 Name: sequential_recordings
—repetitions	Group	A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence. Extends: RepetitionsTable Quantity: 0 or 1 Name: repetitions
—experimental_conditions	Group	A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions. Extends: ExperimentalConditionsTable Quantity: 0 or 1 Name: experimental_conditions

2.6.2.32. Groups: /general/intracellular_ephys/<IntracellularElectrode>

An intracellular electrode.

• Extends: IntracellularElectrode

• Quantity: 0 or more

2.6.2.33. Groups: /general/intracellular_ephys/sweep_table

[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions tables provide enhanced support for experiment metadata.

• Extends: SweepTable

• Quantity: 0 or 1

• Name: sweep_table

2.6.2.34. Groups: /general/intracellular_ephys/intracellular_recordings

A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response are recorded as as part of an experiment. In this case both, the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.

• Extends: IntracellularRecordingsTable

• Quantity: 0 or 1

• Name: intracellular_recordings

2.6.2.35. Groups: /general/intracellular_ephys/simultaneous_recordings

A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes

• Extends: SimultaneousRecordingsTable

• Quantity: 0 or 1

• Name: simultaneous_recordings

2.6.2.36. Groups: /general/intracellular_ephys/sequential_recordings

A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.

• Extends: SequentialRecordingsTable

• Quantity: 0 or 1

• Name: sequential_recordings

2.6.2.37. Groups: /general/intracellular_ephys/repetitions

A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.

• Extends: RepetitionsTable

• Quantity: 0 or 1

• Name: repetitions

2.6.2.38. Groups: /general/intracellular_ephys/experimental_conditions

A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions.

• Extends: ExperimentalConditionsTable

• Quantity: 0 or 1

• Name: experimental_conditions

2.6.2.39. Groups: /general/optogenetics

Metadata describing optogenetic stimuluation.

• Quantity: 0 or 1

• Name: optogenetics

Table 2.42 Groups contained in <optogenetics>

Id	Type	Description
optogenetics	Group	Top level Group for optogenetics Quantity: 0 or 1 Name: optogenetics
—<OptogeneticStimulusSite>	Group	An optogenetic stimulation site. Extends: OptogeneticStimulusSite Quantity: 0 or more

2.6.2.40. Groups: /general/optogenetics/<OptogeneticStimulusSite>

An optogenetic stimulation site.

• Extends: OptogeneticStimulusSite

• Quantity: 0 or more

2.6.2.41. Groups: /general/optophysiology

Metadata related to optophysiology.

• Quantity: 0 or 1

• Name: optophysiology

Table 2.43 Groups contained in <optophysiology>

Id	Type	Description
optophysiology	Group	Top level Group for optophysiology Quantity: 0 or 1 Name: optophysiology
—<ImagingPlane>	Group	An imaging plane. Extends: ImagingPlane Quantity: 0 or more

2.6.2.42. Groups: /general/optophysiology/<ImagingPlane>

An imaging plane.

• Extends: ImagingPlane

• Quantity: 0 or more

2.6.2.43. Groups: /intervals

Experimental intervals, whether that be logically distinct sub-experiments having a particular scientific goal, trials (see trials subgroup) during an experiment, or epochs (see epochs subgroup) deriving from analysis of data.

• Quantity: 0 or 1

• Name: intervals

Table 2.44 Groups contained in <intervals>

Id	Type	Description
intervals	Group	Top level Group for intervals Quantity: 0 or 1 Name: intervals
—epochs	Group	Time intervals marking coarse-grained experimental phases or subdivisions of a recording session, such as baseline, task, rest, or sleep stages. Extends: TimeIntervals Quantity: 0 or 1 Name: epochs
—trials	Group	Time intervals corresponding to repeated experimental units with consistent structure, such as individual stimulus-response-reward cycles. Extends: TimeIntervals Quantity: 0 or 1 Name: trials
—invalid_times	Group	Time intervals that should be removed from analysis. Extends: TimeIntervals Quantity: 0 or 1 Name: invalid_times
—<TimeIntervals>	Group	Optional additional table(s) for describing other experimental time intervals. Extends: TimeIntervals Quantity: 0 or more

2.6.2.44. Groups: /intervals/epochs

Time intervals marking coarse-grained experimental phases or subdivisions of a recording session, such as baseline, task, rest, or sleep stages.

• Extends: TimeIntervals

• Quantity: 0 or 1

• Name: epochs

2.6.2.45. Groups: /intervals/trials

Time intervals corresponding to repeated experimental units with consistent structure, such as individual stimulus-response-reward cycles.

• Extends: TimeIntervals

• Quantity: 0 or 1

• Name: trials

2.6.2.46. Groups: /intervals/invalid_times

Time intervals that should be removed from analysis.

• Extends: TimeIntervals

• Quantity: 0 or 1

• Name: invalid_times

2.6.2.47. Groups: /intervals/<TimeIntervals>

Optional additional table(s) for describing other experimental time intervals.

• Extends: TimeIntervals

• Quantity: 0 or more

2.6.2.48. Groups: /events

Primary experimental event tables for the session, stored as EventsTable instances. This location is intended for event data that are ready to be used in downstream analysis. It replaces the deprecated BehavioralEvents placement. Events emitted directly by the acquisition system (TTL edges, hardware event channels) belong in /acquisition/. Events derived by user processing (filtering, detection algorithms, annotation with experimental context) belong in a ProcessingModule under /processing/. For periods with required start and stop times, see /intervals/. For continuous acquired signals or stimulus templates from which events may have been derived, see /acquisition/ or /stimulus/. For more guidance on choosing between /events/, /acquisition/, /processing/, and /analysis/, see the schema docs FAQ.

• Quantity: 0 or 1

• Name: events

Table 2.45 Groups contained in <events>

Id	Type	Description
events	Group	Top level Group for events Quantity: 0 or 1 Name: events
—<EventsTable>	Group	An EventsTable holding a collection of event times of a particular type (e.g., licks, rewards, stimulus presentations) along with their per-event metadata. Extends: EventsTable Quantity: 0 or more

2.6.2.49. Groups: /events/<EventsTable>

An EventsTable holding a collection of event times of a particular type (e.g., licks, rewards, stimulus presentations) along with their per-event metadata.

• Extends: EventsTable

• Quantity: 0 or more

2.6.2.50. Groups: /units

Data about sorted spike units.

• Extends: Units

• Quantity: 0 or 1

• Name: units

2.6.3. LabMetaData

Overview: Lab-specific meta-data.

LabMetaData extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.file.yaml

• Source Specification: see Section 3.7.3

2.6.4. Subject

Overview: Information about the animal or person from which the data was measured.

Subject extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.file.yaml

• Source Specification: see Section 3.7.4

Table 2.46 Datasets, Links, and Attributes contained in <Subject>

Id	Type	Description
<Subject>	Group	Top level Group for <Subject> Neurodata Type: Subject Extends: NWBContainer
—age	Dataset	Age of subject. Can be supplied instead of ‘date_of_birth’. The ISO 8601 Duration format is recommended, e.g., ‘P90D’ for 90 days old. If the precise age is unknown, an age range can be given by ‘[lower bound]/[upper bound]’ e.g. ‘P10D/P20D’ would mean that the age is in between 10 and 20 days. If only the lower bound is known, then including only the slash after that lower bound can be used to indicate a missing bound. For instance, ‘P90Y/’ would indicate that the age is 90 years or older. Quantity: 0 or 1 Data Type: text Name: age
——reference	Attribute	Age is with reference to this event. Can be ‘birth’ or ‘gestational’. If reference is omitted, ‘birth’ is implied. Data Type: text Required: False Default Value: birth Name: reference
—date_of_birth	Dataset	Date of birth of subject. Can be supplied instead of ‘age’. Quantity: 0 or 1 Data Type: isodatetime Name: date_of_birth
—description	Dataset	Description of subject and where subject came from (e.g., breeder, if animal). Quantity: 0 or 1 Data Type: text Name: description
—genotype	Dataset	Genetic strain. If absent, assume Wild Type (WT). Quantity: 0 or 1 Data Type: text Name: genotype
—sex	Dataset	Gender of subject. Quantity: 0 or 1 Data Type: text Name: sex
—species	Dataset	Species of subject. Quantity: 0 or 1 Data Type: text Name: species
—strain	Dataset	Strain of subject. Quantity: 0 or 1 Data Type: text Name: strain
—subject_id	Dataset	ID of animal/person used/participating in experiment (lab convention). Quantity: 0 or 1 Data Type: text Name: subject_id
—weight	Dataset	Weight at time of experiment, at time of surgery and at other important times. Quantity: 0 or 1 Data Type: text Name: weight

2.7. Miscellaneous neurodata_types.

Miscellaneous types.

2.7.1. AbstractFeatureSeries

Overview: 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.

AbstractFeatureSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.1

Table 2.47 Datasets, Links, and Attributes contained in <AbstractFeatureSeries>

Id	Type	Description
<AbstractFeatureSeries>	Group	Top level Group for <AbstractFeatureSeries> Neurodata Type: AbstractFeatureSeries Extends: TimeSeries
—data	Dataset	Values of each feature at each time. Data Type: numeric Dimensions: [[‘num_times’], [‘num_times’, ‘num_features’]] Shape: [[None], [None, None]] Name: data
——unit	Attribute	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’”. Data Type: text Required: False Default Value: see ‘feature_units’ Name: unit
—feature_units	Dataset	Units of each feature. Quantity: 0 or 1 Data Type: text Dimensions: [‘num_features’] Shape: [None] Name: feature_units
—features	Dataset	Description of the features represented in TimeSeries::data. Data Type: text Dimensions: [‘num_features’] Shape: [None] Name: features

2.7.2. AnnotationSeries

Overview: DEPRECATED. Use an EventsTable instead. 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.

AnnotationSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.2

Table 2.48 Datasets, Links, and Attributes contained in <AnnotationSeries>

Id	Type	Description
<AnnotationSeries>	Group	Top level Group for <AnnotationSeries> Neurodata Type: AnnotationSeries Extends: TimeSeries
—data	Dataset	Annotations made during an experiment. Data Type: text Dimensions: [‘num_times’] Shape: [None] Name: data
——resolution	Attribute	Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0. Data Type: float32 Value: -1.0 Name: resolution
——unit	Attribute	Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to ‘n/a’. Data Type: text Value: n/a Name: unit

2.7.3. IntervalSeries

Overview: 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.

IntervalSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.3

Table 2.49 Datasets, Links, and Attributes contained in <IntervalSeries>

Id	Type	Description
<IntervalSeries>	Group	Top level Group for <IntervalSeries> Neurodata Type: IntervalSeries Extends: TimeSeries
—data	Dataset	Use values >0 if interval started, <0 if interval ended. Data Type: int8 Dimensions: [‘num_times’] Shape: [None] Name: data
——resolution	Attribute	Smallest meaningful difference between values in data. Annotations have no units, so the value is fixed to -1.0. Data Type: float32 Value: -1.0 Name: resolution
——unit	Attribute	Base unit of measurement for working with the data. Annotations have no units, so the value is fixed to ‘n/a’. Data Type: text Value: n/a Name: unit

2.7.4. FrequencyBandsTable

Overview: Table for describing the bands that DecompositionSeries was generated from. There should be one row in this table for each band.

FrequencyBandsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.4

Table 2.50 Datasets, Links, and Attributes contained in <FrequencyBandsTable>

Id	Type	Description
<FrequencyBandsTable>	Group	Top level Group for <FrequencyBandsTable> Neurodata Type: FrequencyBandsTable Extends: DynamicTable
—band_name	Dataset	Name of the band, e.g. theta. Extends: VectorData Data Type: text Name: band_name
—band_limits	Dataset	Low and high limit of each band in Hz. If it is a Gaussian filter, use 2 SD on either side of the center. Extends: VectorData Data Type: float32 Dimensions: [‘num_bands’, ‘low, high’] Shape: [None, 2] Name: band_limits
—band_mean	Dataset	The mean Gaussian filters, in Hz. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Dimensions: [‘num_bands’] Shape: [None] Name: band_mean
—band_stdev	Dataset	The standard deviation of Gaussian filters, in Hz. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Dimensions: [‘num_bands’] Shape: [None] Name: band_stdev

2.7.5. DecompositionSeries

Overview: Spectral analysis of a time series, e.g. of an LFP or a speech signal.

DecompositionSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.5

Table 2.51 Datasets, Links, and Attributes contained in <DecompositionSeries>

Id	Type	Description
<DecompositionSeries>	Group	Top level Group for <DecompositionSeries> Neurodata Type: DecompositionSeries Extends: TimeSeries
—data	Dataset	Data decomposed into frequency bands. Data Type: numeric Dimensions: [‘num_times’, ‘num_channels’, ‘num_bands’] Shape: [None, None, None] Name: data
——unit	Attribute	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’. Data Type: text Required: False Default Value: no unit Name: unit
—metric	Dataset	The metric used, e.g. phase, amplitude, power. Data Type: text Name: metric
—source_channels	Dataset	DynamicTableRegion pointer to the channels that this decomposition series was generated from. Extends: DynamicTableRegion Quantity: 0 or 1 Name: source_channels
—source_timeseries	Link	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. Target Type TimeSeries Name: source_timeseries

Table 2.52 Groups contained in <DecompositionSeries>

Id	Type	Description
<DecompositionSeries>	Group	Top level Group for <DecompositionSeries> Neurodata Type: DecompositionSeries Extends: TimeSeries
—source_timeseries	Link	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. Target Type TimeSeries Name: source_timeseries
—bands	Group	Table for describing the bands that this series was generated from. Extends: FrequencyBandsTable Quantity: 0 or 1 Name: bands

2.7.5.1. Groups: bands

Table for describing the bands that this series was generated from.

• Extends: FrequencyBandsTable

• Quantity: 0 or 1

• Name: bands

2.7.6. Units

Overview: Data about spiking units. Event times of observed units (e.g. cell, synapse, etc.) should be concatenated and stored in spike_times.

Units extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Default Name: Units

• Inherits from: DynamicTable, Container

• Source filename: nwb.misc.yaml

• Source Specification: see Section 3.8.6

Table 2.53 Datasets, Links, and Attributes contained in <Units>

Id	Type	Description
<Units>	Group	Top level Group for <Units> Neurodata Type: Units Extends: DynamicTable Default Name: Units
—spike_times_index	Dataset	Index into the spike_times dataset. Extends: VectorIndex Quantity: 0 or 1 Name: spike_times_index
—spike_times	Dataset	Spike times for each unit, in seconds, relative to the session reference time (i.e. session_start_time or, if defined, timestamps_reference_time). Times should be stored in ascending order. Extends: VectorData Quantity: 0 or 1 Data Type: float64 Name: spike_times
——resolution	Attribute	The temporal resolution of the spike times, in seconds. This is typically the sampling period (1/sampling_rate) of the acquisition data from which spikes were extracted. If the acquisition data was downsampled before spike sorting, the resolution should be based on the downsampled sampling rate (lower sampling rate, larger resolution value). If interpolation was applied during spike sorting, then spike times may fall between samples of the acquisition data, so the resolution should be the interpolation step size (higher sampling rate, smaller resolution value). Data Type: float64 Required: False Name: resolution
—obs_intervals_index	Dataset	Index into the obs_intervals dataset. Extends: VectorIndex Quantity: 0 or 1 Name: obs_intervals_index
—obs_intervals	Dataset	Observation intervals for each unit, in seconds, relative to the session reference time (i.e. session_start_time or, if defined, timestamps_reference_time). Intervals should be in ascending order and non-overlapping. Extends: VectorData Quantity: 0 or 1 Data Type: float64 Dimensions: [‘num_intervals’, ‘start|end’] Shape: [None, 2] Name: obs_intervals
—electrodes_index	Dataset	Index into electrodes. Extends: VectorIndex Quantity: 0 or 1 Name: electrodes_index
—electrodes	Dataset	Electrode that each spike unit came from, specified using a DynamicTableRegion. Extends: DynamicTableRegion Quantity: 0 or 1 Name: electrodes
—electrode_group	Dataset	Electrode group that each spike unit came from. Extends: VectorData Quantity: 0 or 1 Data Type: object reference to ElectrodeGroup Name: electrode_group
—waveform_mean	Dataset	Spike waveform mean for each spike unit. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Dimensions: [[‘num_units’, ‘num_samples’], [‘num_units’, ‘num_samples’, ‘num_electrodes’]] Shape: [[None, None], [None, None, None]] Name: waveform_mean
——sampling_rate	Attribute	Sampling rate, in hertz. Data Type: float32 Required: False Name: sampling_rate
——unit	Attribute	Unit of measurement. This value is fixed to ‘volts’. Data Type: text Value: volts Name: unit
—waveform_sd	Dataset	Spike waveform standard deviation for each spike unit. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Dimensions: [[‘num_units’, ‘num_samples’], [‘num_units’, ‘num_samples’, ‘num_electrodes’]] Shape: [[None, None], [None, None, None]] Name: waveform_sd
——sampling_rate	Attribute	Sampling rate, in hertz. Data Type: float32 Required: False Name: sampling_rate
——unit	Attribute	Unit of measurement. This value is fixed to ‘volts’. Data Type: text Value: volts Name: unit
—waveforms	Dataset	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 the same as the order of the electrodes referenced in the ‘electrodes’ column of this table. The number of samples for each waveform must be the same. Extends: VectorData Quantity: 0 or 1 Data Type: numeric Dimensions: [‘num_waveforms’, ‘num_samples’] Shape: [None, None] Name: waveforms
——sampling_rate	Attribute	Sampling rate, in hertz. Data Type: float32 Required: False Name: sampling_rate
——unit	Attribute	Unit of measurement. This value is fixed to ‘volts’. Data Type: text Value: volts Name: unit
—waveforms_index	Dataset	Index into the ‘waveforms’ dataset. One value for every spike event. See ‘waveforms’ for more detail. Extends: VectorIndex Quantity: 0 or 1 Name: waveforms_index
—waveforms_index_index	Dataset	Index into the ‘waveforms_index’ dataset. One value for every unit (row in the table). See ‘waveforms’ for more detail. Extends: VectorIndex Quantity: 0 or 1 Name: waveforms_index_index

2.8. Behavior

This source module contains neurodata_types for behavior data.

