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

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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