nwb-linkml/nwb_linkml/schema/core.nwb.retinotopy.yaml
sneakers-the-rat 4faaa8efe8 I believe that's a full translation
or at least all the semantics are present. it's not pretty by any stretch of the imagination
2023-08-25 00:22:47 -07:00

333 lines
11 KiB
YAML

name: core.nwb.retinotopy
id: core.nwb.retinotopy
imports:
- core.nwb.base
- nwb.language
default_prefix: core.nwb.retinotopy/
classes:
ImagingRetinotopy:
name: ImagingRetinotopy
description: 'Intrinsic signal optical imaging or widefield imaging for measuring
retinotopy. Stores orthogonal maps (e.g., altitude/azimuth; radius/theta) of
responses to specific stimuli and a combined polarity map from which to identify
visual areas. This group does not store the raw responses imaged during retinotopic
mapping or the stimuli presented, but rather the resulting phase and power maps
after applying a Fourier transform on the averaged responses. Note: for data
consistency, all images and arrays are stored in the format [row][column] and
[row, col], which equates to [y][x]. Field of view and dimension arrays may
appear backward (i.e., y before x).'
is_a: NWBDataInterface
attributes:
axis_1_phase_map:
name: axis_1_phase_map
description: Phase response to stimulus on the first measured axis.
multivalued: false
range: ImagingRetinotopy_axis_1_phase_map
required: true
axis_1_power_map:
name: axis_1_power_map
description: Power response on the first measured axis. Response is scaled
so 0.0 is no power in the response and 1.0 is maximum relative power.
multivalued: false
range: ImagingRetinotopy_axis_1_power_map
required: false
axis_2_phase_map:
name: axis_2_phase_map
description: Phase response to stimulus on the second measured axis.
multivalued: false
range: ImagingRetinotopy_axis_2_phase_map
required: true
axis_2_power_map:
name: axis_2_power_map
description: Power response on the second measured axis. Response is scaled
so 0.0 is no power in the response and 1.0 is maximum relative power.
multivalued: false
range: ImagingRetinotopy_axis_2_power_map
required: false
axis_descriptions:
name: axis_descriptions
description: Two-element array describing the contents of the two response
axis fields. Description should be something like ['altitude', 'azimuth']
or '['radius', 'theta'].
multivalued: false
range: ImagingRetinotopy_axis_descriptions
required: true
focal_depth_image:
name: focal_depth_image
description: 'Gray-scale image taken with same settings/parameters (e.g.,
focal depth, wavelength) as data collection. Array format: [rows][columns].'
multivalued: false
range: ImagingRetinotopy_focal_depth_image
required: false
sign_map:
name: sign_map
description: Sine of the angle between the direction of the gradient in axis_1
and axis_2.
multivalued: false
range: ImagingRetinotopy_sign_map
required: false
vasculature_image:
name: vasculature_image
description: 'Gray-scale anatomical image of cortical surface. Array structure:
[rows][columns]'
multivalued: false
range: ImagingRetinotopy_vasculature_image
required: true
ImagingRetinotopy_axis_1_phase_map:
name: ImagingRetinotopy_axis_1_phase_map
description: Phase response to stimulus on the first measured axis.
attributes:
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
unit:
name: unit
description: Unit that axis data is stored in (e.g., degrees).
range: text
array:
name: array
range: ImagingRetinotopy_axis_1_phase_map_Array
ImagingRetinotopy_axis_1_phase_map_Array:
name: ImagingRetinotopy_axis_1_phase_map_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: float32
required: false
num_cols:
name: num_cols
range: float32
required: false
ImagingRetinotopy_axis_1_power_map:
name: ImagingRetinotopy_axis_1_power_map
description: Power response on the first measured axis. Response is scaled so
0.0 is no power in the response and 1.0 is maximum relative power.
attributes:
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
unit:
name: unit
description: Unit that axis data is stored in (e.g., degrees).
range: text
array:
name: array
range: ImagingRetinotopy_axis_1_power_map_Array
ImagingRetinotopy_axis_1_power_map_Array:
name: ImagingRetinotopy_axis_1_power_map_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: float32
required: false
num_cols:
name: num_cols
range: float32
required: false
ImagingRetinotopy_axis_2_phase_map:
name: ImagingRetinotopy_axis_2_phase_map
description: Phase response to stimulus on the second measured axis.