2.8.1. SpatialSeries

Overview: 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.

SpatialSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.1

Table 2.54 Datasets, Links, and Attributes contained in <SpatialSeries>

Id	Type	Description
<SpatialSeries>	Group	Top level Group for <SpatialSeries> Neurodata Type: SpatialSeries Extends: TimeSeries
—data	Dataset	1-D or 2-D array storing position or direction relative to some reference frame. Data Type: numeric Dimensions: [[‘num_times’], [‘num_times’, ‘x’], [‘num_times’, ‘x,y’], [‘num_times’, ‘x,y,z’]] Shape: [[None], [None, 1], [None, 2], [None, 3]] Name: data
——unit	Attribute	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’. Data Type: text Required: False Default Value: meters Name: unit
—reference_frame	Dataset	Description defining what exactly ‘straight-ahead’ means. Quantity: 0 or 1 Data Type: text Name: reference_frame

2.8.2. BehavioralEpochs

Overview: 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.

BehavioralEpochs extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: BehavioralEpochs

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.2

Table 2.55 Groups contained in <BehavioralEpochs>

Id	Type	Description
<BehavioralEpochs>	Group	Top level Group for <BehavioralEpochs> Neurodata Type: BehavioralEpochs Extends: NWBDataInterface Default Name: BehavioralEpochs
—<IntervalSeries>	Group	IntervalSeries object containing start and stop times of epochs. Extends: IntervalSeries Quantity: 1 or more

2.8.2.1. Groups: <IntervalSeries>

IntervalSeries object containing start and stop times of epochs.

• Extends: IntervalSeries

• Quantity: 1 or more

2.8.3. BehavioralEvents

Overview: DEPRECATED. Use an EventsTable instead. TimeSeries for storing behavioral events. See description of BehavioralEpochs for more details.

BehavioralEvents extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: BehavioralEvents

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.3

Table 2.56 Groups contained in <BehavioralEvents>

Id	Type	Description
<BehavioralEvents>	Group	Top level Group for <BehavioralEvents> Neurodata Type: BehavioralEvents Extends: NWBDataInterface Default Name: BehavioralEvents
—<TimeSeries>	Group	TimeSeries object containing behavioral events. Extends: TimeSeries Quantity: 1 or more

2.8.3.1. Groups: <TimeSeries>

TimeSeries object containing behavioral events.

• Extends: TimeSeries

• Quantity: 1 or more

2.8.4. BehavioralTimeSeries

Overview: TimeSeries for storing behavioral time series data. See description of BehavioralEpochs for more details.

BehavioralTimeSeries extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: BehavioralTimeSeries

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.4

Table 2.57 Groups contained in <BehavioralTimeSeries>

Id	Type	Description
<BehavioralTimeSeries>	Group	Top level Group for <BehavioralTimeSeries> Neurodata Type: BehavioralTimeSeries Extends: NWBDataInterface Default Name: BehavioralTimeSeries
—<TimeSeries>	Group	TimeSeries object containing continuous behavioral data. Extends: TimeSeries Quantity: 1 or more

2.8.4.1. Groups: <TimeSeries>

TimeSeries object containing continuous behavioral data.

• Extends: TimeSeries

• Quantity: 1 or more

2.8.5. PupilTracking

Overview: Eye-tracking data, representing pupil size.

PupilTracking extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: PupilTracking

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.5

Table 2.58 Groups contained in <PupilTracking>

Id	Type	Description
<PupilTracking>	Group	Top level Group for <PupilTracking> Neurodata Type: PupilTracking Extends: NWBDataInterface Default Name: PupilTracking
—<TimeSeries>	Group	TimeSeries object containing time series data on pupil size. Extends: TimeSeries Quantity: 1 or more

2.8.5.1. Groups: <TimeSeries>

TimeSeries object containing time series data on pupil size.

• Extends: TimeSeries

• Quantity: 1 or more

2.8.6. EyeTracking

Overview: Eye-tracking data, representing direction of gaze.

EyeTracking extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: EyeTracking

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.6

Table 2.59 Groups contained in <EyeTracking>

Id	Type	Description
<EyeTracking>	Group	Top level Group for <EyeTracking> Neurodata Type: EyeTracking Extends: NWBDataInterface Default Name: EyeTracking
—<SpatialSeries>	Group	SpatialSeries object containing data measuring direction of gaze. Extends: SpatialSeries Quantity: 1 or more

2.8.6.1. Groups: <SpatialSeries>

SpatialSeries object containing data measuring direction of gaze.

• Extends: SpatialSeries

• Quantity: 1 or more

2.8.7. CompassDirection

Overview: 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.

CompassDirection extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: CompassDirection

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.7

Table 2.60 Groups contained in <CompassDirection>

Id	Type	Description
<CompassDirection>	Group	Top level Group for <CompassDirection> Neurodata Type: CompassDirection Extends: NWBDataInterface Default Name: CompassDirection
—<SpatialSeries>	Group	SpatialSeries object containing direction of gaze travel. Extends: SpatialSeries Quantity: 1 or more

2.8.7.1. Groups: <SpatialSeries>

SpatialSeries object containing direction of gaze travel.

• Extends: SpatialSeries

• Quantity: 1 or more

2.8.8. Position

Overview: Position data, whether along the x, x/y or x/y/z axis.

Position extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: Position

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.behavior.yaml

• Source Specification: see Section 3.9.8

Table 2.61 Groups contained in <Position>

Id	Type	Description
<Position>	Group	Top level Group for <Position> Neurodata Type: Position Extends: NWBDataInterface Default Name: Position
—<SpatialSeries>	Group	SpatialSeries object containing position data. Extends: SpatialSeries Quantity: 1 or more

2.8.8.1. Groups: <SpatialSeries>

SpatialSeries object containing position data.

• Extends: SpatialSeries

• Quantity: 1 or more

2.9. Extracellular electrophysiology

This source module contains neurodata_types for extracellular electrophysiology data.

2.9.1. ElectricalSeries

Overview: 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.

ElectricalSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Subtypes: SpikeEventSeries

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.1

Table 2.62 Datasets, Links, and Attributes contained in <ElectricalSeries>

Id	Type	Description
<ElectricalSeries>	Group	Top level Group for <ElectricalSeries> Neurodata Type: ElectricalSeries Extends: TimeSeries
—filtering	Attribute	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. Data Type: text Required: False Name: filtering
—data	Dataset	Recorded voltage data. Data Type: numeric Dimensions: [[‘num_times’], [‘num_times’, ‘num_channels’], [‘num_times’, ‘num_channels’, ‘num_samples’]] Shape: [[None], [None, None], [None, None, None]] Name: data
——unit	Attribute	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’. Data Type: text Value: volts Name: unit
—electrodes	Dataset	DynamicTableRegion pointer to the electrodes that this time series was generated from. Extends: DynamicTableRegion Name: electrodes
—channel_conversion	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [‘num_channels’] Shape: [None] Name: channel_conversion
——axis	Attribute	The zero-indexed axis of the ‘data’ dataset that the channel-specific conversion factor corresponds to. This value is fixed to 1. Data Type: int32 Value: 1 Name: axis

2.9.2. SpikeEventSeries

Overview: 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 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).

SpikeEventSeries extends ElectricalSeries and includes all elements of ElectricalSeries with the following additions or changes.

• Extends: ElectricalSeries

• Primitive Type: Group

• Inherits from: ElectricalSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.2

Table 2.63 Datasets, Links, and Attributes contained in <SpikeEventSeries>

Id	Type	Description
<SpikeEventSeries>	Group	Top level Group for <SpikeEventSeries> Neurodata Type: SpikeEventSeries Extends: ElectricalSeries
—data	Dataset	Spike waveforms. Data Type: numeric Dimensions: [[‘num_events’, ‘num_samples’], [‘num_events’, ‘num_channels’, ‘num_samples’]] Shape: [[None, None], [None, None, None]] Name: data
——unit	Attribute	Unit of measurement for waveforms, which is fixed to ‘volts’. Data Type: text Value: volts Name: unit
—timestamps	Dataset	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. Data Type: float64 Dimensions: [‘num_times’] Shape: [None] Name: timestamps
——interval	Attribute	Value is ‘1’ Data Type: int32 Value: 1 Name: interval
——unit	Attribute	Unit of measurement for timestamps, which is fixed to ‘seconds’. Data Type: text Value: seconds Name: unit

2.9.3. FeatureExtraction

Overview: Features, such as PC1 and PC2, that are extracted from signals stored in a SpikeEventSeries or other source.

FeatureExtraction extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: FeatureExtraction

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.3

Table 2.64 Datasets, Links, and Attributes contained in <FeatureExtraction>

Id	Type	Description
<FeatureExtraction>	Group	Top level Group for <FeatureExtraction> Neurodata Type: FeatureExtraction Extends: NWBDataInterface Default Name: FeatureExtraction
—description	Dataset	Description of features (eg, ‘’PC1’’) for each of the extracted features. Data Type: text Dimensions: [‘num_features’] Shape: [None] Name: description
—features	Dataset	Multi-dimensional array of features extracted from each event. Data Type: float32 Dimensions: [‘num_events’, ‘num_channels’, ‘num_features’] Shape: [None, None, None] Name: features
—times	Dataset	Times of events that features correspond to (can be a link). Data Type: float64 Dimensions: [‘num_events’] Shape: [None] Name: times
—electrodes	Dataset	DynamicTableRegion pointer to the electrodes that this time series was generated from. Extends: DynamicTableRegion Name: electrodes

2.9.4. EventDetection

Overview: Detected spike events from voltage trace(s).

EventDetection extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: EventDetection

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.4

Table 2.65 Datasets, Links, and Attributes contained in <EventDetection>

Id	Type	Description
<EventDetection>	Group	Top level Group for <EventDetection> Neurodata Type: EventDetection Extends: NWBDataInterface Default Name: EventDetection
—detection_method	Dataset	Description of how events were detected, such as voltage threshold, or dV/dT threshold, as well as relevant values. Data Type: text Name: detection_method
—source_idx	Dataset	Indices (zero-based) into the linked source ElectricalSeries::data array corresponding to time of event or time and channel 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. Data Type: int32 Dimensions: [[‘num_events’], [‘num_events’, ‘time_index, channel_index’]] Shape: [[None], [None, 2]] Name: source_idx
—times	Dataset	DEPRECATED. Timestamps of events, in seconds. Quantity: 0 or 1 Data Type: float64 Dimensions: [‘num_events’] Shape: [None] Name: times
——unit	Attribute	Unit of measurement for event times, which is fixed to ‘seconds’. Data Type: text Value: seconds Name: unit
—source_electricalseries	Link	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. Target Type ElectricalSeries Name: source_electricalseries

Table 2.66 Groups contained in <EventDetection>

Id	Type	Description
<EventDetection>	Group	Top level Group for <EventDetection> Neurodata Type: EventDetection Extends: NWBDataInterface Default Name: EventDetection
—source_electricalseries	Link	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. Target Type ElectricalSeries Name: source_electricalseries

2.9.5. EventWaveform

Overview: DEPRECATED. 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.

EventWaveform extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: EventWaveform

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.5

Table 2.67 Groups contained in <EventWaveform>

Id	Type	Description
<EventWaveform>	Group	Top level Group for <EventWaveform> Neurodata Type: EventWaveform Extends: NWBDataInterface Default Name: EventWaveform
—<SpikeEventSeries>	Group	SpikeEventSeries object(s) containing detected spike event waveforms. Extends: SpikeEventSeries Quantity: 1 or more

2.9.5.1. Groups: <SpikeEventSeries>

SpikeEventSeries object(s) containing detected spike event waveforms.

• Extends: SpikeEventSeries

• Quantity: 1 or more

2.9.6. FilteredEphys

Overview: 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.

FilteredEphys extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: FilteredEphys

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.6

Table 2.68 Groups contained in <FilteredEphys>

Id	Type	Description
<FilteredEphys>	Group	Top level Group for <FilteredEphys> Neurodata Type: FilteredEphys Extends: NWBDataInterface Default Name: FilteredEphys
—<ElectricalSeries>	Group	ElectricalSeries object(s) containing filtered electrophysiology data. Extends: ElectricalSeries Quantity: 1 or more

2.9.6.1. Groups: <ElectricalSeries>

ElectricalSeries object(s) containing filtered electrophysiology data.

• Extends: ElectricalSeries

• Quantity: 1 or more

2.9.7. LFP

Overview: 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.

LFP extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: LFP

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.7

Table 2.69 Groups contained in <LFP>

Id	Type	Description
<LFP>	Group	Top level Group for <LFP> Neurodata Type: LFP Extends: NWBDataInterface Default Name: LFP
—<ElectricalSeries>	Group	ElectricalSeries object(s) containing LFP data for one or more channels. Extends: ElectricalSeries Quantity: 1 or more

2.9.7.1. Groups: <ElectricalSeries>

ElectricalSeries object(s) containing LFP data for one or more channels.

• Extends: ElectricalSeries

• Quantity: 1 or more

2.9.8. ElectrodeGroup

Overview: A physical grouping of electrodes, e.g., a shank of an array. An electrode group is typically used to describe electrodes that are physically connected on a single device and are often (but not always) used together for analysis, such as for spike sorting. Note that this is descriptive metadata; electrodes from different groups can still be spike-sorted together if needed.

ElectrodeGroup extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.8

Table 2.70 Datasets, Links, and Attributes contained in <ElectrodeGroup>

Id	Type	Description
<ElectrodeGroup>	Group	Top level Group for <ElectrodeGroup> Neurodata Type: ElectrodeGroup Extends: NWBContainer
—description	Attribute	Description of this electrode group. Data Type: text Name: description
—location	Attribute	Location of electrode group. Specify the area, layer, comments on estimation of area/layer, etc. Use standard atlas names for anatomical regions when possible. Data Type: text Name: location
—position	Dataset	stereotaxic or common framework coordinates Quantity: 0 or 1 Data Type: Compound data type with the following elements: x: x coordinate (dtype= float32 ) y: y coordinate (dtype= float32 ) z: z coordinate (dtype= float32 ) Name: position
—device	Link	Link to the device that was used to record from this electrode group. Target Type Device Name: device

Table 2.71 Groups contained in <ElectrodeGroup>

Id	Type	Description
<ElectrodeGroup>	Group	Top level Group for <ElectrodeGroup> Neurodata Type: ElectrodeGroup Extends: NWBContainer
—device	Link	Link to the device that was used to record from this electrode group. Target Type Device Name: device

2.9.9. ElectrodesTable

Overview: A table of all electrodes (i.e. channels) used for recording. Introduced in NWB 2.8.0. Replaces the “electrodes” table (neurodata_type_inc DynamicTable, no neurodata_type_def) that is part of NWBFile.

ElectrodesTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.9

Table 2.72 Datasets, Links, and Attributes contained in <ElectrodesTable>

Id	Type	Description
<ElectrodesTable>	Group	Top level Group for <ElectrodesTable> Neurodata Type: ElectrodesTable Extends: DynamicTable
—location	Dataset	Location of the electrode (channel). 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. Extends: VectorData Data Type: text Name: location
—group	Dataset	Reference to the ElectrodeGroup this electrode is a part of. Extends: VectorData Data Type: object reference to ElectrodeGroup Name: group
—group_name	Dataset	Name of the ElectrodeGroup this electrode is a part of. Extends: VectorData Quantity: 0 or 1 Data Type: text Name: group_name
—x	Dataset	x coordinate of the channel location in the brain (+x is posterior). Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: x
—y	Dataset	y coordinate of the channel location in the brain (+y is inferior). Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: y
—z	Dataset	z coordinate of the channel location in the brain (+z is right). Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: z
—imp	Dataset	Impedance of the channel, in ohms. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: imp
—filtering	Dataset	Description of hardware filtering, including the filter name and frequency cutoffs. Extends: VectorData Quantity: 0 or 1 Data Type: text Name: filtering
—rel_x	Dataset	x coordinate in electrode group. Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: rel_x
—rel_y	Dataset	y coordinate in electrode group. Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: rel_y
—rel_z	Dataset	z coordinate in electrode group. Units should be specified in microns. Extends: VectorData Quantity: 0 or 1 Data Type: float32 Name: rel_z
—reference	Dataset	Description of the reference electrode and/or reference scheme used for this electrode, e.g., “stainless steel skull screw” or “online common average referencing”. Extends: VectorData Quantity: 0 or 1 Data Type: text Name: reference

2.9.10. ClusterWaveforms

Overview: 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.

ClusterWaveforms extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: ClusterWaveforms

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.10

Table 2.73 Datasets, Links, and Attributes contained in <ClusterWaveforms>

Id	Type	Description
<ClusterWaveforms>	Group	Top level Group for <ClusterWaveforms> Neurodata Type: ClusterWaveforms Extends: NWBDataInterface Default Name: ClusterWaveforms
—waveform_filtering	Dataset	Filtering applied to data before generating mean/sd Data Type: text Name: waveform_filtering
—waveform_mean	Dataset	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) Data Type: float32 Dimensions: [‘num_clusters’, ‘num_samples’] Shape: [None, None] Name: waveform_mean
—waveform_sd	Dataset	Stdev of waveforms for each cluster, using the same indices as in mean Data Type: float32 Dimensions: [‘num_clusters’, ‘num_samples’] Shape: [None, None] Name: waveform_sd
—clustering_interface	Link	Link to Clustering interface that was the source of the clustered data Target Type Clustering Name: clustering_interface

Table 2.74 Groups contained in <ClusterWaveforms>

Id	Type	Description
<ClusterWaveforms>	Group	Top level Group for <ClusterWaveforms> Neurodata Type: ClusterWaveforms Extends: NWBDataInterface Default Name: ClusterWaveforms
—clustering_interface	Link	Link to Clustering interface that was the source of the clustered data Target Type Clustering Name: clustering_interface

2.9.11. Clustering

Overview: DEPRECATED Clustered spike data, whether from automatic clustering tools (e.g., klustakwik) or as a result of manual sorting.

