nwb-linkml/nwb_schema_language/src/data/tests/nwb.ophys.yaml

groups:
- neurodata_type_def: OnePhotonSeries
  neurodata_type_inc: ImageSeries
  doc: Image stack recorded over time from 1-photon microscope.
  attributes:
  - name: pmt_gain
    dtype: float32
    doc: Photomultiplier gain.
    required: false
  - name: scan_line_rate
    dtype: float32
    doc: Lines imaged per second. This is also stored in /general/optophysiology but
      is kept here as it is useful information for analysis, and so good to be stored
      w/ the actual data.
    required: false
  - name: exposure_time
    dtype: float32
    doc: Exposure time of the sample; often the inverse of the frequency.
    required: false
  - name: binning
    dtype: uint8
    doc: Amount of pixels combined into 'bins'; could be 1, 2, 4, 8, etc.
    required: false
  - name: power
    dtype: float32
    doc: Power of the excitation in mW, if known.
    required: false
  - name: intensity
    dtype: float32
    doc: Intensity of the excitation in mW/mm^2, if known.
    required: false
  links:
  - name: imaging_plane
    target_type: ImagingPlane
    doc: Link to ImagingPlane object from which this TimeSeries data was generated.

- neurodata_type_def: TwoPhotonSeries
  neurodata_type_inc: ImageSeries
  doc: Image stack recorded over time from 2-photon microscope.
  attributes:
  - name: pmt_gain
    dtype: float32
    doc: Photomultiplier gain.
    required: false
  - name: scan_line_rate
    dtype: float32
    doc: Lines imaged per second. This is also stored in /general/optophysiology but
      is kept here as it is useful information for analysis, and so good to be stored
      w/ the actual data.
    required: false
  datasets:
  - name: field_of_view
    dtype: float32
    dims:
    - - width|height
    - - width|height|depth
    shape:
    - - 2
    - - 3
    doc: Width, height and depth of image, or imaged area, in meters.
    quantity: '?'
  links:
  - name: imaging_plane
    target_type: ImagingPlane
    doc: Link to ImagingPlane object from which this TimeSeries data was generated.

- neurodata_type_def: RoiResponseSeries
  neurodata_type_inc: TimeSeries
  doc: ROI responses over an imaging plane. The first dimension represents time.
    The second dimension, if present, represents ROIs.
  datasets:
  - name: data
    dtype: numeric
    dims:
    - - num_times
    - - num_times
      - num_ROIs
    shape:
    - - null
    - - null
      - null
    doc: Signals from ROIs.
  - name: rois
    neurodata_type_inc: DynamicTableRegion
    doc: DynamicTableRegion referencing into an ROITable containing information on the ROIs
      stored in this timeseries.

- neurodata_type_def: DfOverF
  neurodata_type_inc: NWBDataInterface
  default_name: DfOverF
  doc: dF/F information about a region of interest (ROI). Storage hierarchy of dF/F
    should be the same as for segmentation (i.e., same names for ROIs and for image
    planes).
  groups:
  - neurodata_type_inc: RoiResponseSeries
    doc: RoiResponseSeries object(s) containing dF/F for a ROI.
    quantity: '+'

- neurodata_type_def: Fluorescence
  neurodata_type_inc: NWBDataInterface
  default_name: Fluorescence
  doc: Fluorescence information about a region of interest (ROI). Storage hierarchy
    of fluorescence should be the same as for segmentation (ie, same names for ROIs
    and for image planes).
  groups:
  - neurodata_type_inc: RoiResponseSeries
    doc: RoiResponseSeries object(s) containing fluorescence data for a ROI.
    quantity: '+'

- neurodata_type_def: ImageSegmentation
  neurodata_type_inc: NWBDataInterface
  default_name: ImageSegmentation
  doc: Stores pixels in an image that represent different regions of interest (ROIs)
    or masks. All segmentation for a given imaging plane is stored together, with
    storage for multiple imaging planes (masks) supported. Each ROI is stored in its
    own subgroup, with the ROI group containing both a 2D mask and a list of pixels
    that make up this mask. Segments can also be used for masking neuropil. If segmentation
    is allowed to change with time, a new imaging plane (or module) is required and
    ROI names should remain consistent between them.
  groups:
  - neurodata_type_inc: PlaneSegmentation
    doc: Results from image segmentation of a specific imaging plane.
    quantity: '+'

