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

name: core.nwb.ophys
id: core.nwb.ophys
imports:
- core.nwb.image
- core.nwb.base
- hdmf-common.table
- nwb.language
default_prefix: core.nwb.ophys/
classes:
  OnePhotonSeries:
    name: OnePhotonSeries
    description: Image stack recorded over time from 1-photon microscope.
    is_a: ImageSeries
    attributes:
      pmt_gain:
        name: pmt_gain
        description: Photomultiplier gain.
        range: float32
      scan_line_rate:
        name: scan_line_rate
        description: 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.
        range: float32
      exposure_time:
        name: exposure_time
        description: Exposure time of the sample; often the inverse of the frequency.
        range: float32
      binning:
        name: binning
        description: Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.
        range: uint8
      power:
        name: power
        description: Power of the excitation in mW, if known.
        range: float32
      intensity:
        name: intensity
        description: Intensity of the excitation in mW/mm^2, if known.
        range: float32
  TwoPhotonSeries:
    name: TwoPhotonSeries
    description: Image stack recorded over time from 2-photon microscope.
    is_a: ImageSeries
    attributes:
      pmt_gain:
        name: pmt_gain
        description: Photomultiplier gain.
        range: float32
      scan_line_rate:
        name: scan_line_rate
        description: 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.
        range: float32
      field_of_view:
        name: field_of_view
        description: Width, height and depth of image, or imaged area, in meters.
        multivalued: false
        range: TwoPhotonSeries_field_of_view
        required: false
  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:
    name: RoiResponseSeries
    description: ROI responses over an imaging plane. The first dimension represents
      time. The second dimension, if present, represents ROIs.
    is_a: TimeSeries
    attributes:
      data:
        name: data
        description: Signals from ROIs.
        multivalued: false
        range: RoiResponseSeries_data
        required: true
      rois:
        name: rois
        description: DynamicTableRegion referencing into an ROITable containing information
          on the ROIs stored in this timeseries.
        multivalued: false
        range: RoiResponseSeries_rois
        required: true
  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
  DfOverF:
    name: DfOverF
    description: 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).
    is_a: NWBDataInterface
    attributes:
      RoiResponseSeries:
        name: RoiResponseSeries
        description: RoiResponseSeries object(s) containing dF/F for a ROI.
        multivalued: true
        range: RoiResponseSeries
        required: true
  Fluorescence:
    name: Fluorescence
    description: 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).
    is_a: NWBDataInterface
    attributes:
      RoiResponseSeries:
        name: RoiResponseSeries
        description: RoiResponseSeries object(s) containing fluorescence data for
          a ROI.
        multivalued: true
        range: RoiResponseSeries
        required: true
  ImageSegmentation:
    name: ImageSegmentation
    description: 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.
    is_a: NWBDataInterface
    attributes:
      PlaneSegmentation:
        name: PlaneSegmentation
        description: Results from image segmentation of a specific imaging plane.
        multivalued: true
        range: PlaneSegmentation
        required: true
  PlaneSegmentation:
    name: PlaneSegmentation
    description: Results from image segmentation of a specific imaging plane.
    is_a: DynamicTable
    attributes:
      image_mask:
        name: 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.
        multivalued: false
        range: PlaneSegmentation_image_mask
        required: false
      pixel_mask_index:
        name: pixel_mask_index
        description: Index into pixel_mask.
        multivalued: false
        range: PlaneSegmentation_pixel_mask_index
        required: false
      pixel_mask:
        name: pixel_mask
        description: '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'
        multivalued: false
        range: PlaneSegmentation_pixel_mask
        required: false
      voxel_mask_index:
        name: voxel_mask_index
        description: Index into voxel_mask.
        multivalued: false
        range: PlaneSegmentation_voxel_mask_index
        required: false
      voxel_mask:
        name: voxel_mask
        description: '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'
        multivalued: false
        range: PlaneSegmentation_voxel_mask
        required: false
      reference_images:
        name: reference_images
        description: Image stacks that the segmentation masks apply to.
        multivalued: false
        range: PlaneSegmentation_reference_images
        required: true
  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
    attributes:
      array:
        name: array
        range: PlaneSegmentation_image_mask_Array
  PlaneSegmentation_image_mask_Array:
    name: PlaneSegmentation_image_mask_Array
    is_a: Arraylike
    attributes:
      num_roi:
        name: num_roi
        range: AnyType
        required: true
      num_x:
        name: num_x
        range: AnyType
        required: true
      num_y:
        name: num_y
        range: AnyType
        required: true
      num_z:
        name: num_z
        range: AnyType
        required: false
  PlaneSegmentation_pixel_mask_index:
    name: PlaneSegmentation_pixel_mask_index
    description: Index into pixel_mask.