Clustering extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: Clustering

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ecephys.yaml

• Source Specification: see Section 3.10.11

Table 2.75 Datasets, Links, and Attributes contained in <Clustering>

Id	Type	Description
<Clustering>	Group	Top level Group for <Clustering> Neurodata Type: Clustering Extends: NWBDataInterface Default Name: Clustering
—description	Dataset	Description of clusters or clustering, (e.g. cluster 0 is noise, clusters curated using Klusters, etc) Data Type: text Name: description
—num	Dataset	Cluster number of each event Data Type: int32 Dimensions: [‘num_events’] Shape: [None] Name: num
—peak_over_rms	Dataset	Maximum ratio of waveform peak to RMS on any channel in the cluster (provides a basic clustering metric). Data Type: float32 Dimensions: [‘num_clusters’] Shape: [None] Name: peak_over_rms
—times	Dataset	Times of clustered events, in seconds. This may be a link to times field in associated FeatureExtraction module. Data Type: float64 Dimensions: [‘num_events’] Shape: [None] Name: times

2.10. Intracellular electrophysiology

This source module contains neurodata_types for intracellular electrophysiology data.

2.10.1. PatchClampSeries

Overview: An abstract base class for patch-clamp data - stimulus or response, current or voltage.

PatchClampSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Subtypes: VoltageClampStimulusSeries, CurrentClampStimulusSeries, CurrentClampSeries, VoltageClampSeries, IZeroClampSeries

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.1

Table 2.76 Datasets, Links, and Attributes contained in <PatchClampSeries>

Id	Type	Description
<PatchClampSeries>	Group	Top level Group for <PatchClampSeries> Neurodata Type: PatchClampSeries Extends: TimeSeries
—stimulus_description	Attribute	Protocol/stimulus name for this patch-clamp dataset. Data Type: text Name: stimulus_description
—sweep_number	Attribute	Sweep number, allows to group different PatchClampSeries together. Data Type: uint32 Required: False Name: sweep_number
—data	Dataset	Recorded voltage or current. Data Type: numeric Dimensions: [‘num_times’] Shape: [None] Name: data
——unit	Attribute	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’. Data Type: text Name: unit
—gain	Dataset	Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt (c-clamp). Quantity: 0 or 1 Data Type: float32 Name: gain
—electrode	Link	Link to IntracellularElectrode object that describes the electrode that was used to apply or record this data. Target Type IntracellularElectrode Name: electrode

Table 2.77 Groups contained in <PatchClampSeries>

Id	Type	Description
<PatchClampSeries>	Group	Top level Group for <PatchClampSeries> Neurodata Type: PatchClampSeries Extends: TimeSeries
—electrode	Link	Link to IntracellularElectrode object that describes the electrode that was used to apply or record this data. Target Type IntracellularElectrode Name: electrode

2.10.2. CurrentClampSeries

Overview: Voltage data from an intracellular current-clamp recording. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected.

CurrentClampSeries extends PatchClampSeries and includes all elements of PatchClampSeries with the following additions or changes.

• Extends: PatchClampSeries

• Primitive Type: Group

• Inherits from: PatchClampSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Subtypes: IZeroClampSeries

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.2

Table 2.78 Datasets, Links, and Attributes contained in <CurrentClampSeries>

Id	Type	Description
<CurrentClampSeries>	Group	Top level Group for <CurrentClampSeries> Neurodata Type: CurrentClampSeries Extends: PatchClampSeries
—data	Dataset	Recorded voltage. Name: data
——unit	Attribute	Base unit of measurement for working with the data. which 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’ and add ‘offset’. Data Type: text Value: volts Name: unit
—bias_current	Dataset	Bias current, in amps. Quantity: 0 or 1 Data Type: float32 Name: bias_current
—bridge_balance	Dataset	Bridge balance, in ohms. Quantity: 0 or 1 Data Type: float32 Name: bridge_balance
—capacitance_compensation	Dataset	Capacitance compensation, in farads. Quantity: 0 or 1 Data Type: float32 Name: capacitance_compensation

2.10.3. IZeroClampSeries

Overview: Voltage data from an intracellular recording when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell.

IZeroClampSeries extends CurrentClampSeries and includes all elements of CurrentClampSeries with the following additions or changes.

• Extends: CurrentClampSeries

• Primitive Type: Group

• Inherits from: CurrentClampSeries, PatchClampSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.3

Table 2.79 Datasets, Links, and Attributes contained in <IZeroClampSeries>

Id	Type	Description
<IZeroClampSeries>	Group	Top level Group for <IZeroClampSeries> Neurodata Type: IZeroClampSeries Extends: CurrentClampSeries
—stimulus_description	Attribute	An IZeroClampSeries has no stimulus, so this attribute is automatically set to “N/A” Data Type: text Value: N/A Name: stimulus_description
—bias_current	Dataset	Bias current, in amps, fixed to 0.0. Data Type: float32 Name: bias_current
—bridge_balance	Dataset	Bridge balance, in ohms, fixed to 0.0. Data Type: float32 Name: bridge_balance
—capacitance_compensation	Dataset	Capacitance compensation, in farads, fixed to 0.0. Data Type: float32 Name: capacitance_compensation

2.10.4. CurrentClampStimulusSeries

Overview: Stimulus current applied during current clamp recording.

CurrentClampStimulusSeries extends PatchClampSeries and includes all elements of PatchClampSeries with the following additions or changes.

• Extends: PatchClampSeries

• Primitive Type: Group

• Inherits from: PatchClampSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.4

Table 2.80 Datasets, Links, and Attributes contained in <CurrentClampStimulusSeries>

Id	Type	Description
<CurrentClampStimulusSeries>	Group	Top level Group for <CurrentClampStimulusSeries> Neurodata Type: CurrentClampStimulusSeries Extends: PatchClampSeries
—data	Dataset	Stimulus current applied. Name: data
——unit	Attribute	Base unit of measurement for working with the data. which is fixed to ‘amperes’. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply ‘data’ by ‘conversion’ and add ‘offset’. Data Type: text Value: amperes Name: unit

2.10.5. VoltageClampSeries

Overview: Current data from an intracellular voltage-clamp recording. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected.

VoltageClampSeries extends PatchClampSeries and includes all elements of PatchClampSeries with the following additions or changes.

• Extends: PatchClampSeries

• Primitive Type: Group

• Inherits from: PatchClampSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.5

Table 2.81 Datasets, Links, and Attributes contained in <VoltageClampSeries>

Id	Type	Description
<VoltageClampSeries>	Group	Top level Group for <VoltageClampSeries> Neurodata Type: VoltageClampSeries Extends: PatchClampSeries
—data	Dataset	Recorded current. Name: data
——unit	Attribute	Base unit of measurement for working with the data. which is fixed to ‘amperes’. Actual stored values are not necessarily stored in these units. To access the data in these units, multiply ‘data’ by ‘conversion’ and add ‘offset’. Data Type: text Value: amperes Name: unit
—capacitance_fast	Dataset	Fast capacitance, in farads. Quantity: 0 or 1 Data Type: float32 Name: capacitance_fast
——unit	Attribute	Unit of measurement for capacitance_fast, which is fixed to ‘farads’. Data Type: text Value: farads Name: unit
—capacitance_slow	Dataset	Slow capacitance, in farads. Quantity: 0 or 1 Data Type: float32 Name: capacitance_slow
——unit	Attribute	Unit of measurement for capacitance_fast, which is fixed to ‘farads’. Data Type: text Value: farads Name: unit
—resistance_comp_bandwidth	Dataset	Resistance compensation bandwidth, in hertz. Quantity: 0 or 1 Data Type: float32 Name: resistance_comp_bandwidth
——unit	Attribute	Unit of measurement for resistance_comp_bandwidth, which is fixed to ‘hertz’. Data Type: text Value: hertz Name: unit
—resistance_comp_correction	Dataset	Resistance compensation correction, in percent. Quantity: 0 or 1 Data Type: float32 Name: resistance_comp_correction
——unit	Attribute	Unit of measurement for resistance_comp_correction, which is fixed to ‘percent’. Data Type: text Value: percent Name: unit
—resistance_comp_prediction	Dataset	Resistance compensation prediction, in percent. Quantity: 0 or 1 Data Type: float32 Name: resistance_comp_prediction
——unit	Attribute	Unit of measurement for resistance_comp_prediction, which is fixed to ‘percent’. Data Type: text Value: percent Name: unit
—whole_cell_capacitance_comp	Dataset	Whole cell capacitance compensation, in farads. Quantity: 0 or 1 Data Type: float32 Name: whole_cell_capacitance_comp
——unit	Attribute	Unit of measurement for whole_cell_capacitance_comp, which is fixed to ‘farads’. Data Type: text Value: farads Name: unit
—whole_cell_series_resistance_comp	Dataset	Whole cell series resistance compensation, in ohms. Quantity: 0 or 1 Data Type: float32 Name: whole_cell_series_resistance_comp
——unit	Attribute	Unit of measurement for whole_cell_series_resistance_comp, which is fixed to ‘ohms’. Data Type: text Value: ohms Name: unit

2.10.6. VoltageClampStimulusSeries

Overview: Stimulus voltage applied during a voltage clamp recording.

VoltageClampStimulusSeries extends PatchClampSeries and includes all elements of PatchClampSeries with the following additions or changes.

• Extends: PatchClampSeries

• Primitive Type: Group

• Inherits from: PatchClampSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.6

Table 2.82 Datasets, Links, and Attributes contained in <VoltageClampStimulusSeries>

Id	Type	Description
<VoltageClampStimulusSeries>	Group	Top level Group for <VoltageClampStimulusSeries> Neurodata Type: VoltageClampStimulusSeries Extends: PatchClampSeries
—data	Dataset	Stimulus voltage applied. Name: data
——unit	Attribute	Base unit of measurement for working with the data. which 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’ and add ‘offset’. Data Type: text Value: volts Name: unit

2.10.7. IntracellularElectrode

Overview: An intracellular electrode and its metadata.

IntracellularElectrode extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.7

Table 2.83 Datasets, Links, and Attributes contained in <IntracellularElectrode>

Id	Type	Description
<IntracellularElectrode>	Group	Top level Group for <IntracellularElectrode> Neurodata Type: IntracellularElectrode Extends: NWBContainer
—cell_id	Dataset	unique ID of the cell Quantity: 0 or 1 Data Type: text Name: cell_id
—description	Dataset	Description of electrode (e.g., whole-cell, sharp, etc.). Data Type: text Name: description
—filtering	Dataset	Electrode specific filtering. Quantity: 0 or 1 Data Type: text Name: filtering
—initial_access_resistance	Dataset	Initial access resistance. Quantity: 0 or 1 Data Type: text Name: initial_access_resistance
—location	Dataset	Location of the electrode. 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. Quantity: 0 or 1 Data Type: text Name: location
—resistance	Dataset	Electrode resistance, in ohms. Quantity: 0 or 1 Data Type: text Name: resistance
—seal	Dataset	Information about seal used for recording. Quantity: 0 or 1 Data Type: text Name: seal
—slice	Dataset	Information about slice used for recording. Quantity: 0 or 1 Data Type: text Name: slice
—device	Link	Device that was used to record from this electrode. Target Type Device Name: device

Table 2.84 Groups contained in <IntracellularElectrode>

Id	Type	Description
<IntracellularElectrode>	Group	Top level Group for <IntracellularElectrode> Neurodata Type: IntracellularElectrode Extends: NWBContainer
—device	Link	Device that was used to record from this electrode. Target Type Device Name: device

2.10.8. SweepTable

Overview: [DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables. Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions tables provide enhanced support for experiment metadata.

SweepTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.8

Table 2.85 Datasets, Links, and Attributes contained in <SweepTable>

Id	Type	Description
<SweepTable>	Group	Top level Group for <SweepTable> Neurodata Type: SweepTable Extends: DynamicTable
—sweep_number	Dataset	Sweep number of the PatchClampSeries in that row. Extends: VectorData Data Type: uint32 Name: sweep_number
—series	Dataset	The PatchClampSeries with the sweep number in that row. Extends: VectorData Data Type: object reference to PatchClampSeries Name: series
—series_index	Dataset	Index for series. Extends: VectorIndex Name: series_index

2.10.9. IntracellularElectrodesTable

Overview: Table for storing intracellular electrode related metadata.

IntracellularElectrodesTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.9

Table 2.86 Datasets, Links, and Attributes contained in <IntracellularElectrodesTable>

Id	Type	Description
<IntracellularElectrodesTable>	Group	Top level Group for <IntracellularElectrodesTable> Neurodata Type: IntracellularElectrodesTable Extends: DynamicTable
—description	Attribute	Description of what is in this dynamic table. Data Type: text Value: Table for storing intracellular electrode related metadata. Name: description
—electrode	Dataset	Column for storing the reference to the intracellular electrode. Extends: VectorData Data Type: object reference to IntracellularElectrode Name: electrode

2.10.10. IntracellularStimuliTable

Overview: Table for storing intracellular stimulus related metadata.

IntracellularStimuliTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.10

Table 2.87 Datasets, Links, and Attributes contained in <IntracellularStimuliTable>

Id	Type	Description
<IntracellularStimuliTable>	Group	Top level Group for <IntracellularStimuliTable> Neurodata Type: IntracellularStimuliTable Extends: DynamicTable
—description	Attribute	Description of what is in this dynamic table. Data Type: text Value: Table for storing intracellular stimulus related metadata. Name: description
—stimulus	Dataset	Column storing the reference to the recorded stimulus for the recording (rows). Extends: TimeSeriesReferenceVectorData Name: stimulus
—stimulus_template	Dataset	Column storing the reference to the stimulus template for the recording (rows). Extends: TimeSeriesReferenceVectorData Quantity: 0 or 1 Name: stimulus_template

2.10.11. IntracellularResponsesTable

Overview: Table for storing intracellular response related metadata.

IntracellularResponsesTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.11

Table 2.88 Datasets, Links, and Attributes contained in <IntracellularResponsesTable>

Id	Type	Description
<IntracellularResponsesTable>	Group	Top level Group for <IntracellularResponsesTable> Neurodata Type: IntracellularResponsesTable Extends: DynamicTable
—description	Attribute	Description of what is in this dynamic table. Data Type: text Value: Table for storing intracellular response related metadata. Name: description
—response	Dataset	Column storing the reference to the recorded response for the recording (rows) Extends: TimeSeriesReferenceVectorData Name: response

2.10.12. IntracellularRecordingsTable

Overview: A table to group together a stimulus and response from a single electrode and a single simultaneous recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response. In some cases, however, only a stimulus or a response is recorded as part of an experiment. In this case, both the stimulus and response will point to the same TimeSeries while the idx_start and count of the invalid column will be set to -1, thus, indicating that no values have been recorded for the stimulus or response, respectively. Note, a recording MUST contain at least a stimulus or a response. Typically the stimulus and response are PatchClampSeries. However, the use of AD/DA channels that are not associated to an electrode is also common in intracellular electrophysiology, in which case other TimeSeries may be used.

IntracellularRecordingsTable extends AlignedDynamicTable and includes all elements of AlignedDynamicTable with the following additions or changes.

• Extends: AlignedDynamicTable

• Primitive Type: Group

• Name: intracellular_recordings

• Inherits from: AlignedDynamicTable, DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.12

Table 2.89 Datasets, Links, and Attributes contained in <IntracellularRecordingsTable>

Id	Type	Description
intracellular_recordings	Group	Top level Group for intracellular_recordings Neurodata Type: IntracellularRecordingsTable Extends: AlignedDynamicTable Name: intracellular_recordings
—description	Attribute	Description of the contents of this table. Inherited from AlignedDynamicTable and overwritten here to fix the value of the attribute. Data Type: text Value: A table to group together a stimulus and response from a single electrode and a single simultaneous recording and for storing metadata about the intracellular recording. Name: description

Table 2.90 Groups contained in <IntracellularRecordingsTable>

Id	Type	Description
intracellular_recordings	Group	Top level Group for intracellular_recordings Neurodata Type: IntracellularRecordingsTable Extends: AlignedDynamicTable Name: intracellular_recordings
—electrodes	Group	Table for storing intracellular electrode related metadata. Extends: IntracellularElectrodesTable Name: electrodes
—stimuli	Group	Table for storing intracellular stimulus related metadata. Extends: IntracellularStimuliTable Name: stimuli
—responses	Group	Table for storing intracellular response related metadata. Extends: IntracellularResponsesTable Name: responses

2.10.12.1. Groups: electrodes

Table for storing intracellular electrode related metadata.

• Extends: IntracellularElectrodesTable

• Name: electrodes

2.10.12.2. Groups: stimuli

Table for storing intracellular stimulus related metadata.

• Extends: IntracellularStimuliTable

• Name: stimuli

2.10.12.3. Groups: responses

Table for storing intracellular response related metadata.

• Extends: IntracellularResponsesTable

• Name: responses

2.10.13. SimultaneousRecordingsTable

Overview: A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes.

SimultaneousRecordingsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Name: simultaneous_recordings

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.13

Table 2.91 Datasets, Links, and Attributes contained in <SimultaneousRecordingsTable>

Id	Type	Description
simultaneous_recordings	Group	Top level Group for simultaneous_recordings Neurodata Type: SimultaneousRecordingsTable Extends: DynamicTable Name: simultaneous_recordings
—recordings	Dataset	A reference to one or more rows in the IntracellularRecordingsTable table. Extends: DynamicTableRegion Name: recordings
——table	Attribute	Reference to the IntracellularRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. Data Type: object reference to IntracellularRecordingsTable Name: table
—recordings_index	Dataset	Index dataset for the recordings column. Extends: VectorIndex Name: recordings_index

2.10.14. SequentialRecordingsTable

Overview: A table for grouping different sequential recordings from the SimultaneousRecordingsTable table together. This is typically used to group together sequential recordings where a sequence of stimuli of the same type with varying parameters have been presented in a sequence.

SequentialRecordingsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Name: sequential_recordings

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.14

Table 2.92 Datasets, Links, and Attributes contained in <SequentialRecordingsTable>

Id	Type	Description
sequential_recordings	Group	Top level Group for sequential_recordings Neurodata Type: SequentialRecordingsTable Extends: DynamicTable Name: sequential_recordings
—simultaneous_recordings	Dataset	A reference to one or more rows in the SimultaneousRecordingsTable table. Extends: DynamicTableRegion Name: simultaneous_recordings
——table	Attribute	Reference to the SimultaneousRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. Data Type: object reference to SimultaneousRecordingsTable Name: table
—simultaneous_recordings_index	Dataset	Index dataset for the simultaneous_recordings column. Extends: VectorIndex Name: simultaneous_recordings_index
—stimulus_type	Dataset	The type of stimulus used for the sequential recording. Extends: VectorData Data Type: text Name: stimulus_type

2.10.15. RepetitionsTable

Overview: A table for grouping different sequential intracellular recordings together. With each SequentialRecording typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.

RepetitionsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Name: repetitions

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.15

Table 2.93 Datasets, Links, and Attributes contained in <RepetitionsTable>

Id	Type	Description
repetitions	Group	Top level Group for repetitions Neurodata Type: RepetitionsTable Extends: DynamicTable Name: repetitions
—sequential_recordings	Dataset	A reference to one or more rows in the SequentialRecordingsTable table. Extends: DynamicTableRegion Name: sequential_recordings
——table	Attribute	Reference to the SequentialRecordingsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. Data Type: object reference to SequentialRecordingsTable Name: table
—sequential_recordings_index	Dataset	Index dataset for the sequential_recordings column. Extends: VectorIndex Name: sequential_recordings_index

2.10.16. ExperimentalConditionsTable

Overview: A table for grouping different intracellular recording repetitions together that belong to the same experimental condition.

ExperimentalConditionsTable extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Name: experimental_conditions

• Inherits from: DynamicTable, Container

• Source filename: nwb.icephys.yaml

• Source Specification: see Section 3.11.16

Table 2.94 Datasets, Links, and Attributes contained in <ExperimentalConditionsTable>

Id	Type	Description
experimental_conditions	Group	Top level Group for experimental_conditions Neurodata Type: ExperimentalConditionsTable Extends: DynamicTable Name: experimental_conditions
—repetitions	Dataset	A reference to one or more rows in the RepetitionsTable table. Extends: DynamicTableRegion Name: repetitions
——table	Attribute	Reference to the RepetitionsTable table that this table region applies to. This specializes the attribute inherited from DynamicTableRegion to fix the type of table that can be referenced here. Data Type: object reference to RepetitionsTable Name: table
—repetitions_index	Dataset	Index dataset for the repetitions column. Extends: VectorIndex Name: repetitions_index

2.11. Optogenetics

This source module contains neurodata_types for opto-genetics data.

2.11.1. OptogeneticSeries

Overview: An optogenetic stimulus.

OptogeneticSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ogen.yaml

• Source Specification: see Section 3.12.1

Table 2.95 Datasets, Links, and Attributes contained in <OptogeneticSeries>

Id	Type	Description
<OptogeneticSeries>	Group	Top level Group for <OptogeneticSeries> Neurodata Type: OptogeneticSeries Extends: TimeSeries
—data	Dataset	Applied power for optogenetic stimulus, in watts. Shape can be 1D or 2D. 2D data is meant to be used in an extension of OptogeneticSeries that defines what the second dimension represents. Data Type: numeric Dimensions: [[‘num_times’], [‘num_times’, ‘num_rois’]] Shape: [[None], [None, None]] Name: data
——unit	Attribute	Unit of measurement for data, which is fixed to ‘watts’. Data Type: text Value: watts Name: unit
—site	Link	Link to OptogeneticStimulusSite object that describes the site to which this stimulus was applied. Target Type OptogeneticStimulusSite Name: site

Table 2.96 Groups contained in <OptogeneticSeries>

Id	Type	Description
<OptogeneticSeries>	Group	Top level Group for <OptogeneticSeries> Neurodata Type: OptogeneticSeries Extends: TimeSeries
—site	Link	Link to OptogeneticStimulusSite object that describes the site to which this stimulus was applied. Target Type OptogeneticStimulusSite Name: site

2.11.2. OptogeneticStimulusSite

Overview: A site of optogenetic stimulation.

OptogeneticStimulusSite extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.ogen.yaml

• Source Specification: see Section 3.12.2

Table 2.97 Datasets, Links, and Attributes contained in <OptogeneticStimulusSite>

Id	Type	Description
<OptogeneticStimulusSite>	Group	Top level Group for <OptogeneticStimulusSite> Neurodata Type: OptogeneticStimulusSite Extends: NWBContainer
—description	Dataset	Description of stimulation site. Data Type: text Name: description
—excitation_lambda	Dataset	Excitation wavelength, in nm. Data Type: float32 Name: excitation_lambda
—location	Dataset	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. Data Type: text Name: location
—device	Link	Device that generated the stimulus. Target Type Device Name: device

Table 2.98 Groups contained in <OptogeneticStimulusSite>

Id	Type	Description
<OptogeneticStimulusSite>	Group	Top level Group for <OptogeneticStimulusSite> Neurodata Type: OptogeneticStimulusSite Extends: NWBContainer
—device	Link	Device that generated the stimulus. Target Type Device Name: device

2.12. Optical physiology

This source module contains neurodata_types for optical physiology data.

2.12.1. OnePhotonSeries

Overview: Image stack recorded over time from 1-photon microscope.

OnePhotonSeries extends ImageSeries and includes all elements of ImageSeries with the following additions or changes.

• Extends: ImageSeries

• Primitive Type: Group

• Inherits from: ImageSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.1

Table 2.99 Datasets, Links, and Attributes contained in <OnePhotonSeries>

Id	Type	Description
<OnePhotonSeries>	Group	Top level Group for <OnePhotonSeries> Neurodata Type: OnePhotonSeries Extends: ImageSeries
—pmt_gain	Attribute	Photomultiplier gain. Data Type: float32 Required: False Name: pmt_gain
—scan_line_rate	Attribute	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. Data Type: float32 Required: False Name: scan_line_rate
—exposure_time	Attribute	Exposure time of the sample; often the inverse of the frequency. Data Type: float32 Required: False Name: exposure_time
—binning	Attribute	Amount of pixels combined into ‘bins’; could be 1, 2, 4, 8, etc. Data Type: uint8 Required: False Name: binning
—power	Attribute	Power of the excitation in mW, if known. Data Type: float32 Required: False Name: power
—intensity	Attribute	Intensity of the excitation in mW/mm^2, if known. Data Type: float32 Required: False Name: intensity
—data	Dataset	Time-series of microscopy data indexed as data[time, width, height]. Indexing convention: width: first spatial axis (horizontal direction, columns) height: second spatial axis (vertical direction, rows) For raster-scanning systems (two-photon, confocal, one-photon laser scanning): width: fast scan direction (horizontal) height: slow scan direction (vertical) Coordinate system diagram: height ^ (slow) | | +-----------------+ | | | | | Image plane | | | | | +-----------------+ | 0 ----------------------> width (fast) For non-raster systems (wide-field, light-sheet, random-access), width and height are arbitrary coordinates of the image plane. Note: This indexing convention conflicts with standard matrix[row, column] notation for array access where the first index moves vertically through rows and the second moves horizontally through columns. In the schema, data[time, width, height] means that the first spatial index moves horizontally (width) through columns and the second spatial index moves vertically (height) through rows. In summary, incrementing the first spatial index moves you horizontally across the image, while in matrix notation it would move you vertically across the rows of the image. Data Type: numeric Dimensions: [[‘time’, ‘width’, ‘height’], [‘time’, ‘width’, ‘height’, ‘depth’]] Shape: [[None, None, None], [None, None, None, None]] Name: data
—imaging_plane	Link	Link to ImagingPlane object from which this TimeSeries data was generated. Target Type ImagingPlane Name: imaging_plane

Table 2.100 Groups contained in <OnePhotonSeries>

Id	Type	Description
<OnePhotonSeries>	Group	Top level Group for <OnePhotonSeries> Neurodata Type: OnePhotonSeries Extends: ImageSeries
—imaging_plane	Link	Link to ImagingPlane object from which this TimeSeries data was generated. Target Type ImagingPlane Name: imaging_plane

2.12.2. TwoPhotonSeries

Overview: Image stack recorded over time from 2-photon microscope.

TwoPhotonSeries extends ImageSeries and includes all elements of ImageSeries with the following additions or changes.

• Extends: ImageSeries

• Primitive Type: Group

• Inherits from: ImageSeries, TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.2

Table 2.101 Datasets, Links, and Attributes contained in <TwoPhotonSeries>

Id	Type	Description
<TwoPhotonSeries>	Group	Top level Group for <TwoPhotonSeries> Neurodata Type: TwoPhotonSeries Extends: ImageSeries
—pmt_gain	Attribute	Photomultiplier gain. Data Type: float32 Required: False Name: pmt_gain
—scan_line_rate	Attribute	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. Data Type: float32 Required: False Name: scan_line_rate
—data	Dataset	Time-series of microscopy data indexed as data[time, width, height]. Indexing convention: width: first spatial axis (horizontal direction, columns) height: second spatial axis (vertical direction, rows) For raster-scanning systems (two-photon, confocal, one-photon laser scanning): width: fast scan direction (horizontal) height: slow scan direction (vertical) Coordinate system diagram: height ^ (slow) | | +-----------------+ | | | | | Image plane | | | | | +-----------------+ | 0 ----------------------> width (fast) For non-raster systems (wide-field, light-sheet, random-access), width and height are arbitrary coordinates of the image plane. Note: This indexing convention conflicts with standard matrix[row, column] notation for array access where the first index moves vertically through rows and the second moves horizontally through columns. In the schema, data[time, width, height] means that the first spatial index moves horizontally (width) through columns and the second spatial index moves vertically (height) through rows. Data Type: numeric Dimensions: [[‘time’, ‘width’, ‘height’], [‘time’, ‘width’, ‘height’, ‘depth’]] Shape: [[None, None, None], [None, None, None, None]] Name: data
—field_of_view	Dataset	Physical dimensions of the imaging field of view in width, height, and optionally depth directions, in meters. The width dimension corresponds to the faster scanning axis, and the height dimension corresponds to the slower scanning axis. Quantity: 0 or 1 Data Type: float32 Dimensions: [[‘width|height’], [‘width|height|depth’]] Shape: [[2], [3]] Name: field_of_view
—imaging_plane	Link	Link to ImagingPlane object from which this TimeSeries data was generated. Target Type ImagingPlane Name: imaging_plane

Table 2.102 Groups contained in <TwoPhotonSeries>

Id	Type	Description
<TwoPhotonSeries>	Group	Top level Group for <TwoPhotonSeries> Neurodata Type: TwoPhotonSeries Extends: ImageSeries
—imaging_plane	Link	Link to ImagingPlane object from which this TimeSeries data was generated. Target Type ImagingPlane Name: imaging_plane

2.12.3. RoiResponseSeries

Overview: ROI responses over an imaging plane. The first dimension represents time. The second dimension, if present, represents ROIs.

RoiResponseSeries extends TimeSeries and includes all elements of TimeSeries with the following additions or changes.

• Extends: TimeSeries

• Primitive Type: Group

• Inherits from: TimeSeries, NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.3

Table 2.103 Datasets, Links, and Attributes contained in <RoiResponseSeries>

Id	Type	Description
<RoiResponseSeries>	Group	Top level Group for <RoiResponseSeries> Neurodata Type: RoiResponseSeries Extends: TimeSeries
—data	Dataset	Signals from ROIs. Data Type: numeric Dimensions: [[‘num_times’], [‘num_times’, ‘num_ROIs’]] Shape: [[None], [None, None]] Name: data
—rois	Dataset	DynamicTableRegion referencing into an ROITable containing information on the ROIs stored in this timeseries. Extends: DynamicTableRegion Name: rois

2.12.4. DfOverF

Overview: 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).

DfOverF extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: DfOverF

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.4

Table 2.104 Groups contained in <DfOverF>

Id	Type	Description
<DfOverF>	Group	Top level Group for <DfOverF> Neurodata Type: DfOverF Extends: NWBDataInterface Default Name: DfOverF
—<RoiResponseSeries>	Group	RoiResponseSeries object(s) containing dF/F for a ROI. Extends: RoiResponseSeries Quantity: 1 or more

2.12.4.1. Groups: <RoiResponseSeries>

RoiResponseSeries object(s) containing dF/F for a ROI.

• Extends: RoiResponseSeries

• Quantity: 1 or more

2.12.5. Fluorescence

Overview: 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).

Fluorescence extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: Fluorescence

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.5

Table 2.105 Groups contained in <Fluorescence>

Id	Type	Description
<Fluorescence>	Group	Top level Group for <Fluorescence> Neurodata Type: Fluorescence Extends: NWBDataInterface Default Name: Fluorescence
—<RoiResponseSeries>	Group	RoiResponseSeries object(s) containing fluorescence data for a ROI. Extends: RoiResponseSeries Quantity: 1 or more

2.12.5.1. Groups: <RoiResponseSeries>

RoiResponseSeries object(s) containing fluorescence data for a ROI.

• Extends: RoiResponseSeries

• Quantity: 1 or more

2.12.6. ImageSegmentation

Overview: 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.

ImageSegmentation extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: ImageSegmentation

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.6

Table 2.106 Groups contained in <ImageSegmentation>

Id	Type	Description
<ImageSegmentation>	Group	Top level Group for <ImageSegmentation> Neurodata Type: ImageSegmentation Extends: NWBDataInterface Default Name: ImageSegmentation
—<PlaneSegmentation>	Group	Results from image segmentation of a specific imaging plane. Extends: PlaneSegmentation Quantity: 1 or more

2.12.6.1. Groups: <PlaneSegmentation>

Results from image segmentation of a specific imaging plane.

• Extends: PlaneSegmentation

• Quantity: 1 or more

2.12.7. PlaneSegmentation

Overview: Results from image segmentation of a specific imaging plane. At least one of image_mask, pixel_mask, or voxel_mask is required.

PlaneSegmentation extends DynamicTable and includes all elements of DynamicTable with the following additions or changes.

• Extends: DynamicTable

• Primitive Type: Group

• Inherits from: DynamicTable, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.7

Table 2.107 Datasets, Links, and Attributes contained in <PlaneSegmentation>

Id	Type	Description
<PlaneSegmentation>	Group	Top level Group for <PlaneSegmentation> Neurodata Type: PlaneSegmentation Extends: DynamicTable
—image_mask	Dataset	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. At least one of image_mask, pixel_mask, or voxel_mask is required. Extends: VectorData Quantity: 0 or 1 Dimensions: [[‘num_roi’, ‘num_x’, ‘num_y’], [‘num_roi’, ‘num_x’, ‘num_y’, ‘num_z’]] Shape: [[None, None, None], [None, None, None, None]] Name: image_mask
—pixel_mask_index	Dataset	Index into pixel_mask. Extends: VectorIndex Quantity: 0 or 1 Name: pixel_mask_index
—pixel_mask	Dataset	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. At least one of image_mask, pixel_mask, or voxel_mask is required. Extends: VectorData Quantity: 0 or 1 Data Type: Compound data type with the following elements: x: Pixel x-coordinate. (dtype= uint32 ) y: Pixel y-coordinate. (dtype= uint32 ) weight: Weight of the pixel. (dtype= float32 ) Name: pixel_mask
—voxel_mask_index	Dataset	Index into voxel_mask. Extends: VectorIndex Quantity: 0 or 1 Name: voxel_mask_index
—voxel_mask	Dataset	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. At least one of image_mask, pixel_mask, or voxel_mask is required. Extends: VectorData Quantity: 0 or 1 Data Type: Compound data type with the following elements: x: Voxel x-coordinate. (dtype= uint32 ) y: Voxel y-coordinate. (dtype= uint32 ) z: Voxel z-coordinate. (dtype= uint32 ) weight: Weight of the voxel. (dtype= float32 ) Name: voxel_mask
—imaging_plane	Link	Link to ImagingPlane object from which this data was generated. Target Type ImagingPlane Name: imaging_plane

Table 2.108 Groups contained in <PlaneSegmentation>

Id	Type	Description
<PlaneSegmentation>	Group	Top level Group for <PlaneSegmentation> Neurodata Type: PlaneSegmentation Extends: DynamicTable
—imaging_plane	Link	Link to ImagingPlane object from which this data was generated. Target Type ImagingPlane Name: imaging_plane
—reference_images	Group	Image stacks that the segmentation masks apply to. Name: reference_images

2.12.7.1. Groups: reference_images

Image stacks that the segmentation masks apply to.