- neurodata_type_def: PlaneSegmentation
  neurodata_type_inc: DynamicTable
  doc: Results from image segmentation of a specific imaging plane.
  datasets:
  - name: image_mask
    neurodata_type_inc: VectorData
    dims:
    - - num_roi
      - num_x
      - num_y
    - - num_roi
      - num_x
      - num_y
      - num_z
    shape:
    - - null
      - null
      - null
    - - null
      - null
      - null
      - null
    doc: ROI masks for each ROI. Each image mask is the size of the original imaging
      plane (or volume) and members of the ROI are finite non-zero.
    quantity: '?'
  - name: pixel_mask_index
    neurodata_type_inc: VectorIndex
    doc: Index into pixel_mask.
    quantity: '?'
  - name: pixel_mask
    neurodata_type_inc: VectorData
    dtype:
    - name: x
      dtype: uint32
      doc: Pixel x-coordinate.
    - name: y
      dtype: uint32
      doc: Pixel y-coordinate.
    - name: weight
      dtype: float32
      doc: Weight of the pixel.
    doc: 'Pixel masks for each ROI: a list of indices and weights for the ROI. Pixel
      masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation'
    quantity: '?'
  - name: voxel_mask_index
    neurodata_type_inc: VectorIndex
    doc: Index into voxel_mask.
    quantity: '?'
  - name: voxel_mask
    neurodata_type_inc: VectorData
    dtype:
    - name: x
      dtype: uint32
      doc: Voxel x-coordinate.
    - name: y
      dtype: uint32
      doc: Voxel y-coordinate.
    - name: z
      dtype: uint32
      doc: Voxel z-coordinate.
    - name: weight
      dtype: float32
      doc: Weight of the voxel.
    doc: 'Voxel masks for each ROI: a list of indices and weights for the ROI. Voxel
      masks are concatenated and parsing of this dataset is maintained by the PlaneSegmentation'
    quantity: '?'
  groups:
  - name: reference_images
    doc: Image stacks that the segmentation masks apply to.
    groups:
    - neurodata_type_inc: ImageSeries
      doc: One or more image stacks that the masks apply to (can be one-element
        stack).
      quantity: '*'
  links:
  - name: imaging_plane
    target_type: ImagingPlane
    doc: Link to ImagingPlane object from which this data was generated.

