test.extensions.yaml

groups:
- neurodata_type_def: SpatialLightModulator
  neurodata_type_inc: Device
  name: slm
  doc: Spatial light monitor used in the experiment.
  quantity: '?'
  attributes:
  - name: size
    dtype: numeric
    dims:
    - - width
      - height
    - - width
      - height
      - depth
    shape:
    - - 2
    - - 3
    doc: Resolution of SpatialLightModulator (in pixels), formatted as [width, height]
      or [width, height, depth].
    required: false
- neurodata_type_def: PhotostimulationDevice
  neurodata_type_inc: Device
  doc: Device used to generate photostimulation.
  attributes:
  - name: type
    dtype: text
    doc: Device used for optogenetic stimulation ('laser' or 'LED').
  - name: wavelength
    dtype: numeric
    doc: Excitation wavelength of stimulation light (nanometers).
    required: false
  - name: opsin
    dtype: text
    doc: Type of opsin used for photoactivation.
    required: false
  - name: power
    dtype: numeric
    doc: Incident power of stimulation device (in milliwatts).
    required: false
  - name: peak_pulse_energy
    dtype: numeric
    doc: 'If device is pulsed laser: pulse energy  (in microjoules).'
    required: false
  - name: pulse_rate
    dtype: numeric
    doc: 'If device is pulsed laser: pulse rate (in kHz) used for stimulation.'
    required: false
  groups:
  - neurodata_type_def: SpatialLightModulator
    neurodata_type_inc: Device
    name: slm
    doc: Spatial light monitor used in the experiment.
    quantity: '?'
    attributes:
    - name: size
      dtype: numeric
      dims:
      - - width
        - height
      - - width
        - height
        - depth
      shape:
      - - 2
      - - 3
      doc: Resolution of SpatialLightModulator (in pixels), formatted as [width, height]
        or [width, height, depth].
      required: false
- neurodata_type_def: HolographicPattern
  neurodata_type_inc: NWBContainer
  name: pattern
  doc: 'Container to store the pattern used in a photostimulation experiment. '
  attributes:
  - name: dimension
    dtype: numeric
    dims:
    - - width
      - height
    - - width
      - height
      - depth
    shape:
    - - 2
    - - 3
    doc: Number of pixels on x, y, (and z) axes. Calculated automatically when ROI
      is input using 'image_mask_roi.' Required when using 'pixel_roi.'
    required: false
  - name: roi_size
    dtype: numeric
    doc: Size of a single stimulation ROI in pixels. If a scalar is provided, the
      ROI is assumed to be a circle (for 2D patterns) or cylinder (for 3D patterns)
      centered at the corresponding coordinates, with diameter 'roi_size'. If 'roi_size'
      is a two or three dimensional array, the ROI is assumed to be a rectangle or
      cuboid, with dimensions [width, height] or [width, height, depth]. This parameter
      is required when using 'pixel_roi'.
    required: false
  datasets:
  - name: image_mask_roi
    dims:
    - - num_rows
      - num_cols
    - - num_rows
      - num_cols
      - depth
    shape:
    - - null
      - null
    - - null
      - null
      - null
    doc: 'ROIs designated using a mask of size [width, height] (2D stimulation) or
      [width, height, depth] (3D stimulation), where for a given pixel a value of
      1 indicates stimulation, and a value of 0 indicates no stimulation. '
    quantity: '?'
  - name: pixel_roi
    shape:
    - - null
      - null
    - - null
      - null
      - null
    doc: ROIs designated as a list specifying the pixel ([x1, y1], [x2, y2], …) or
      voxel ([x1, y1, z1], [x2, y2, z2], …) of each ROI, where the items in the list
      are the coordinates of the center of the ROI. The size of each ROI is specified
      via the required 'roi_size' parameter.
    quantity: '?'
    attributes:
    - name: roi_size
      dtype: numeric
      doc: Size of a single stimulation ROI in pixels. If a scalar is provided, the
        ROI is assumed to be a circle (for 2D patterns) or cylinder (for 3D patterns)
        centered at the corresponding coordinates, with diameter 'roi_size'. If 'roi_size'
        is a two or three dimensional array, the ROI is assumed to be a rectangle
        or cuboid, with dimensions [width, height] or [width, height, depth]. This
        parameter is required when using 'pixel_roi'.
      required: false
- neurodata_type_def: HolographicPattern2
  neurodata_type_inc: PlaneSegmentation
  doc: 'Container to store the pattern used in a photostimulation experiment. '
- neurodata_type_def: HolographicSegmentation
  neurodata_type_inc: NWBDataInterface
  name: holographic_segmentation
  doc: 'Container to store the pattern used in a photostimulation experiment. '
  attributes:
  - name: dimension
    dtype: numeric
    dims:
    - - width
      - height
    - - width
      - height
      - depth
    shape:
    - - 2
    - - 3
    doc: Number of pixels on x, y, (and z) axes. Calculated automatically when ROI
      is input using 'image_mask_roi.' Required when using 'pixel_roi.'
    required: false
  groups:
  - neurodata_type_def: HolographicPattern2
    neurodata_type_inc: PlaneSegmentation
    doc: 'Container to store the pattern used in a photostimulation experiment. '
- neurodata_type_def: PhotostimulationSeries
  neurodata_type_inc: TimeSeries
  doc: 'TimeSeries object for photostimulus presentation. '
  quantity: '*'
  attributes:
  - name: format
    dtype: text
    doc: Format of data denoting stimulus presentation. Can be either 'interval' or
      'series'.