• Name: reference_images

Table 2.109 Groups contained in <reference_images>

Id	Type	Description
reference_images	Group	Top level Group for reference_images Name: reference_images
—<ImageSeries>	Group	One or more image stacks that the masks apply to (can be one-element stack). Extends: ImageSeries Quantity: 0 or more

2.12.7.2. Groups: reference_images/<ImageSeries>

One or more image stacks that the masks apply to (can be one-element stack).

• Extends: ImageSeries

• Quantity: 0 or more

2.12.8. ImagingPlane

Overview: An imaging plane and its metadata.

ImagingPlane extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.8

Table 2.110 Datasets, Links, and Attributes contained in <ImagingPlane>

Id	Type	Description
<ImagingPlane>	Group	Top level Group for <ImagingPlane> Neurodata Type: ImagingPlane Extends: NWBContainer
—description	Dataset	Description of the imaging plane. Quantity: 0 or 1 Data Type: text Name: description
—excitation_lambda	Dataset	Excitation wavelength, in nm. Data Type: float32 Name: excitation_lambda
—imaging_rate	Dataset	Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored there instead. Quantity: 0 or 1 Data Type: float32 Name: imaging_rate
—indicator	Dataset	Calcium indicator. Data Type: text Name: indicator
—location	Dataset	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. Data Type: text Name: location
—manifold	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [[‘height’, ‘width’, ‘x, y, z’], [‘height’, ‘width’, ‘depth’, ‘x, y, z’]] Shape: [[None, None, 3], [None, None, None, 3]] Name: manifold
——conversion	Attribute	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. Data Type: float32 Required: False Default Value: 1.0 Name: conversion
——unit	Attribute	Base unit of measurement for working with the data. The default value is ‘meters’. Data Type: text Required: False Default Value: meters Name: unit
—origin_coords	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [[‘x, y’], [‘x, y, z’]] Shape: [[2], [3]] Name: origin_coords
——unit	Attribute	Measurement units for origin_coords. The default value is ‘meters’. Data Type: text Required: False Default Value: meters Name: unit
—grid_spacing	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [[‘x, y’], [‘x, y, z’]] Shape: [[2], [3]] Name: grid_spacing
——unit	Attribute	Measurement units for grid_spacing. The default value is ‘meters’. Data Type: text Required: False Default Value: meters Name: unit
—reference_frame	Dataset	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: 0 or 1 Data Type: text Name: reference_frame
—device	Link	Link to the Device object that was used to record from this electrode. Target Type Device Name: device

Table 2.111 Groups contained in <ImagingPlane>

Id	Type	Description
<ImagingPlane>	Group	Top level Group for <ImagingPlane> Neurodata Type: ImagingPlane Extends: NWBContainer
—device	Link	Link to the Device object that was used to record from this electrode. Target Type Device Name: device
—<OpticalChannel>	Group	An optical channel used to record from an imaging plane. Extends: OpticalChannel Quantity: 1 or more

2.12.8.1. Groups: <OpticalChannel>

An optical channel used to record from an imaging plane.

• Extends: OpticalChannel

• Quantity: 1 or more

2.12.9. OpticalChannel

Overview: An optical channel used to record from an imaging plane.

OpticalChannel extends NWBContainer and includes all elements of NWBContainer with the following additions or changes.

• Extends: NWBContainer

• Primitive Type: Group

• Inherits from: NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.9

Table 2.112 Datasets, Links, and Attributes contained in <OpticalChannel>

Id	Type	Description
<OpticalChannel>	Group	Top level Group for <OpticalChannel> Neurodata Type: OpticalChannel Extends: NWBContainer
—description	Dataset	Description or other notes about the channel. Data Type: text Name: description
—emission_lambda	Dataset	Emission wavelength for channel, in nm. Data Type: float32 Name: emission_lambda

2.12.10. MotionCorrection

Overview: 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).

MotionCorrection extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: MotionCorrection

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.10

Table 2.113 Groups contained in <MotionCorrection>

Id	Type	Description
<MotionCorrection>	Group	Top level Group for <MotionCorrection> Neurodata Type: MotionCorrection Extends: NWBDataInterface Default Name: MotionCorrection
—<CorrectedImageStack>	Group	Results from motion correction of an image stack. Extends: CorrectedImageStack Quantity: 1 or more

2.12.10.1. Groups: <CorrectedImageStack>

Results from motion correction of an image stack.

• Extends: CorrectedImageStack

• Quantity: 1 or more

2.12.11. CorrectedImageStack

Overview: Results from motion correction of an image stack.

CorrectedImageStack extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.ophys.yaml

• Source Specification: see Section 3.13.11

Table 2.114 Datasets, Links, and Attributes contained in <CorrectedImageStack>

Id	Type	Description
<CorrectedImageStack>	Group	Top level Group for <CorrectedImageStack> Neurodata Type: CorrectedImageStack Extends: NWBDataInterface
—original	Link	Link to ImageSeries object that is being registered. Target Type ImageSeries Name: original

Table 2.115 Groups contained in <CorrectedImageStack>

Id	Type	Description
<CorrectedImageStack>	Group	Top level Group for <CorrectedImageStack> Neurodata Type: CorrectedImageStack Extends: NWBDataInterface
—original	Link	Link to ImageSeries object that is being registered. Target Type ImageSeries Name: original
—corrected	Group	Image stack with frames shifted to the common coordinates. Extends: ImageSeries Name: corrected
—xy_translation	Group	Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image. Extends: TimeSeries Name: xy_translation

2.12.11.1. Groups: corrected

Image stack with frames shifted to the common coordinates.

• Extends: ImageSeries

• Name: corrected

2.12.11.2. Groups: xy_translation

Stores the x,y delta necessary to align each frame to the common coordinates, for example, to align each frame to a reference image.

• Extends: TimeSeries

• Name: xy_translation

2.13. Retinotopy

This source module contains neurodata_type for retinotopy data.

2.13.1. ImagingRetinotopy

Overview: DEPRECATED. 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).

ImagingRetinotopy extends NWBDataInterface and includes all elements of NWBDataInterface with the following additions or changes.

• Extends: NWBDataInterface

• Primitive Type: Group

• Default Name: ImagingRetinotopy

• Inherits from: NWBDataInterface, NWBContainer, Container

• Source filename: nwb.retinotopy.yaml

• Source Specification: see Section 3.14.1

Table 2.116 Datasets, Links, and Attributes contained in <ImagingRetinotopy>

Id	Type	Description
<ImagingRetinotopy>	Group	Top level Group for <ImagingRetinotopy> Neurodata Type: ImagingRetinotopy Extends: NWBDataInterface Default Name: ImagingRetinotopy
—axis_1_phase_map	Dataset	Phase response to stimulus on the first measured axis. Data Type: float32 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: axis_1_phase_map
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——unit	Attribute	Unit that axis data is stored in (e.g., degrees). Data Type: text Name: unit
—axis_1_power_map	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: axis_1_power_map
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——unit	Attribute	Unit that axis data is stored in (e.g., degrees). Data Type: text Name: unit
—axis_2_phase_map	Dataset	Phase response to stimulus on the second measured axis. Data Type: float32 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: axis_2_phase_map
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——unit	Attribute	Unit that axis data is stored in (e.g., degrees). Data Type: text Name: unit
—axis_2_power_map	Dataset	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: 0 or 1 Data Type: float32 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: axis_2_power_map
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——unit	Attribute	Unit that axis data is stored in (e.g., degrees). Data Type: text Name: unit
—axis_descriptions	Dataset	Two-element array describing the contents of the two response axis fields. Description should be something like [‘altitude’, ‘azimuth’] or ‘[‘radius’, ‘theta’]. Data Type: text Dimensions: [‘axis_1, axis_2’] Shape: [2] Name: axis_descriptions
—focal_depth_image	Dataset	Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns]. Quantity: 0 or 1 Data Type: uint16 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: focal_depth_image
——bits_per_pixel	Attribute	Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value. Data Type: int32 Name: bits_per_pixel
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——focal_depth	Attribute	Focal depth offset, in meters. Data Type: float32 Name: focal_depth
——format	Attribute	Format of image. Right now only ‘raw’ is supported. Data Type: text Name: format
—sign_map	Dataset	Sine of the angle between the direction of the gradient in axis_1 and axis_2. Quantity: 0 or 1 Data Type: float32 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: sign_map
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
—vasculature_image	Dataset	Gray-scale anatomical image of cortical surface. Array structure: [rows][columns] Data Type: uint16 Dimensions: [‘num_rows’, ‘num_cols’] Shape: [None, None] Name: vasculature_image
——bits_per_pixel	Attribute	Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value Data Type: int32 Name: bits_per_pixel
——dimension	Attribute	Number of rows and columns in the image. Additional Information: row, column representation is equivalent to height, width. Data Type: int32 Dimensions: [‘num_rows, num_cols’] Shape: [2] Name: dimension
——field_of_view	Attribute	Size of viewing area, in meters. Data Type: float32 Dimensions: [‘height, width’] Shape: [2] Name: field_of_view
——format	Attribute	Format of image. Right now only ‘raw’ is supported. Data Type: text Name: format

3. Schema Sources

Source Specification: see Section 3.1

3.1. Namespace – NWB core

Description: see Section 1.1

YAML Specification:

name: core
doc: NWB namespace
schema:
- namespace: hdmf-common
- doc: This source module contains base data types used throughout the NWB 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 event data.
  source: nwb.event.yaml
  title: Events
- doc: This source module contains neurodata_types for image data.
  source: nwb.image.yaml
  title: Image data
- doc: Main NWB file specification.
  source: nwb.file.yaml
  title: NWB 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
full_name: NWB core
version: 2.10.0-alpha
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

3.2. Base data types

This source module contains base data types used throughout the NWB data format.

3.2.1. NWBData

Extends: Data

Description: see Section 2.1.1

YAML Specification:

neurodata_type_def: NWBData
neurodata_type_inc: Data
doc: An abstract data type for a dataset.

3.2.2. TimeSeriesReferenceVectorData

Extends: VectorData

Description: see Section 2.1.2

YAML Specification:

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.

3.2.3. BaseImage

Extends: NWBData

Description: see Section 2.1.3

YAML Specification:

neurodata_type_def: BaseImage
neurodata_type_inc: NWBData
doc: An abstract base type for image data. Parent type for Image and
  ExternalImage types.
attributes:
- name: description
  dtype: text
  doc: Description of the image.
  required: false

3.2.4. Image

Extends: BaseImage

Description: see Section 2.1.4

YAML Specification:

neurodata_type_def: Image
neurodata_type_inc: BaseImage
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: A type for storing image data directly. 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

3.2.5. ExternalImage

Extends: BaseImage

Description: see Section 2.1.5

YAML Specification:

neurodata_type_def: ExternalImage
neurodata_type_inc: BaseImage
dtype: text
doc: A type for referencing an external image file. The single file path or URI
  to the external image file should be stored in the dataset. This type should
  NOT be used if the image is stored in another NWB file and that file is linked
  to this file.
attributes:
- name: image_mode
  dtype: text
  doc: Image mode (color mode) of the image, e.g., "RGB", "RGBA", "grayscale",
    and "LA".
  required: false
- name: image_format
  dtype: text
  doc: Common name of the image file format. Only widely readable, open file
    formats are allowed. Allowed values are "PNG", "JPEG", and "GIF".

3.2.6. ImageReferences

Extends: NWBData

Description: see Section 2.1.6

YAML Specification:

neurodata_type_def: ImageReferences
neurodata_type_inc: NWBData
dtype:
  target_type: BaseImage
  reftype: object
dims:
- num_images
shape:
- null
doc: Ordered dataset of references to BaseImage (e.g., Image or ExternalImage)
  objects.

3.2.7. NWBContainer

Extends: Container

Description: see Section 2.1.7

YAML Specification:

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.

3.2.8. NWBDataInterface

Extends: NWBContainer

Description: see Section 2.1.8

YAML Specification:

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.

3.2.9. TimeSeries

Extends: NWBDataInterface

Description: see Section 2.1.9

YAML Specification:

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. For storing
      instantaneous event information, it is recommended to use an EventsTable
      instead of a TimeSeries with continuity set to "instantaneous".
    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: '?'

3.2.10. ProcessingModule

Extends: NWBContainer

Description: see Section 2.1.10

YAML Specification:

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: '*'

3.2.11. Images

Extends: NWBDataInterface

Description: see Section 2.1.11

YAML Specification:

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: BaseImage
  doc: Images stored in this collection.
  quantity: +
- name: order_of_images
  neurodata_type_inc: ImageReferences
  doc: Ordered dataset of references to BaseImage objects stored in the parent
    group. Each 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: '?'

3.3. Devices

This source module contains neurodata_types for device data.

3.3.1. Device

Extends: NWBContainer

Description: see Section 2.2.1

YAML Specification:

neurodata_type_def: Device
neurodata_type_inc: NWBContainer
doc: Metadata about a specific instance of a data acquisition device, e.g.,
  recording system, electrode, microscope. Link to a DeviceModel.model to
  represent information about the model of the device.
attributes:
- name: description
  dtype: text
  doc: Description of the device as free-form text. If there is any
    software/firmware associated with the device, the names and versions of
    those can be added to NWBFile.was_generated_by.
  required: false
- name: manufacturer
  dtype: text
  doc: DEPRECATED. The name of the manufacturer of the device, e.g., Imec,
    Plexon, Thorlabs. Instead of using this field, store the value in
    DeviceModel.manufacturer and link to that DeviceModel from this Device.
  required: false
- name: model_number
  dtype: text
  doc: DEPRECATED. The model number (or part/product number) of the device,
    e.g., PRB_1_4_0480_1, PLX-VP-32-15SE(75)-(260-80)(460-10)-300-(1)CON/32m-V,
    BERGAMO. Instead of using this field, store the value in
    DeviceModel.model_number and link to that DeviceModel from this Device.
  required: false
- name: model_name
  dtype: text
  doc: DEPRECATED. The model name of the device, e.g., Neuropixels 1.0, V-Probe,
    Bergamo III. Instead of using this field, create and add a new DeviceModel
    named the model name and link to that DeviceModel from this Device.
  required: false
- name: serial_number
  dtype: text
  doc: The serial number of the device.
  required: false
links:
- name: model
  target_type: DeviceModel
  doc: The model of the device.
  quantity: '?'

3.3.2. DeviceModel

Extends: NWBContainer

Description: see Section 2.2.2

YAML Specification:

neurodata_type_def: DeviceModel
neurodata_type_inc: NWBContainer
doc: Model properties of a data acquisition device, e.g., recording system,
  electrode, microscope. This should be extended for specific types of device
  models to include additional attributes specific to each type. The name of the
  DeviceModel should be the most common representation of the model name, e.g.,
  Neuropixels 1.0, V-Probe, Bergamo III.
attributes:
- name: manufacturer
  dtype: text
  doc: The name of the manufacturer of the device model, e.g., Imec, Plexon,
    Thorlabs.
- name: model_number
  dtype: text
  doc: The model number (or part/product number) of the device, e.g.,
    PRB_1_4_0480_1, PLX-VP-32-15SE(75)-(260-80)(460-10)-300-(1)CON/32m-V,
    BERGAMO.
  required: false
- name: description
  dtype: text
  doc: Description of the device model as free-form text.
  required: false

3.4. Epochs

This source module contains neurodata_types for epoch data.

3.4.1. TimeIntervals

Extends: DynamicTable

Description: see Section 2.3.1

YAML Specification:

neurodata_type_def: TimeIntervals
neurodata_type_inc: DynamicTable
doc: A column-based table to store information about time intervals, one
  interval per row. Use `TimeIntervals` when each row naturally has a start and
  stop time and represents a contiguous period of time, often encompassing an
  experimental condition. Rows can optionally reference `TimeSeries` data via
  the `timeseries` column. Examples include trials, epochs, behavioral states
  (e.g., "running", "resting"), and invalid recording windows.
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: '?'

3.5. Events

This source module contains neurodata_types for event data.

3.5.1. TimestampVectorData

Extends: VectorData

Description: see Section 2.4.1

YAML Specification:

neurodata_type_def: TimestampVectorData
neurodata_type_inc: VectorData
dtype: float
dims:
- num_times
shape:
- null
doc: A 1-dimensional VectorData that stores timestamps in seconds from the
  session start time. Timestamp are not required to be sorted in time.
attributes:
- name: unit
  dtype: text
  value: seconds
  doc: The unit of measurement for the timestamps, fixed to 'seconds'.
- name: resolution
  dtype: float
  doc: The temporal resolution of the timestamps, in seconds. This is typically
    the sampling period (1 / sampling_rate), also known as the clock period, of
    the data acquisition system from which the timestamps were recorded or
    derived.
  required: false

3.5.2. DurationVectorData

Extends: VectorData

Description: see Section 2.4.2

YAML Specification:

neurodata_type_def: DurationVectorData
neurodata_type_inc: VectorData
dtype: float
dims:
- num_times
shape:
- null
doc: A 1-dimensional VectorData that stores durations in seconds.
attributes:
- name: unit
  dtype: text
  value: seconds
  doc: The unit of measurement for the durations, fixed to 'seconds'.
- name: resolution
  dtype: float
  doc: The temporal resolution of the durations, in seconds. This is typically
    the sampling period (1 / sampling_rate), also known as the clock period, of
    the data acquisition system from which the durations were recorded or
    derived.
  required: false

3.5.3. EventsTable

Extends: DynamicTable

Description: see Section 2.4.3

YAML Specification:

neurodata_type_def: EventsTable
neurodata_type_inc: DynamicTable
doc: A column-based table to store information about events, one event per row.
  Use `EventsTable` when each row is anchored at a single timestamp and duration
  is absent, optional, or mixed across rows. Additional columns may be added to
  store metadata about each event, such as the duration of the event. Examples
  include TTL pulses, licks, rewards, stimulus onsets, and detected ripples.
attributes:
- name: description
  dtype: text
  doc: A description of the events stored in the table, including information
    about how the event times were computed, especially if the times are the
    result of processing or filtering raw data. For example, if the experimenter
    is encoding different types of events using a strobed or N-bit encoding,
    then the description should describe which channels were used and how the
    event time is computed, e.g., as the rise time of the first bit.
datasets:
- name: timestamp
  neurodata_type_inc: TimestampVectorData
  doc: Column containing the time that each event occurred, in seconds, from the
    session start time.
- name: duration
  neurodata_type_inc: DurationVectorData
  doc: Optional column containing the duration of each event, in seconds. A
    value of NaN can be used for events without a duration or with a duration
    that is not yet specified.
  quantity: '?'
- name: annotation
  neurodata_type_inc: VectorData
  dtype: text
  dims:
  - num_times
  shape:
  - null
  doc: Column containing user annotations about events.
  quantity: '?'