attributes:
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
unit:
name: unit
description: Unit that axis data is stored in (e.g., degrees).
range: text
array:
name: array
range: ImagingRetinotopy_axis_2_phase_map_Array
ImagingRetinotopy_axis_2_phase_map_Array:
name: ImagingRetinotopy_axis_2_phase_map_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: float32
required: false
num_cols:
name: num_cols
range: float32
required: false
ImagingRetinotopy_axis_2_power_map:
name: ImagingRetinotopy_axis_2_power_map
description: Power response on the second measured axis. Response is scaled so
0.0 is no power in the response and 1.0 is maximum relative power.
attributes:
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
unit:
name: unit
description: Unit that axis data is stored in (e.g., degrees).
range: text
array:
name: array
range: ImagingRetinotopy_axis_2_power_map_Array
ImagingRetinotopy_axis_2_power_map_Array:
name: ImagingRetinotopy_axis_2_power_map_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: float32
required: false
num_cols:
name: num_cols
range: float32
required: false
ImagingRetinotopy_axis_descriptions:
name: ImagingRetinotopy_axis_descriptions
description: Two-element array describing the contents of the two response axis
fields. Description should be something like ['altitude', 'azimuth'] or '['radius',
'theta'].
attributes:
array:
name: array
range: ImagingRetinotopy_axis_descriptions_Array
ImagingRetinotopy_axis_descriptions_Array:
name: ImagingRetinotopy_axis_descriptions_Array
is_a: Arraylike
attributes:
axis_1, axis_2:
name: axis_1, axis_2
range: text
required: true
minimum_cardinality: 2
maximum_cardinality: 2
ImagingRetinotopy_focal_depth_image:
name: ImagingRetinotopy_focal_depth_image
description: 'Gray-scale image taken with same settings/parameters (e.g., focal
depth, wavelength) as data collection. Array format: [rows][columns].'
attributes:
bits_per_pixel:
name: bits_per_pixel
description: Number of bits used to represent each value. This is necessary
to determine maximum (white) pixel value.
range: int32
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
focal_depth:
name: focal_depth
description: Focal depth offset, in meters.
range: float32
format:
name: format
description: Format of image. Right now only 'raw' is supported.
range: text
array:
name: array
range: ImagingRetinotopy_focal_depth_image_Array
ImagingRetinotopy_focal_depth_image_Array:
name: ImagingRetinotopy_focal_depth_image_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: uint16
required: false
num_cols:
name: num_cols
range: uint16
required: false
ImagingRetinotopy_sign_map:
name: ImagingRetinotopy_sign_map
description: Sine of the angle between the direction of the gradient in axis_1
and axis_2.
attributes:
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
array:
name: array
range: ImagingRetinotopy_sign_map_Array
ImagingRetinotopy_sign_map_Array:
name: ImagingRetinotopy_sign_map_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: float32
required: false
num_cols:
name: num_cols
range: float32
required: false
ImagingRetinotopy_vasculature_image:
name: ImagingRetinotopy_vasculature_image
description: 'Gray-scale anatomical image of cortical surface. Array structure:
[rows][columns]'
attributes:
bits_per_pixel:
name: bits_per_pixel
description: Number of bits used to represent each value. This is necessary
to determine maximum (white) pixel value
range: int32
dimension:
name: dimension
description: 'Number of rows and columns in the image. NOTE: row, column representation
is equivalent to height, width.'
range: int32
field_of_view:
name: field_of_view
description: Size of viewing area, in meters.
range: float32
format:
name: format
description: Format of image. Right now only 'raw' is supported.
range: text
array:
name: array
range: ImagingRetinotopy_vasculature_image_Array
ImagingRetinotopy_vasculature_image_Array:
name: ImagingRetinotopy_vasculature_image_Array
is_a: Arraylike
attributes:
num_rows:
name: num_rows
range: uint16
required: false
num_cols:
name: num_cols
range: uint16
required: false