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
- core.nwb.device
- nwb.language
- core.nwb.ophys.include
- core.nwb.ophys
prefixes:
  core.nwb.ophys:
    prefix_prefix: core.nwb.ophys
    prefix_reference: https://example.com/core.nwb.ophys/
default_prefix: core.nwb.ophys
classes:
  OnePhotonSeries:
    name: OnePhotonSeries
    description: Image stack recorded over time from 1-photon microscope.
    is_a: ImageSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      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
    tree_root: true
  TwoPhotonSeries:
    name: TwoPhotonSeries
    description: Image stack recorded over time from 2-photon microscope.
    is_a: ImageSeries
    attributes:
      name:
        name: name
        range: string
        required: true
      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
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      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
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      roi_response_series:
        name: roi_response_series
        description: RoiResponseSeries object(s) containing dF/F for a ROI.
        multivalued: true
        range: RoiResponseSeries
        required: true
    tree_root: 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:
      name:
        name: name
        range: string
        required: true
      roi_response_series:
        name: roi_response_series
        description: RoiResponseSeries object(s) containing fluorescence data for
          a ROI.
        multivalued: true
        range: RoiResponseSeries
        required: true
    tree_root: 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:
      name:
        name: name
        range: string
        required: true
      plane_segmentation:
        name: plane_segmentation
        description: Results from image segmentation of a specific imaging plane.
        multivalued: true
        range: PlaneSegmentation
        required: true
    tree_root: true
  PlaneSegmentation:
    name: PlaneSegmentation
    description: Results from image segmentation of a specific imaging plane.
    is_a: DynamicTable
    attributes:
      name:
        name: name
        range: string
        required: true
      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: true
        range: AnyType
      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: true
        range: AnyType
      reference_images:
        name: reference_images
        description: Image stacks that the segmentation masks apply to.
        multivalued: true
        any_of:
        - range: ImageSeries
    tree_root: true
  ImagingPlane:
    name: ImagingPlane
    description: An imaging plane and its metadata.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description of the imaging plane.
        multivalued: false
        range: text
        required: false
      excitation_lambda:
        name: excitation_lambda
        description: Excitation wavelength, in nm.
        multivalued: false
        range: float32
        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: float32
        required: false
      indicator:
        name: indicator
        description: Calcium indicator.
        multivalued: false
        range: text
        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: text
        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: text
        required: false
      optical_channel:
        name: optical_channel
        description: An optical channel used to record from an imaging plane.
        multivalued: true
        range: OpticalChannel
        required: true
    tree_root: true
  OpticalChannel:
    name: OpticalChannel
    description: An optical channel used to record from an imaging plane.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
      description:
        name: description
        description: Description or other notes about the channel.
        multivalued: false
        range: text
        required: true
      emission_lambda:
        name: emission_lambda
        description: Emission wavelength for channel, in nm.
        multivalued: false
        range: float32
        required: true
    tree_root: true
  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:
      name:
        name: name
        range: string
        required: true
      corrected_image_stack:
        name: corrected_image_stack
        description: Reuslts from motion correction of an image stack.
        multivalued: true
        range: CorrectedImageStack
        required: true
    tree_root: true
  CorrectedImageStack:
    name: CorrectedImageStack
    description: Reuslts from motion correction of an image stack.
    is_a: NWBDataInterface
    attributes:
      name:
        name: name
        range: string
        required: true
      corrected:
        name: corrected
        description: Image stack with frames shifted to the common coordinates.
        multivalued: false
        range: ImageSeries
        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: TimeSeries
        required: true
    tree_root: true