3.6. Image data

This source module contains neurodata_types for image data.

3.6.1. GrayscaleImage

Extends: Image

Description: see Section 2.5.1

YAML Specification:

neurodata_type_def: GrayscaleImage
neurodata_type_inc: Image
dtype: numeric
dims:
- x
- y
shape:
- null
- null
doc: A grayscale image.

3.6.2. RGBImage

Extends: Image

Description: see Section 2.5.2

YAML Specification:

neurodata_type_def: RGBImage
neurodata_type_inc: Image
dtype: numeric
dims:
- x
- y
- r, g, b
shape:
- null
- null
- 3
doc: A color image.

3.6.3. RGBAImage

Extends: Image

Description: see Section 2.5.3

YAML Specification:

neurodata_type_def: RGBAImage
neurodata_type_inc: Image
dtype: numeric
dims:
- x
- y
- r, g, b, a
shape:
- null
- null
- 4
doc: A color image with transparency.

3.6.4. ImageSeries

Extends: TimeSeries

Description: see Section 2.5.4

YAML Specification:

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 facilitate 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: num_samples
  dtype: uint32
  doc: Total number of frames across all external files. This is required when
    format='external' and timing is described using starting_time and rate,
    since data is empty and its first dimension cannot be used to determine the
    number of frames. When timestamps is provided, len(timestamps) already
    serves this purpose.
  quantity: '?'
- 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: '?'

3.6.5. ImageMaskSeries

Extends: ImageSeries

Description: see Section 2.5.5

YAML Specification:

neurodata_type_def: ImageMaskSeries
neurodata_type_inc: ImageSeries
doc: DEPRECATED. 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.

3.6.6. OpticalSeries

Extends: ImageSeries

Description: see Section 2.5.6

YAML Specification:

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: '?'

3.6.7. IndexSeries

Extends: TimeSeries

Description: see Section 2.5.7

YAML Specification:

neurodata_type_def: IndexSeries
neurodata_type_inc: TimeSeries
doc: Stores indices that reference images defined in other containers. The
  primary purpose of the IndexSeries is to allow images stored in an Images
  container to be referenced in a specific sequence through the 'indexed_images'
  link. This approach avoids duplicating image data when the same image needs to
  be presented multiple times or when images need to be shown in a different
  order than they are stored. Since images in an Images container do not have an
  inherent order, the Images container needs to include an 'order_of_images'
  dataset (of type ImageReferences) when being referenced by an IndexSeries.
  This dataset establishes the ordered sequence that the indices in IndexSeries
  refer to. The 'data' field stores the index into this ordered sequence, and
  the 'timestamps' array indicates the precise presentation time of each indexed
  image during an experiment. This can be used for displaying individual images
  or creating movie segments by referencing a sequence of images with the
  appropriate timestamps. While IndexSeries can also reference frames from an
  ImageSeries through the 'indexed_timeseries' link, this usage is discouraged
  and will be deprecated in favor of using Images containers with
  'order_of_images'.
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: '?'

3.7. NWB file

Main NWB file specification.

3.7.1. ScratchData

Extends: NWBData

Description: see Section 2.6.1

YAML Specification:

neurodata_type_def: ScratchData
neurodata_type_inc: NWBData
doc: Any one-off datasets
attributes:
- name: notes
  dtype: text
  doc: Any notes the user has about the dataset being stored

3.7.2. NWBFile

Extends: NWBContainer

Description: see Section 2.6.2

YAML Specification:

neurodata_type_def: NWBFile
neurodata_type_inc: NWBContainer
name: root
doc: An NWB file storing cellular-based neurophysiology data from a single
  experimental session.
attributes:
- name: nwb_version
  dtype: text
  value: 2.10.0-alpha
  doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be
    the name of the format with trailing major, minor and patch numbers.
datasets:
- name: file_create_date
  dtype: isodatetime
  dims:
  - num_modifications
  shape:
  - null
  doc: 'A record of the date the file was created and of subsequent modifications.
    The date is stored in UTC with local timezone offset as ISO 8601 extended formatted
    strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no
    timezone offset. Date accuracy is up to milliseconds. The file can be created
    after the experiment was run, so this may differ from the experiment start time.
    Each modification to the nwb file adds a new entry to the array.'
- name: identifier
  dtype: text
  doc: A unique text identifier for the file. For example, concatenated lab
    name, file creation date/time and experimentalist, or a hash of these and/or
    other values. The goal is that the string should be unique to all other
    files.
- name: session_description
  dtype: text
  doc: A description of the experimental session and data in the file.
- name: session_start_time
  dtype: isodatetime
  doc: 'Date and time of the experiment/session start. The date is stored in UTC with
    local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00.
    Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to
    milliseconds.'
- name: timestamps_reference_time
  dtype: isodatetime
  doc: 'Date and time corresponding to time zero of all timestamps. The date is stored
    in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00.
    Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to
    milliseconds. All times stored in the file use this time as reference (i.e., time
    zero).'
groups:
- name: acquisition
  doc: Data streams recorded from the system, including ephys, ophys, tracking,
    etc. This group should be read-only after the experiment is completed and
    timestamps are corrected to a common timebase. The data stored here may be
    links to raw data stored in external NWB files. This will allow keeping
    bulky raw data out of the file while preserving the option of keeping
    some/all in the file. Acquired data includes tracking and experimental data
    streams (i.e., everything measured from the system). If bulky data is stored
    in the /acquisition group, the data can exist in a separate NWB file that is
    linked to by the file being used for processing and analysis.
  groups:
  - neurodata_type_inc: NWBDataInterface
    doc: Acquired, raw data.
    quantity: '*'
  - neurodata_type_inc: DynamicTable
    doc: Tabular data that is relevant to acquisition
    quantity: '*'
- name: analysis
  doc: Lab-specific and custom scientific analysis of data. There is no defined
    format for the content of this group - the format is up to the individual
    user/lab. To facilitate sharing analysis data between labs, the contents
    here should be stored in standard types (e.g., neurodata_types) and
    appropriately documented. The file can store lab-specific and custom data
    analysis without restriction on its form or schema, reducing data formatting
    restrictions on end users. Such data should be placed in the analysis group.
    The analysis data should be documented so that it could be shared with other
    labs.
  groups:
  - neurodata_type_inc: NWBContainer
    doc: Custom analysis results.
    quantity: '*'
  - neurodata_type_inc: DynamicTable
    doc: Tabular data that is relevant to data stored in analysis
    quantity: '*'
- name: scratch
  doc: A place to store one-off analysis results. Data placed here is not
    intended for sharing. By placing data here, users acknowledge that there is
    no guarantee that their data meets any standard.
  quantity: '?'
  datasets:
  - neurodata_type_inc: ScratchData
    doc: Any one-off datasets
    quantity: '*'
  groups:
  - neurodata_type_inc: NWBContainer
    doc: Any one-off containers
    quantity: '*'
  - neurodata_type_inc: DynamicTable
    doc: Any one-off tables
    quantity: '*'
- name: processing
  doc: The home for ProcessingModules. These modules perform intermediate
    analysis of data that is necessary to perform before scientific analysis.
    Examples include spike clustering, extracting position from tracking data,
    stitching together image slices. ProcessingModules can be large and express
    many data sets from relatively complex analysis (e.g., spike detection and
    clustering) or small, representing extraction of position information from
    tracking video, or even binary lick/no-lick decisions. Common software tools
    (e.g., klustakwik, MClust) are expected to read/write data here.
    'Processing' refers to intermediate analysis of the acquired data to make it
    more amenable to scientific analysis.
  groups:
  - neurodata_type_inc: ProcessingModule
    doc: Intermediate analysis of acquired data.
    quantity: '*'
- name: stimulus
  doc: Data pushed into the system (eg, video stimulus, sound, voltage, etc) and
    secondary representations of that data (eg, measurements of something used
    as a stimulus). This group should be made read-only after experiment
    complete and timestamps are corrected to common timebase. Stores both
    presented stimuli and stimulus templates, the latter in case the same
    stimulus is presented multiple times, or is pulled from an external stimulus
    library. Stimuli are here defined as any signal that is pushed into the
    system as part of the experiment (eg, sound, video, voltage, etc). Many
    different experiments can use the same stimuli, and stimuli can be reused
    during an experiment. The stimulus group is organized so that one version of
    template stimuli can be stored and these be used multiple times. These
    templates can exist in the present file or can be linked to a remote library
    file.
  groups:
  - name: presentation
    doc: Stimuli presented during the experiment.
    groups:
    - neurodata_type_inc: TimeSeries
      doc: TimeSeries objects containing data of presented stimuli.
      quantity: '*'
    - neurodata_type_inc: NWBDataInterface
      doc: Generic NWB data interfaces, usually from an extension, containing
        data of presented stimuli.
      quantity: '*'
    - neurodata_type_inc: DynamicTable
      doc: DynamicTable objects containing data of presented stimuli.
      quantity: '*'
  - name: templates
    doc: Template stimuli. Timestamps in templates are based on stimulus design
      and are relative to the beginning of the stimulus. When templates are
      used, the stimulus instances must convert presentation times to the
      experiment`s time reference frame.
    groups:
    - neurodata_type_inc: TimeSeries
      doc: TimeSeries objects containing template data of presented stimuli.
      quantity: '*'
    - neurodata_type_inc: Images
      doc: Images objects containing images of presented stimuli.
      quantity: '*'
- name: general
  doc: Experimental metadata, including protocol, notes and description of
    hardware device(s).  The metadata stored in this section should be used to
    describe the experiment. Metadata necessary for interpreting the data is
    stored with the data. General experimental metadata, including animal
    strain, experimental protocols, experimenter, devices, etc, are stored under
    'general'. Core metadata (e.g., that required to interpret data fields) is
    stored with the data itself, and implicitly defined by the file
    specification (e.g., time is in seconds). The strategy used here for storing
    non-core metadata is to use free-form text fields, such as would appear in
    sentences or paragraphs from a Methods section. Metadata fields are text to
    enable them to be more general, for example to represent ranges instead of
    numerical values. Machine-readable metadata is stored as attributes to these
    free-form datasets. All entries in the below table are to be included when
    data is present. Unused groups (e.g., intracellular_ephys in an
    optophysiology experiment) should not be created unless there is data to
    store within them.
  datasets:
  - name: data_collection
    dtype: text
    doc: Notes about data collection and analysis.
    quantity: '?'
  - name: experiment_description
    dtype: text
    doc: General description of the experiment.
    quantity: '?'
  - name: experimenter
    dtype: text
    dims:
    - num_experimenters
    shape:
    - null
    doc: Name of person(s) who performed the experiment. Can also specify roles
      of different people involved.
    quantity: '?'
  - name: institution
    dtype: text
    doc: Institution(s) where experiment was performed.
    quantity: '?'
  - name: keywords
    dtype: text
    dims:
    - num_keywords
    shape:
    - null
    doc: Terms to search over.
    quantity: '?'
  - name: lab
    dtype: text
    doc: Laboratory where experiment was performed.
    quantity: '?'
  - name: notes
    dtype: text
    doc: Notes about the experiment.
    quantity: '?'
  - name: pharmacology
    dtype: text
    doc: Description of drugs used, including how and when they were
      administered. Anesthesia(s), painkiller(s), etc., plus dosage,
      concentration, etc.
    quantity: '?'
  - name: protocol
    dtype: text
    doc: Experimental protocol, if applicable. e.g., include IACUC protocol
      number.
    quantity: '?'
  - name: related_publications
    dtype: text
    dims:
    - num_publications
    shape:
    - null
    doc: Publication information. PMID, DOI, URL, etc.
    quantity: '?'
  - name: session_id
    dtype: text
    doc: Lab-specific ID for the session.
    quantity: '?'
  - name: slices
    dtype: text
    doc: Description of slices, including information about preparation
      thickness, orientation, temperature, and bath solution.
    quantity: '?'
  - name: source_script
    dtype: text
    doc: Script file or link to public source code used to create this NWB file.
    quantity: '?'
    attributes:
    - name: file_name
      dtype: text
      doc: Name of script file.
  - name: was_generated_by
    dtype: text
    dims:
    - num_sources
    - name, version
    shape:
    - null
    - 2
    doc: Name and version of software package(s) used to generate data contained
      in this NWB File. For each software package or library, include the name
      of the software as the first value and the version as the second value.
    quantity: '?'
  - name: stimulus
    dtype: text
    doc: Notes about stimuli, such as how and where they were presented.
    quantity: '?'
  - name: surgery
    dtype: text
    doc: Narrative description about surgery/surgeries, including date(s) and
      who performed surgery.
    quantity: '?'
  - name: virus
    dtype: text
    doc: Information about virus(es) used in experiments, including virus ID,
      source, date made, injection location, volume, etc.
    quantity: '?'
  groups:
  - name: external_resources
    neurodata_type_inc: HERD
    doc: This is the HERD structure for this specific NWBFile, storing the
      mapped external resources.
    quantity: '?'
  - neurodata_type_inc: LabMetaData
    doc: Place-holder than can be extended so that lab-specific meta-data can be
      placed in /general.
    quantity: '*'
  - name: devices
    doc: Description of hardware devices used during experiment, e.g., monitors,
      ADC boards, microscopes, etc.
    quantity: '?'
    groups:
    - neurodata_type_inc: Device
      doc: Data acquisition devices.
      quantity: '*'
    - name: models
      doc: Collection of data acquisition device models.
      quantity: '?'
      groups:
      - neurodata_type_inc: DeviceModel
        doc: Data acquisition device models.
        quantity: '*'
  - name: subject
    neurodata_type_inc: Subject
    doc: Information about the animal or person from which the data was
      measured.
    quantity: '?'
  - name: extracellular_ephys
    doc: Metadata related to extracellular electrophysiology.
    quantity: '?'
    groups:
    - neurodata_type_inc: ElectrodeGroup
      doc: Physical group of electrodes.
      quantity: '*'
    - name: electrodes
      neurodata_type_inc: ElectrodesTable
      doc: A table of all electrodes (i.e. channels) used for recording. Changed
        in NWB 2.9.0 to use the newly added ElectrodesTable neurodata type
        instead of a DynamicTable with added columns.
      quantity: '?'
  - name: intracellular_ephys
    doc: Metadata related to intracellular electrophysiology.
    quantity: '?'
    datasets:
    - name: filtering
      dtype: text
      doc: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description
        of filtering used. Includes filtering type and parameters, frequency fall-off,
        etc. If this changes between TimeSeries, filter description should be stored
        as a text attribute for each TimeSeries.'
      quantity: '?'
    groups:
    - neurodata_type_inc: IntracellularElectrode
      doc: An intracellular electrode.
      quantity: '*'
    - name: sweep_table
      neurodata_type_inc: SweepTable
      doc: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
        is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
        tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
        tables provide enhanced support for experiment metadata.'
      quantity: '?'
    - name: intracellular_recordings
      neurodata_type_inc: IntracellularRecordingsTable
      doc: A table to group together a stimulus and response from a single
        electrode and a single simultaneous recording. Each row in the table
        represents a single recording consisting typically of a stimulus and a
        corresponding response. In some cases, however, only a stimulus or a
        response are recorded as as part of an experiment. In this case both,
        the stimulus and response will point to the same TimeSeries while the
        idx_start and count of the invalid column will be set to -1, thus,
        indicating that no values have been recorded for the stimulus or
        response, respectively. Note, a recording MUST contain at least a
        stimulus or a response. Typically the stimulus and response are
        PatchClampSeries. However, the use of AD/DA channels that are not
        associated to an electrode is also common in intracellular
        electrophysiology, in which case other TimeSeries may be used.
      quantity: '?'
    - name: simultaneous_recordings
      neurodata_type_inc: SimultaneousRecordingsTable
      doc: A table for grouping different intracellular recordings from the
        IntracellularRecordingsTable table together that were recorded
        simultaneously from different electrodes
      quantity: '?'
    - name: sequential_recordings
      neurodata_type_inc: SequentialRecordingsTable
      doc: A table for grouping different sequential recordings from the
        SimultaneousRecordingsTable table together. This is typically used to
        group together sequential recordings where the a sequence of stimuli of
        the same type with varying parameters have been presented in a sequence.
      quantity: '?'
    - name: repetitions
      neurodata_type_inc: RepetitionsTable
      doc: A table for grouping different sequential intracellular recordings
        together. With each SequentialRecording typically representing a
        particular type of stimulus, the RepetitionsTable table is typically
        used to group sets of stimuli applied in sequence.
      quantity: '?'
    - name: experimental_conditions
      neurodata_type_inc: ExperimentalConditionsTable
      doc: A table for grouping different intracellular recording repetitions
        together that belong to the same experimental experimental_conditions.
      quantity: '?'
  - name: optogenetics
    doc: Metadata describing optogenetic stimuluation.
    quantity: '?'
    groups:
    - neurodata_type_inc: OptogeneticStimulusSite
      doc: An optogenetic stimulation site.
      quantity: '*'
  - name: optophysiology
    doc: Metadata related to optophysiology.
    quantity: '?'
    groups:
    - neurodata_type_inc: ImagingPlane
      doc: An imaging plane.
      quantity: '*'
- name: intervals
  doc: Experimental intervals, whether that be logically distinct
    sub-experiments having a particular scientific goal, trials (see trials
    subgroup) during an experiment, or epochs (see epochs subgroup) deriving
    from analysis of data.
  quantity: '?'
  groups:
  - name: epochs
    neurodata_type_inc: TimeIntervals
    doc: Time intervals marking coarse-grained experimental phases or
      subdivisions of a recording session, such as baseline, task, rest, or
      sleep stages.
    quantity: '?'
  - name: trials
    neurodata_type_inc: TimeIntervals
    doc: Time intervals corresponding to repeated experimental units with
      consistent structure, such as individual stimulus-response-reward cycles.
    quantity: '?'
  - name: invalid_times
    neurodata_type_inc: TimeIntervals
    doc: Time intervals that should be removed from analysis.
    quantity: '?'
  - neurodata_type_inc: TimeIntervals
    doc: Optional additional table(s) for describing other experimental time
      intervals.
    quantity: '*'
- name: events
  doc: Primary experimental event tables for the session, stored as
    `EventsTable` instances. This location is intended for event data that are
    ready to be used in downstream analysis. It replaces the deprecated
    `BehavioralEvents` placement. Events emitted directly by the acquisition
    system (TTL edges, hardware event channels) belong in `/acquisition/`.
    Events derived by user processing (filtering, detection algorithms,
    annotation with experimental context) belong in a `ProcessingModule` under
    `/processing/`. For periods with required start and stop times, see
    `/intervals/`. For continuous acquired signals or stimulus templates from
    which events may have been derived, see `/acquisition/` or `/stimulus/`. For
    more guidance on choosing between `/events/`, `/acquisition/`,
    `/processing/`, and `/analysis/`, see the schema docs FAQ.
  quantity: '?'
  groups:
  - neurodata_type_inc: EventsTable
    doc: An EventsTable holding a collection of event times of a particular type
      (e.g., licks, rewards, stimulus presentations) along with their per-event
      metadata.
    quantity: '*'
- name: units
  neurodata_type_inc: Units
  doc: Data about sorted spike units.
  quantity: '?'