- neurodata_type_def: ImagingPlane
  neurodata_type_inc: NWBContainer
  doc: An imaging plane and its metadata.
  datasets:
  - name: description
    dtype: text
    doc: Description of the imaging plane.
    quantity: '?'
  - name: excitation_lambda
    dtype: float32
    doc: Excitation wavelength, in nm.
  - name: imaging_rate
    dtype: float32
    doc: Rate that images are acquired, in Hz. If the corresponding TimeSeries is present, the rate should be stored
      there instead.
    quantity: '?'
  - name: indicator
    dtype: text
    doc: Calcium indicator.
  - name: location
    dtype: text
    doc: Location of the imaging plane. Specify the area, layer, comments on estimation
      of area/layer, stereotaxic coordinates if in vivo, etc. Use standard atlas
      names for anatomical regions when possible.
  - name: manifold
    dtype: float32
    dims:
    - - height
      - width
      - x, y, z
    - - height
      - width
      - depth
      - x, y, z
    shape:
    - - null
      - null
      - 3
    - - null
      - null
      - null
      - 3
    doc: "DEPRECATED Physical position of each pixel. 'xyz' represents the position\
      \ of the pixel relative to the defined coordinate space. Deprecated in favor of origin_coords and grid_spacing."
    quantity: '?'
    attributes:
    - name: conversion
      dtype: float32
      default_value: 1.0
      doc: Scalar to multiply each element in data to convert it to the specified 'unit'.
        If the data are stored in acquisition system units or other units
        that require a conversion to be interpretable, multiply the data by 'conversion'
        to convert the data to the specified 'unit'. e.g. if the data acquisition system
        stores values in this object as pixels from x = -500 to 499, y = -500 to 499
        that correspond to a 2 m x 2 m range, then the 'conversion' multiplier to get
        from raw data acquisition pixel units to meters is 2/1000.
      required: false
    - name: unit
      dtype: text
      default_value: meters
      doc: Base unit of measurement for working with the data. The default value is 'meters'.
      required: false
  - name: origin_coords
    dtype: float32
    dims:
    - - x, y
    - - x, y, z
    shape:
    - - 2
    - - 3
    doc: Physical location of the first element of the imaging plane (0, 0) for 2-D data or (0, 0, 0) for 3-D data.
      See also reference_frame for what the physical location is relative to (e.g., bregma).
    quantity: '?'
    attributes:
    - name: unit
      dtype: text
      default_value: meters
      doc: Measurement units for origin_coords. The default value is 'meters'.
  - name: grid_spacing
    dtype: float32
    dims:
    - - x, y
    - - x, y, z
    shape:
    - - 2
    - - 3
    doc: Space between pixels in (x, y) or voxels in (x, y, z) directions, in the specified unit.
      Assumes imaging plane is a regular grid. See also reference_frame to interpret the grid.
    quantity: '?'
    attributes:
    - name: unit
      dtype: text
      default_value: meters
      doc: Measurement units for grid_spacing. The default value is 'meters'.
  - name: reference_frame
    dtype: text
    doc: Describes reference frame of origin_coords and grid_spacing.
      For example, this can be a text description of the anatomical location and orientation of the grid
      defined by origin_coords and grid_spacing or the vectors needed to transform or rotate the grid to
      a common anatomical axis (e.g., AP/DV/ML). This field is necessary to interpret origin_coords and grid_spacing.
      If origin_coords and grid_spacing are not present, then this field is not required.
      For example, if the microscope takes 10 x 10 x 2 images, where the first value of the data matrix
      (index (0, 0, 0)) corresponds to (-1.2, -0.6, -2) mm relative to bregma, the spacing between pixels is 0.2 mm in
      x, 0.2 mm in y and 0.5 mm in z, and larger numbers in x means more anterior, larger numbers in y means more
      rightward, and larger numbers in z means more ventral, then enter the following --
      origin_coords = (-1.2, -0.6, -2)
      grid_spacing = (0.2, 0.2, 0.5)
      reference_frame = "Origin coordinates are relative to bregma. First dimension corresponds to anterior-posterior
      axis (larger index = more anterior). Second dimension corresponds to medial-lateral axis (larger index = more
      rightward). Third dimension corresponds to dorsal-ventral axis (larger index = more ventral)."
    quantity: '?'
  groups:
  - neurodata_type_inc: OpticalChannel
    doc: An optical channel used to record from an imaging plane.
    quantity: '+'
  links:
  - name: device
    target_type: Device
    doc: Link to the Device object that was used to record from this electrode.

- neurodata_type_def: OpticalChannel
  neurodata_type_inc: NWBContainer
  doc: An optical channel used to record from an imaging plane.
  datasets:
  - name: description
    dtype: text
    doc: Description or other notes about the channel.
  - name: emission_lambda
    dtype: float32
    doc: Emission wavelength for channel, in nm.

- neurodata_type_def: MotionCorrection
  neurodata_type_inc: NWBDataInterface
  default_name: MotionCorrection
  doc: 'An image stack where all frames are shifted (registered) to a common coordinate
    system, to account for movement and drift between frames. Note: each frame at
    each point in time is assumed to be 2-D (has only x & y dimensions).'
  groups:
  - neurodata_type_inc: CorrectedImageStack
    doc: Reuslts from motion correction of an image stack.
    quantity: '+'

- neurodata_type_def: CorrectedImageStack
  neurodata_type_inc: NWBDataInterface
  doc: Reuslts from motion correction of an image stack.
  groups:
  - name: corrected
    neurodata_type_inc: ImageSeries
    doc: Image stack with frames shifted to the common coordinates.
  - name: xy_translation
    neurodata_type_inc: TimeSeries
    doc: Stores the x,y delta necessary to align each frame to the common coordinates,
      for example, to align each frame to a reference image.
  links:
  - name: original
    target_type: ImageSeries
    doc: Link to ImageSeries object that is being registered.