nwb-linkml/nwb_linkml/schema/core.nwb.ophys.include.yaml

name: core.nwb.ophys.include
id: core.nwb.ophys.include
imports:
- core.nwb.image
- core.nwb.base
- hdmf-common.table
- core.nwb.device
- nwb.language
- core.nwb.ophys.include
- core.nwb.ophys
default_prefix: core.nwb.ophys.include/
classes:
  TwoPhotonSeries__field_of_view:
    name: TwoPhotonSeries__field_of_view
    description: Width, height and depth of image, or imaged area, in meters.
    attributes:
      array:
        name: array
        range: TwoPhotonSeries__field_of_view__Array
  TwoPhotonSeries__field_of_view__Array:
    name: TwoPhotonSeries__field_of_view__Array
    is_a: Arraylike
    attributes:
      width|height:
        name: width|height
        range: float32
        required: false
        minimum_cardinality: 2
        maximum_cardinality: 2
      width|height|depth:
        name: width|height|depth
        range: float32
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
  RoiResponseSeries__data:
    name: RoiResponseSeries__data
    description: Signals from ROIs.
    attributes:
      array:
        name: array
        range: RoiResponseSeries__data__Array
  RoiResponseSeries__data__Array:
    name: RoiResponseSeries__data__Array
    is_a: Arraylike
    attributes:
      num_times:
        name: num_times
        range: numeric
        required: true
      num_ROIs:
        name: num_ROIs
        range: numeric
        required: false
  RoiResponseSeries__rois:
    name: RoiResponseSeries__rois
    description: DynamicTableRegion referencing into an ROITable containing information
      on the ROIs stored in this timeseries.
    is_a: DynamicTableRegion
  PlaneSegmentation__image_mask:
    name: PlaneSegmentation__image_mask
    description: 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.
    is_a: VectorData
  PlaneSegmentation__pixel_mask_index:
    name: PlaneSegmentation__pixel_mask_index
    description: Index into pixel_mask.
    is_a: VectorIndex
  PlaneSegmentation__voxel_mask_index:
    name: PlaneSegmentation__voxel_mask_index
    description: Index into voxel_mask.
    is_a: VectorIndex
  PlaneSegmentation__reference_images:
    name: PlaneSegmentation__reference_images
    description: Image stacks that the segmentation masks apply to.
    attributes:
      ImageSeries:
        name: ImageSeries
        description: One or more image stacks that the masks apply to (can be one-element
          stack).
        multivalued: true
        range: ImageSeries
        required: false
  ImagingPlane__manifold:
    name: ImagingPlane__manifold
    description: 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.
    attributes:
      conversion:
        name: conversion
        description: 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.
        range: float32
      unit:
        name: unit
        description: Base unit of measurement for working with the data. The default
          value is 'meters'.
        range: text
      array:
        name: array
        range: ImagingPlane__manifold__Array
  ImagingPlane__manifold__Array:
    name: ImagingPlane__manifold__Array
    is_a: Arraylike
    attributes:
      height:
        name: height
        range: float32
        required: true
      width:
        name: width
        range: float32
        required: true
      x, y, z:
        name: x, y, z
        range: float32
        required: true
        minimum_cardinality: 3
        maximum_cardinality: 3
      depth:
        name: depth
        range: float32
        required: false
  ImagingPlane__origin_coords:
    name: ImagingPlane__origin_coords
    description: 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).
    attributes:
      unit:
        name: unit
        description: Measurement units for origin_coords. The default value is 'meters'.
        range: text
      array:
        name: array
        range: ImagingPlane__origin_coords__Array
  ImagingPlane__origin_coords__Array:
    name: ImagingPlane__origin_coords__Array
    is_a: Arraylike
    attributes:
      x, y:
        name: x, y
        range: float32
        required: false
        minimum_cardinality: 2
        maximum_cardinality: 2
      x, y, z:
        name: x, y, z
        range: float32
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
  ImagingPlane__grid_spacing:
    name: ImagingPlane__grid_spacing
    description: 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.
    attributes:
      unit:
        name: unit
        description: Measurement units for grid_spacing. The default value is 'meters'.
        range: text
      array:
        name: array
        range: ImagingPlane__grid_spacing__Array
  ImagingPlane__grid_spacing__Array:
    name: ImagingPlane__grid_spacing__Array
    is_a: Arraylike
    attributes:
      x, y:
        name: x, y
        range: float32
        required: false
        minimum_cardinality: 2
        maximum_cardinality: 2
      x, y, z:
        name: x, y, z
        range: float32
        required: false
        minimum_cardinality: 3
        maximum_cardinality: 3
  CorrectedImageStack__corrected:
    name: CorrectedImageStack__corrected
    description: Image stack with frames shifted to the common coordinates.
    is_a: ImageSeries
  CorrectedImageStack__xy_translation:
    name: CorrectedImageStack__xy_translation
    description: Stores the x,y delta necessary to align each frame to the common
      coordinates, for example, to align each frame to a reference image.
    is_a: TimeSeries