3.7.3. LabMetaData

Extends: NWBContainer

Description: see Section 2.6.3

YAML Specification:

neurodata_type_def: LabMetaData
neurodata_type_inc: NWBContainer
doc: Lab-specific meta-data.

3.7.4. Subject

Extends: NWBContainer

Description: see Section 2.6.4

YAML Specification:

neurodata_type_def: Subject
neurodata_type_inc: NWBContainer
doc: Information about the animal or person from which the data was measured.
datasets:
- name: age
  dtype: text
  doc: Age of subject. Can be supplied instead of 'date_of_birth'. The ISO 8601
    Duration format is recommended, e.g., 'P90D' for 90 days old. If the precise
    age is unknown, an age range can be given by '[lower bound]/[upper bound]'
    e.g. 'P10D/P20D' would mean that the age is in between 10 and 20 days. If
    only the lower bound is known, then including only the slash after that
    lower bound can be used to indicate a missing bound. For instance, 'P90Y/'
    would indicate that the age is 90 years or older.
  quantity: '?'
  attributes:
  - name: reference
    dtype: text
    default_value: birth
    doc: Age is with reference to this event. Can be 'birth' or 'gestational'.
      If reference is omitted, 'birth' is implied.
    required: false
- name: date_of_birth
  dtype: isodatetime
  doc: Date of birth of subject. Can be supplied instead of 'age'.
  quantity: '?'
- name: description
  dtype: text
  doc: Description of subject and where subject came from (e.g., breeder, if
    animal).
  quantity: '?'
- name: genotype
  dtype: text
  doc: Genetic strain. If absent, assume Wild Type (WT).
  quantity: '?'
- name: sex
  dtype: text
  doc: Gender of subject.
  quantity: '?'
- name: species
  dtype: text
  doc: Species of subject.
  quantity: '?'
- name: strain
  dtype: text
  doc: Strain of subject.
  quantity: '?'
- name: subject_id
  dtype: text
  doc: ID of animal/person used/participating in experiment (lab convention).
  quantity: '?'
- name: weight
  dtype: text
  doc: Weight at time of experiment, at time of surgery and at other important
    times.
  quantity: '?'

3.8. Miscellaneous neurodata_types.

Miscellaneous types.

3.8.1. AbstractFeatureSeries

Extends: TimeSeries

Description: see Section 2.7.1

YAML Specification:

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.

3.8.2. AnnotationSeries

Extends: TimeSeries

Description: see Section 2.7.2

YAML Specification:

neurodata_type_def: AnnotationSeries
neurodata_type_inc: TimeSeries
doc: DEPRECATED. Use an EventsTable instead. 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'.

3.8.3. IntervalSeries

Extends: TimeSeries

Description: see Section 2.7.3

YAML Specification:

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'.

3.8.4. FrequencyBandsTable

Extends: DynamicTable

Description: see Section 2.7.4

YAML Specification:

neurodata_type_def: FrequencyBandsTable
neurodata_type_inc: DynamicTable
doc: Table for describing the bands that DecompositionSeries 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.
  quantity: '?'
- name: band_stdev
  neurodata_type_inc: VectorData
  dtype: float32
  dims:
  - num_bands
  shape:
  - null
  doc: The standard deviation of Gaussian filters, in Hz.
  quantity: '?'

3.8.5. DecompositionSeries

Extends: TimeSeries

Description: see Section 2.7.5

YAML Specification:

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'.
    required: false
- 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: FrequencyBandsTable
  doc: Table for describing the bands that this series was generated from.
  quantity: '?'
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: '?'

3.8.6. Units

Extends: DynamicTable

Description: see Section 2.7.6

YAML Specification:

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, relative to the session reference
    time (i.e. session_start_time or, if defined, timestamps_reference_time).
    Times should be stored in ascending order.
  quantity: '?'
  attributes:
  - name: resolution
    dtype: float64
    doc: The temporal resolution of the spike times, in seconds. This is
      typically the sampling period (1/sampling_rate) of the acquisition data
      from which spikes were extracted. If the acquisition data was downsampled
      before spike sorting, the resolution should be based on the downsampled
      sampling rate (lower sampling rate, larger resolution value). If
      interpolation was applied during spike sorting, then spike times may fall
      between samples of the acquisition data, so the resolution should be the
      interpolation step size (higher sampling rate, smaller resolution value).
    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, in seconds, relative to the session
    reference time (i.e. session_start_time or, if defined,
    timestamps_reference_time). Intervals should be in ascending order and
    non-overlapping.
  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'.
- 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'.
- 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
    the same as the order of 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'.
- 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: '?'

3.9. Behavior

This source module contains neurodata_types for behavior data.

3.9.1. SpatialSeries

Extends: TimeSeries

Description: see Section 2.8.1

YAML Specification:

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: '?'

3.9.2. BehavioralEpochs

Extends: NWBDataInterface

Description: see Section 2.8.2

YAML Specification:

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: +

3.9.3. BehavioralEvents

Extends: NWBDataInterface

Description: see Section 2.8.3

YAML Specification:

neurodata_type_def: BehavioralEvents
neurodata_type_inc: NWBDataInterface
default_name: BehavioralEvents
doc: DEPRECATED. Use an EventsTable instead. TimeSeries for storing behavioral
  events. See description of BehavioralEpochs for more details.
groups:
- neurodata_type_inc: TimeSeries
  doc: TimeSeries object containing behavioral events.
  quantity: +

3.9.4. BehavioralTimeSeries

Extends: NWBDataInterface

Description: see Section 2.8.4

YAML Specification:

neurodata_type_def: BehavioralTimeSeries
neurodata_type_inc: NWBDataInterface
default_name: BehavioralTimeSeries
doc: TimeSeries for storing behavioral time series data. See description of
  BehavioralEpochs for more details.
groups:
- neurodata_type_inc: TimeSeries
  doc: TimeSeries object containing continuous behavioral data.
  quantity: +

3.9.5. PupilTracking

Extends: NWBDataInterface

Description: see Section 2.8.5

YAML Specification:

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: +

3.9.6. EyeTracking

Extends: NWBDataInterface

Description: see Section 2.8.6

YAML Specification:

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: +

3.9.7. CompassDirection

Extends: NWBDataInterface

Description: see Section 2.8.7

YAML Specification:

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: +

3.9.8. Position

Extends: NWBDataInterface

Description: see Section 2.8.8

YAML Specification:

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: +

3.10. Extracellular electrophysiology

This source module contains neurodata_types for extracellular electrophysiology data.

3.10.1. ElectricalSeries

Extends: TimeSeries

Description: see Section 2.9.1

YAML Specification:

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.

3.10.2. SpikeEventSeries

Extends: ElectricalSeries

Description: see Section 2.9.2

YAML Specification:

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 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'.

3.10.3. FeatureExtraction

Extends: NWBDataInterface

Description: see Section 2.9.3

YAML Specification:

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.

3.10.4. EventDetection

Extends: NWBDataInterface

Description: see Section 2.9.4

YAML Specification:

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
  - - num_events
    - time_index, channel_index
  shape:
  - - null
  - - null
    - 2
  doc: Indices (zero-based) into the linked source ElectricalSeries::data array
    corresponding to time of event or time and channel 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: DEPRECATED. Timestamps of events, in seconds.
  quantity: '?'
  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.

3.10.5. EventWaveform

Extends: NWBDataInterface

Description: see Section 2.9.5

YAML Specification:

neurodata_type_def: EventWaveform
neurodata_type_inc: NWBDataInterface
default_name: EventWaveform
doc: DEPRECATED. 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: +

3.10.6. FilteredEphys

Extends: NWBDataInterface

Description: see Section 2.9.6

YAML Specification:

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: +

3.10.7. LFP

Extends: NWBDataInterface

Description: see Section 2.9.7

YAML Specification:

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: +

3.10.8. ElectrodeGroup

Extends: NWBContainer

Description: see Section 2.9.8

YAML Specification:

neurodata_type_def: ElectrodeGroup
neurodata_type_inc: NWBContainer
doc: A physical grouping of electrodes, e.g., a shank of an array. An electrode
  group is typically used to describe electrodes that are physically connected
  on a single device and are often (but not always) used together for analysis,
  such as for spike sorting. Note that this is descriptive metadata; electrodes
  from different groups can still be spike-sorted together if needed.
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.

3.10.9. ElectrodesTable

Extends: DynamicTable

Description: see Section 2.9.9

YAML Specification:

neurodata_type_def: ElectrodesTable
neurodata_type_inc: DynamicTable
doc: A table of all electrodes (i.e. channels) used for recording. Introduced in
  NWB 2.8.0. Replaces the "electrodes" table (neurodata_type_inc DynamicTable,
  no neurodata_type_def) that is part of NWBFile.
datasets:
- name: location
  neurodata_type_inc: VectorData
  dtype: text
  doc: Location of the electrode (channel). 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: group
  neurodata_type_inc: VectorData
  dtype:
    target_type: ElectrodeGroup
    reftype: object
  doc: Reference to the ElectrodeGroup this electrode is a part of.
- name: group_name
  neurodata_type_inc: VectorData
  dtype: text
  doc: Name of the ElectrodeGroup this electrode is a part of.
  quantity: '?'
- name: x
  neurodata_type_inc: VectorData
  dtype: float32
  doc: x coordinate of the channel location in the brain (+x is posterior).
    Units should be specified in microns.
  quantity: '?'
- name: y
  neurodata_type_inc: VectorData
  dtype: float32
  doc: y coordinate of the channel location in the brain (+y is inferior). Units
    should be specified in microns.
  quantity: '?'
- name: z
  neurodata_type_inc: VectorData
  dtype: float32
  doc: z coordinate of the channel location in the brain (+z is right). Units
    should be specified in microns.
  quantity: '?'
- name: imp
  neurodata_type_inc: VectorData
  dtype: float32
  doc: Impedance of the channel, in ohms.
  quantity: '?'
- name: filtering
  neurodata_type_inc: VectorData
  dtype: text
  doc: Description of hardware filtering, including the filter name and
    frequency cutoffs.
  quantity: '?'
- name: rel_x
  neurodata_type_inc: VectorData
  dtype: float32
  doc: x coordinate in electrode group. Units should be specified in microns.
  quantity: '?'
- name: rel_y
  neurodata_type_inc: VectorData
  dtype: float32
  doc: y coordinate in electrode group. Units should be specified in microns.
  quantity: '?'
- name: rel_z
  neurodata_type_inc: VectorData
  dtype: float32
  doc: z coordinate in electrode group. Units should be specified in microns.
  quantity: '?'
- name: reference
  neurodata_type_inc: VectorData
  dtype: text
  doc: Description of the reference electrode and/or reference scheme used for
    this electrode, e.g., "stainless steel skull screw" or "online common
    average referencing".
  quantity: '?'

3.10.10. ClusterWaveforms

Extends: NWBDataInterface

Description: see Section 2.9.10

YAML Specification:

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

3.10.11. Clustering

Extends: NWBDataInterface

Description: see Section 2.9.11

YAML Specification:

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.

3.11. Intracellular electrophysiology

This source module contains neurodata_types for intracellular electrophysiology data.

3.11.1. PatchClampSeries

Extends: TimeSeries

Description: see Section 2.10.1

YAML Specification:

neurodata_type_def: PatchClampSeries
neurodata_type_inc: TimeSeries
doc: An abstract base class for patch-clamp data - stimulus or response, current
  or voltage.
attributes:
- name: stimulus_description
  dtype: text
  doc: Protocol/stimulus name for this patch-clamp dataset.
- name: sweep_number
  dtype: uint32
  doc: Sweep number, allows to group different PatchClampSeries together.
  required: false
datasets:
- name: data
  dtype: numeric
  dims:
  - num_times
  shape:
  - null
  doc: Recorded voltage or current.
  attributes:
  - 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: gain
  dtype: float32
  doc: Gain of the recording, in units Volt/Amp (v-clamp) or Volt/Volt
    (c-clamp).
  quantity: '?'
links:
- name: electrode
  target_type: IntracellularElectrode
  doc: Link to IntracellularElectrode object that describes the electrode that
    was used to apply or record this data.

3.11.2. CurrentClampSeries

Extends: PatchClampSeries

Description: see Section 2.10.2

YAML Specification:

neurodata_type_def: CurrentClampSeries
neurodata_type_inc: PatchClampSeries
doc: Voltage data from an intracellular current-clamp recording. A corresponding
  CurrentClampStimulusSeries (stored separately as a stimulus) is used to store
  the current injected.
datasets:
- name: data
  doc: Recorded voltage.
  attributes:
  - name: unit
    dtype: text
    value: volts
    doc: Base unit of measurement for working with the data. which 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' and add
      'offset'.
- name: bias_current
  dtype: float32
  doc: Bias current, in amps.
  quantity: '?'
- name: bridge_balance
  dtype: float32
  doc: Bridge balance, in ohms.
  quantity: '?'
- name: capacitance_compensation
  dtype: float32
  doc: Capacitance compensation, in farads.
  quantity: '?'

3.11.3. IZeroClampSeries

Extends: CurrentClampSeries

Description: see Section 2.10.3

YAML Specification:

neurodata_type_def: IZeroClampSeries
neurodata_type_inc: CurrentClampSeries
doc: Voltage data from an intracellular recording when all current and amplifier
  settings are off (i.e., CurrentClampSeries fields will be zero). There is no
  CurrentClampStimulusSeries associated with an IZero series because the
  amplifier is disconnected and no stimulus can reach the cell.
attributes:
- name: stimulus_description
  dtype: text
  value: N/A
  doc: An IZeroClampSeries has no stimulus, so this attribute is automatically
    set to "N/A"
datasets:
- name: bias_current
  dtype: float32
  value: 0.0
  doc: Bias current, in amps, fixed to 0.0.
- name: bridge_balance
  dtype: float32
  value: 0.0
  doc: Bridge balance, in ohms, fixed to 0.0.
- name: capacitance_compensation
  dtype: float32
  value: 0.0
  doc: Capacitance compensation, in farads, fixed to 0.0.

3.11.4. CurrentClampStimulusSeries

Extends: PatchClampSeries

Description: see Section 2.10.4

YAML Specification:

neurodata_type_def: CurrentClampStimulusSeries
neurodata_type_inc: PatchClampSeries
doc: Stimulus current applied during current clamp recording.
datasets:
- name: data
  doc: Stimulus current applied.
  attributes:
  - name: unit
    dtype: text
    value: amperes
    doc: Base unit of measurement for working with the data. which is fixed to
      'amperes'. Actual stored values are not necessarily stored in these units.
      To access the data in these units, multiply 'data' by 'conversion' and add
      'offset'.