    is_a: VectorIndex
  PlaneSegmentation_pixel_mask:
    name: PlaneSegmentation_pixel_mask
    description: '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'
    is_a: VectorData
  PlaneSegmentation_voxel_mask_index:
    name: PlaneSegmentation_voxel_mask_index
    description: Index into voxel_mask.
    is_a: VectorIndex
  PlaneSegmentation_voxel_mask:
    name: PlaneSegmentation_voxel_mask
    description: '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'
    is_a: VectorData
  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:
    name: ImagingPlane
    description: An imaging plane and its metadata.
    is_a: NWBContainer
    attributes:
      description:
        name: description
        description: Description of the imaging plane.
        multivalued: false
        range: ImagingPlane_description
        required: false
      excitation_lambda:
        name: excitation_lambda
        description: Excitation wavelength, in nm.
        multivalued: false
        range: ImagingPlane_excitation_lambda
        required: true
      imaging_rate:
        name: imaging_rate
        description: Rate that images are acquired, in Hz. If the corresponding TimeSeries
          is present, the rate should be stored there instead.
        multivalued: false
        range: ImagingPlane_imaging_rate
        required: false
      indicator:
        name: indicator
        description: Calcium indicator.
        multivalued: false
        range: ImagingPlane_indicator
        required: true
      location:
        name: location
        description: 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.
        multivalued: false
        range: ImagingPlane_location
        required: true
      manifold:
        name: 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.
        multivalued: false
        range: ImagingPlane_manifold
        required: false
      origin_coords:
        name: 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).
        multivalued: false
        range: ImagingPlane_origin_coords
        required: false
      grid_spacing:
        name: 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.
        multivalued: false
        range: ImagingPlane_grid_spacing
        required: false
      reference_frame:
        name: reference_frame
        description: 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)."
        multivalued: false
        range: ImagingPlane_reference_frame
        required: false
      OpticalChannel:
        name: OpticalChannel
        description: An optical channel used to record from an imaging plane.
        multivalued: true
        range: OpticalChannel
        required: true
  ImagingPlane_description:
    name: ImagingPlane_description
    description: Description of the imaging plane.
  ImagingPlane_excitation_lambda:
    name: ImagingPlane_excitation_lambda
    description: Excitation wavelength, in nm.
  ImagingPlane_imaging_rate:
    name: ImagingPlane_imaging_rate
    description: Rate that images are acquired, in Hz. If the corresponding TimeSeries
      is present, the rate should be stored there instead.
  ImagingPlane_indicator:
    name: ImagingPlane_indicator
    description: Calcium indicator.
  ImagingPlane_location:
    name: ImagingPlane_location
    description: 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.
  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
  ImagingPlane_reference_frame:
    name: ImagingPlane_reference_frame
    description: 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)."
  OpticalChannel:
    name: OpticalChannel
    description: An optical channel used to record from an imaging plane.
    is_a: NWBContainer
    attributes:
      description:
        name: description
        description: Description or other notes about the channel.
        multivalued: false
        range: OpticalChannel_description
        required: true
      emission_lambda:
        name: emission_lambda
        description: Emission wavelength for channel, in nm.
        multivalued: false
        range: OpticalChannel_emission_lambda
        required: true
  OpticalChannel_description:
    name: OpticalChannel_description
    description: Description or other notes about the channel.
  OpticalChannel_emission_lambda:
    name: OpticalChannel_emission_lambda
    description: Emission wavelength for channel, in nm.
  MotionCorrection:
    name: MotionCorrection
    description: '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).'
    is_a: NWBDataInterface
    attributes:
      CorrectedImageStack:
        name: CorrectedImageStack
        description: Reuslts from motion correction of an image stack.
        multivalued: true
        range: CorrectedImageStack
        required: true
  CorrectedImageStack:
    name: CorrectedImageStack
    description: Reuslts from motion correction of an image stack.
    is_a: NWBDataInterface
    attributes:
      corrected:
        name: corrected
        description: Image stack with frames shifted to the common coordinates.
        multivalued: false
        range: CorrectedImageStack_corrected
        required: true
      xy_translation:
        name: 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.
        multivalued: false
        range: CorrectedImageStack_xy_translation
        required: true
  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