  - name: stimulus_duration
    dtype: numeric
    doc: Duration (in sec) the stimulus is presented following onset.
    required: false
  - name: epoch_length
    dtype: numeric
    doc: Length of each epoch (in seconds).
    required: false
  datasets:
  - name: stimulus_method
    dtype: text
    doc: Scanning or scanless method for shaping optogenetic light (e.g., diffraction
      limited points, 3D shot, disks, etc.).
    quantity: '?'
    attributes:
    - name: sweep_pattern
      dtype: text
      doc: Sweeping method, if spatially modulated during stimulation (none, or other).
        Requires 'stim_method' is specified. (ex. logspiral)
    - name: time_per_sweep
      dtype: numeric
      doc: Time to conduct a sweep (in milliseconds).
      required: false
    - name: num_sweeps
      dtype: numeric
      doc: 'Repetition of a sweep pattern for a single stimulation instance. '
      required: false
  groups:
  - neurodata_type_def: HolographicPattern
    neurodata_type_inc: NWBContainer
    name: pattern
    doc: 'Container to store the pattern used in a photostimulation experiment. '
    attributes:
    - name: dimension
      dtype: numeric
      dims:
      - - width
        - height
      - - width
        - height
        - depth
      shape:
      - - 2
      - - 3
      doc: Number of pixels on x, y, (and z) axes. Calculated automatically when ROI
        is input using 'image_mask_roi.' Required when using 'pixel_roi.'
      required: false
    - name: roi_size
      dtype: numeric
      doc: Size of a single stimulation ROI in pixels. If a scalar is provided, the
        ROI is assumed to be a circle (for 2D patterns) or cylinder (for 3D patterns)
        centered at the corresponding coordinates, with diameter 'roi_size'. If 'roi_size'
        is a two or three dimensional array, the ROI is assumed to be a rectangle
        or cuboid, with dimensions [width, height] or [width, height, depth]. This
        parameter is required when using 'pixel_roi'.
      required: false
    datasets:
    - name: image_mask_roi
      dims:
      - - num_rows
        - num_cols
      - - num_rows
        - num_cols
        - depth
      shape:
      - - null
        - null
      - - null
        - null
        - null
      doc: 'ROIs designated using a mask of size [width, height] (2D stimulation)
        or [width, height, depth] (3D stimulation), where for a given pixel a value
        of 1 indicates stimulation, and a value of 0 indicates no stimulation. '
      quantity: '?'
    - name: pixel_roi
      shape:
      - - null
        - null
      - - null
        - null
        - null
      doc: ROIs designated as a list specifying the pixel ([x1, y1], [x2, y2], …)
        or voxel ([x1, y1, z1], [x2, y2, z2], …) of each ROI, where the items in the
        list are the coordinates of the center of the ROI. The size of each ROI is
        specified via the required 'roi_size' parameter.
      quantity: '?'
      attributes:
      - name: roi_size
        dtype: numeric
        doc: Size of a single stimulation ROI in pixels. If a scalar is provided,
          the ROI is assumed to be a circle (for 2D patterns) or cylinder (for 3D
          patterns) centered at the corresponding coordinates, with diameter 'roi_size'.
          If 'roi_size' is a two or three dimensional array, the ROI is assumed to
          be a rectangle or cuboid, with dimensions [width, height] or [width, height,
          depth]. This parameter is required when using 'pixel_roi'.
        required: false
  - neurodata_type_def: HolographicSegmentation
    neurodata_type_inc: NWBDataInterface
    name: holographic_segmentation
    doc: 'Container to store the pattern used in a photostimulation experiment. '
    attributes:
    - name: dimension
      dtype: numeric
      dims:
      - - width
        - height
      - - width
        - height
        - depth
      shape:
      - - 2
      - - 3
      doc: Number of pixels on x, y, (and z) axes. Calculated automatically when ROI
        is input using 'image_mask_roi.' Required when using 'pixel_roi.'
      required: false
    groups:
    - neurodata_type_def: HolographicPattern2
      neurodata_type_inc: PlaneSegmentation
      doc: 'Container to store the pattern used in a photostimulation experiment. '
- neurodata_type_def: PhotostimulationTable
  neurodata_type_inc: DynamicTable
  doc: "Table of to hold all of an experiment's PhotostimulationSeries objects. "
  quantity: '?'
  datasets:
  - name: series
    neurodata_type_inc: VectorData
    dtype:
      target_type: PhotostimulationSeries
      reftype: object
    doc: PhotostimulationSeries object corresponding to the row.
  links:
  - name: device
    target_type: PhotostimulationDevice
    doc: PhotostimulationDevice used in the table's PhotostimulationSeries containers.