3.11.5. VoltageClampSeries

Extends: PatchClampSeries

Description: see Section 2.10.5

YAML Specification:

neurodata_type_def: VoltageClampSeries
neurodata_type_inc: PatchClampSeries
doc: Current data from an intracellular voltage-clamp recording. A corresponding
  VoltageClampStimulusSeries (stored separately as a stimulus) is used to store
  the voltage injected.
datasets:
- name: data
  doc: Recorded current.
  attributes:
  - name: unit
    dtype: text
    value: amperes
    doc: Base unit of measurement for working with the data. which is fixed to
      'amperes'. 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: capacitance_fast
  dtype: float32
  doc: Fast capacitance, in farads.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: farads
    doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
- name: capacitance_slow
  dtype: float32
  doc: Slow capacitance, in farads.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: farads
    doc: Unit of measurement for capacitance_fast, which is fixed to 'farads'.
- name: resistance_comp_bandwidth
  dtype: float32
  doc: Resistance compensation bandwidth, in hertz.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: hertz
    doc: Unit of measurement for resistance_comp_bandwidth, which is fixed to
      'hertz'.
- name: resistance_comp_correction
  dtype: float32
  doc: Resistance compensation correction, in percent.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: percent
    doc: Unit of measurement for resistance_comp_correction, which is fixed to
      'percent'.
- name: resistance_comp_prediction
  dtype: float32
  doc: Resistance compensation prediction, in percent.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: percent
    doc: Unit of measurement for resistance_comp_prediction, which is fixed to
      'percent'.
- name: whole_cell_capacitance_comp
  dtype: float32
  doc: Whole cell capacitance compensation, in farads.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: farads
    doc: Unit of measurement for whole_cell_capacitance_comp, which is fixed to
      'farads'.
- name: whole_cell_series_resistance_comp
  dtype: float32
  doc: Whole cell series resistance compensation, in ohms.
  quantity: '?'
  attributes:
  - name: unit
    dtype: text
    value: ohms
    doc: Unit of measurement for whole_cell_series_resistance_comp, which is
      fixed to 'ohms'.

3.11.6. VoltageClampStimulusSeries

Extends: PatchClampSeries

Description: see Section 2.10.6

YAML Specification:

neurodata_type_def: VoltageClampStimulusSeries
neurodata_type_inc: PatchClampSeries
doc: Stimulus voltage applied during a voltage clamp recording.
datasets:
- name: data
  doc: Stimulus voltage applied.
  attributes:
  - name: unit
    dtype: text
    value: volts
    doc: Base unit of measurement for working with the data. which 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' and add
      'offset'.

3.11.7. IntracellularElectrode

Extends: NWBContainer

Description: see Section 2.10.7

YAML Specification:

neurodata_type_def: IntracellularElectrode
neurodata_type_inc: NWBContainer
doc: An intracellular electrode and its metadata.
datasets:
- name: cell_id
  dtype: text
  doc: unique ID of the cell
  quantity: '?'
- name: description
  dtype: text
  doc: Description of electrode (e.g.,  whole-cell, sharp, etc.).
- name: filtering
  dtype: text
  doc: Electrode specific filtering.
  quantity: '?'
- name: initial_access_resistance
  dtype: text
  doc: Initial access resistance.
  quantity: '?'
- name: location
  dtype: text
  doc: Location of the electrode. 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.
  quantity: '?'
- name: resistance
  dtype: text
  doc: Electrode resistance, in ohms.
  quantity: '?'
- name: seal
  dtype: text
  doc: Information about seal used for recording.
  quantity: '?'
- name: slice
  dtype: text
  doc: Information about slice used for recording.
  quantity: '?'
links:
- name: device
  target_type: Device
  doc: Device that was used to record from this electrode.

3.11.8. SweepTable

Extends: DynamicTable

Description: see Section 2.10.8

YAML Specification:

neurodata_type_def: SweepTable
neurodata_type_inc: DynamicTable
doc: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable is being
  replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable tables.
  Additional SequentialRecordingsTable, RepetitionsTable, and ExperimentalConditions
  tables provide enhanced support for experiment metadata.'
datasets:
- name: sweep_number
  neurodata_type_inc: VectorData
  dtype: uint32
  doc: Sweep number of the PatchClampSeries in that row.
- name: series
  neurodata_type_inc: VectorData
  dtype:
    target_type: PatchClampSeries
    reftype: object
  doc: The PatchClampSeries with the sweep number in that row.
- name: series_index
  neurodata_type_inc: VectorIndex
  doc: Index for series.

3.11.9. IntracellularElectrodesTable

Extends: DynamicTable

Description: see Section 2.10.9

YAML Specification:

neurodata_type_def: IntracellularElectrodesTable
neurodata_type_inc: DynamicTable
doc: Table for storing intracellular electrode related metadata.
attributes:
- name: description
  dtype: text
  value: Table for storing intracellular electrode related metadata.
  doc: Description of what is in this dynamic table.
datasets:
- name: electrode
  neurodata_type_inc: VectorData
  dtype:
    target_type: IntracellularElectrode
    reftype: object
  doc: Column for storing the reference to the intracellular electrode.

3.11.10. IntracellularStimuliTable

Extends: DynamicTable

Description: see Section 2.10.10

YAML Specification:

neurodata_type_def: IntracellularStimuliTable
neurodata_type_inc: DynamicTable
doc: Table for storing intracellular stimulus related metadata.
attributes:
- name: description
  dtype: text
  value: Table for storing intracellular stimulus related metadata.
  doc: Description of what is in this dynamic table.
datasets:
- name: stimulus
  neurodata_type_inc: TimeSeriesReferenceVectorData
  doc: Column storing the reference to the recorded stimulus for the recording
    (rows).
- name: stimulus_template
  neurodata_type_inc: TimeSeriesReferenceVectorData
  doc: Column storing the reference to the stimulus template for the recording
    (rows).
  quantity: '?'

3.11.11. IntracellularResponsesTable

Extends: DynamicTable

Description: see Section 2.10.11

YAML Specification:

neurodata_type_def: IntracellularResponsesTable
neurodata_type_inc: DynamicTable
doc: Table for storing intracellular response related metadata.
attributes:
- name: description
  dtype: text
  value: Table for storing intracellular response related metadata.
  doc: Description of what is in this dynamic table.
datasets:
- name: response
  neurodata_type_inc: TimeSeriesReferenceVectorData
  doc: Column storing the reference to the recorded response for the recording
    (rows)

3.11.12. IntracellularRecordingsTable

Extends: AlignedDynamicTable

Description: see Section 2.10.12

YAML Specification:

neurodata_type_def: IntracellularRecordingsTable
neurodata_type_inc: AlignedDynamicTable
name: intracellular_recordings
doc: A table to group together a stimulus and response from a single electrode
  and a single simultaneous recording. Each row in the table represents a single
  recording consisting typically of a stimulus and a corresponding response. In
  some cases, however, only a stimulus or a response is recorded as part of an
  experiment. In this case, both the stimulus and response will point to the
  same TimeSeries while the idx_start and count of the invalid column will be
  set to -1, thus, indicating that no values have been recorded for the stimulus
  or response, respectively. Note, a recording MUST contain at least a stimulus
  or a response. Typically the stimulus and response are PatchClampSeries.
  However, the use of AD/DA channels that are not associated to an electrode is
  also common in intracellular electrophysiology, in which case other TimeSeries
  may be used.
attributes:
- name: description
  dtype: text
  value: A table to group together a stimulus and response from a single
    electrode and a single simultaneous recording and for storing metadata about
    the intracellular recording.
  doc: Description of the contents of this table. Inherited from
    AlignedDynamicTable and overwritten here to fix the value of the attribute.
groups:
- name: electrodes
  neurodata_type_inc: IntracellularElectrodesTable
  doc: Table for storing intracellular electrode related metadata.
- name: stimuli
  neurodata_type_inc: IntracellularStimuliTable
  doc: Table for storing intracellular stimulus related metadata.
- name: responses
  neurodata_type_inc: IntracellularResponsesTable
  doc: Table for storing intracellular response related metadata.

3.11.13. SimultaneousRecordingsTable

Extends: DynamicTable

Description: see Section 2.10.13

YAML Specification:

neurodata_type_def: SimultaneousRecordingsTable
neurodata_type_inc: DynamicTable
name: simultaneous_recordings
doc: A table for grouping different intracellular recordings from the
  IntracellularRecordingsTable table together that were recorded simultaneously
  from different electrodes.
datasets:
- name: recordings
  neurodata_type_inc: DynamicTableRegion
  doc: A reference to one or more rows in the IntracellularRecordingsTable
    table.
  attributes:
  - name: table
    dtype:
      target_type: IntracellularRecordingsTable
      reftype: object
    doc: Reference to the IntracellularRecordingsTable table that this table
      region applies to. This specializes the attribute inherited from
      DynamicTableRegion to fix the type of table that can be referenced here.
- name: recordings_index
  neurodata_type_inc: VectorIndex
  doc: Index dataset for the recordings column.

3.11.14. SequentialRecordingsTable

Extends: DynamicTable

Description: see Section 2.10.14

YAML Specification:

neurodata_type_def: SequentialRecordingsTable
neurodata_type_inc: DynamicTable
name: sequential_recordings
doc: A table for grouping different sequential recordings from the
  SimultaneousRecordingsTable table together. This is typically used to group
  together sequential recordings where a sequence of stimuli of the same type
  with varying parameters have been presented in a sequence.
datasets:
- name: simultaneous_recordings
  neurodata_type_inc: DynamicTableRegion
  doc: A reference to one or more rows in the SimultaneousRecordingsTable table.
  attributes:
  - name: table
    dtype:
      target_type: SimultaneousRecordingsTable
      reftype: object
    doc: Reference to the SimultaneousRecordingsTable table that this table
      region applies to. This specializes the attribute inherited from
      DynamicTableRegion to fix the type of table that can be referenced here.
- name: simultaneous_recordings_index
  neurodata_type_inc: VectorIndex
  doc: Index dataset for the simultaneous_recordings column.
- name: stimulus_type
  neurodata_type_inc: VectorData
  dtype: text
  doc: The type of stimulus used for the sequential recording.

3.11.15. RepetitionsTable

Extends: DynamicTable

Description: see Section 2.10.15

YAML Specification:

neurodata_type_def: RepetitionsTable
neurodata_type_inc: DynamicTable
name: repetitions
doc: A table for grouping different sequential intracellular recordings
  together. With each SequentialRecording typically representing a particular
  type of stimulus, the RepetitionsTable table is typically used to group sets
  of stimuli applied in sequence.
datasets:
- name: sequential_recordings
  neurodata_type_inc: DynamicTableRegion
  doc: A reference to one or more rows in the SequentialRecordingsTable table.
  attributes:
  - name: table
    dtype:
      target_type: SequentialRecordingsTable
      reftype: object
    doc: Reference to the SequentialRecordingsTable table that this table region
      applies to. This specializes the attribute inherited from
      DynamicTableRegion to fix the type of table that can be referenced here.
- name: sequential_recordings_index
  neurodata_type_inc: VectorIndex
  doc: Index dataset for the sequential_recordings column.

3.11.16. ExperimentalConditionsTable

Extends: DynamicTable

Description: see Section 2.10.16

YAML Specification:

neurodata_type_def: ExperimentalConditionsTable
neurodata_type_inc: DynamicTable
name: experimental_conditions
doc: A table for grouping different intracellular recording repetitions together
  that belong to the same experimental condition.
datasets:
- name: repetitions
  neurodata_type_inc: DynamicTableRegion
  doc: A reference to one or more rows in the RepetitionsTable table.
  attributes:
  - name: table
    dtype:
      target_type: RepetitionsTable
      reftype: object
    doc: Reference to the RepetitionsTable table that this table region applies
      to. This specializes the attribute inherited from DynamicTableRegion to
      fix the type of table that can be referenced here.
- name: repetitions_index
  neurodata_type_inc: VectorIndex
  doc: Index dataset for the repetitions column.

3.12. Optogenetics

This source module contains neurodata_types for opto-genetics data.

3.12.1. OptogeneticSeries

Extends: TimeSeries

Description: see Section 2.11.1

YAML Specification:

neurodata_type_def: OptogeneticSeries
neurodata_type_inc: TimeSeries
doc: An optogenetic stimulus.
datasets:
- name: data
  dtype: numeric
  dims:
  - - num_times
  - - num_times
    - num_rois
  shape:
  - - null
  - - null
    - null
  doc: Applied power for optogenetic stimulus, in watts. Shape can be 1D or 2D.
    2D data is meant to be used in an extension of OptogeneticSeries that
    defines what the second dimension represents.
  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.

3.12.2. OptogeneticStimulusSite

Extends: NWBContainer

Description: see Section 2.11.2

YAML Specification:

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.

3.13. Optical physiology

This source module contains neurodata_types for optical physiology data.

3.13.1. OnePhotonSeries

Extends: ImageSeries

Description: see Section 2.12.1

YAML Specification:

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
datasets:
- name: data
  dtype: numeric
  dims:
  - - time
    - width
    - height
  - - time
    - width
    - height
    - depth
  shape:
  - - null
    - null
    - null
  - - null
    - null
    - null
    - null
  doc: "Time-series of microscopy data indexed as data[time, width, height].\n\nIndexing
    convention:\n  - width: first spatial axis (horizontal direction, columns)\n \
    \ - height: second spatial axis (vertical direction, rows)\n\nFor raster-scanning
    systems (two-photon, confocal, one-photon laser scanning):\n  - width: fast scan
    direction (horizontal)\n  - height: slow scan direction (vertical)\n\nCoordinate
    system diagram::\n\n  height  ^\n  (slow)  |\n          |    +-----------------+\n\
    \          |    |                 |\n          |    |   Image plane   |\n    \
    \      |    |                 |\n          |    +-----------------+\n        \
    \  |\n          0 ----------------------> width (fast)\n\n\nFor non-raster systems
    (wide-field, light-sheet, random-access), width and height\nare arbitrary coordinates
    of the image plane.\n\nNote: This indexing convention conflicts with standard
    matrix[row, column] notation\nfor array access where the first index moves vertically
    through rows and the second moves horizontally\nthrough columns. In the schema,
    data[time, width, height] means that the first spatial\nindex moves horizontally
    (width) through columns and the second spatial index moves\nvertically (height)
    through rows. In summary, incrementing the first spatial index\nmoves you horizontally
    across the image, while in matrix notation it would move you\nvertically across
    the rows of the image.\n"
links:
- name: imaging_plane
  target_type: ImagingPlane
  doc: Link to ImagingPlane object from which this TimeSeries data was
    generated.

3.13.2. TwoPhotonSeries

Extends: ImageSeries

Description: see Section 2.12.2

YAML Specification:

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: data
  dtype: numeric
  dims:
  - - time
    - width
    - height
  - - time
    - width
    - height
    - depth
  shape:
  - - null
    - null
    - null
  - - null
    - null
    - null
    - null
  doc: "Time-series of microscopy data indexed as data[time, width, height].\n\nIndexing
    convention:\n  - width: first spatial axis (horizontal direction, columns)\n \
    \ - height: second spatial axis (vertical direction, rows)\n\nFor raster-scanning
    systems (two-photon, confocal, one-photon laser scanning):\n  - width: fast scan
    direction (horizontal)\n  - height: slow scan direction (vertical)\n\nCoordinate
    system diagram::\n\n  height  ^\n  (slow)  |\n          |    +-----------------+\n\
    \          |    |                 |\n          |    |   Image plane   |\n    \
    \      |    |                 |\n          |    +-----------------+\n        \
    \  |\n          0 ----------------------> width (fast)\n\n\nFor non-raster systems
    (wide-field, light-sheet, random-access), width and height\nare arbitrary coordinates
    of the image plane.\n\nNote: This indexing convention conflicts with standard
    matrix[row, column] notation\nfor array access where the first index moves vertically
    through rows and the second moves horizontally\nthrough columns. In the schema,
    data[time, width, height] means that the first spatial\nindex moves horizontally
    (width) through columns and the second spatial index moves\nvertically (height)
    through rows.\n"
- name: field_of_view
  dtype: float32
  dims:
  - - width|height
  - - width|height|depth
  shape:
  - - 2
  - - 3
  doc: Physical dimensions of the imaging field of view in width, height, and
    optionally depth directions, in meters. The width dimension corresponds to
    the faster scanning axis, and the height dimension corresponds to the slower
    scanning axis.
  quantity: '?'
links:
- name: imaging_plane
  target_type: ImagingPlane
  doc: Link to ImagingPlane object from which this TimeSeries data was
    generated.

3.13.3. RoiResponseSeries

Extends: TimeSeries

Description: see Section 2.12.3

YAML Specification:

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.

3.13.4. DfOverF

Extends: NWBDataInterface

Description: see Section 2.12.4

YAML Specification:

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: +

3.13.5. Fluorescence

Extends: NWBDataInterface

Description: see Section 2.12.5

YAML Specification:

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: +

3.13.6. ImageSegmentation

Extends: NWBDataInterface

Description: see Section 2.12.6

YAML Specification:

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: +

3.13.7. PlaneSegmentation

Extends: DynamicTable

Description: see Section 2.12.7

YAML Specification:

neurodata_type_def: PlaneSegmentation
neurodata_type_inc: DynamicTable
doc: Results from image segmentation of a specific imaging plane. At least one
  of `image_mask`, `pixel_mask`, or `voxel_mask` is required.
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. At
    least one of `image_mask`, `pixel_mask`, or `voxel_mask` is required.
  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.
    At least one of `image_mask`, `pixel_mask`, or `voxel_mask` is required.'
  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.
    At least one of `image_mask`, `pixel_mask`, or `voxel_mask` is required.'
  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.

3.13.8. ImagingPlane

Extends: NWBContainer

Description: see Section 2.12.8

YAML Specification:

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'.
    required: false
- 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'.
    required: false
- 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.

3.13.9. OpticalChannel

Extends: NWBContainer

Description: see Section 2.12.9

YAML Specification:

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.

3.13.10. MotionCorrection

Extends: NWBDataInterface

Description: see Section 2.12.10

YAML Specification:

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: Results from motion correction of an image stack.
  quantity: +

3.13.11. CorrectedImageStack

Extends: NWBDataInterface

Description: see Section 2.12.11

YAML Specification:

neurodata_type_def: CorrectedImageStack
neurodata_type_inc: NWBDataInterface
doc: Results 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.

3.14. Retinotopy

This source module contains neurodata_type for retinotopy data.

3.14.1. ImagingRetinotopy

Extends: NWBDataInterface

Description: see Section 2.13.1

YAML Specification:

neurodata_type_def: ImagingRetinotopy
neurodata_type_inc: NWBDataInterface
default_name: ImagingRetinotopy
doc: 'DEPRECATED. 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.