pynwb.retinotopy module¶
-
class
pynwb.retinotopy.
RetinotopyImage
(name, data, bits_per_pixel, dimension, format, field_of_view)[source]¶ Bases:
pynwb.core.NWBData
Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]
Parameters: - name (
str
) – Name of this retinotopy image - data (
Iterable
) – Data field. - bits_per_pixel (
int
) – Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value. - dimension (
Iterable
) – Number of rows and columns in the image. - format (
Iterable
) – Format of image. Right now only “raw” supported. - field_of_view (
Iterable
) – Size of viewing area, in meters.
- name (
-
class
pynwb.retinotopy.
FocalDepthImage
(name, data, bits_per_pixel, dimension, format, field_of_view, focal_depth)[source]¶ Bases:
pynwb.retinotopy.RetinotopyImage
Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns].
Parameters: - name (
str
) – Name of this retinotopy image - data (
Iterable
) – Data field. - bits_per_pixel (
int
) – Number of bits used to represent each value. This is necessary to determine maximum (white) pixel value. - dimension (
Iterable
) – Number of rows and columns in the image. - format (
Iterable
) – Format of image. Right now only “raw” supported. - field_of_view (
Iterable
) – Size of viewing area, in meters. - focal_depth (float) – Focal depth offset, in meters.
- name (
-
class
pynwb.retinotopy.
RetinotopyMap
(name, data, field_of_view, dimension)[source]¶ Bases:
pynwb.core.NWBData
Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude)
Parameters:
-
class
pynwb.retinotopy.
AxisMap
(name, data, field_of_view, unit, dimension)[source]¶ Bases:
pynwb.retinotopy.RetinotopyMap
Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) with unit
Parameters:
-
class
pynwb.retinotopy.
ImagingRetinotopy
(sign_map, axis_1_phase_map, axis_1_power_map, axis_2_phase_map, axis_2_power_map, axis_descriptions, focal_depth_image, vasculature_image, name='ImagingRetinotopy')[source]¶ Bases:
pynwb.core.NWBDataInterface
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).
Parameters: - sign_map (
RetinotopyMap
) – Sine of the angle between the direction of the gradient in axis_1 and axis_2. - axis_1_phase_map (
AxisMap
) – Phase response to stimulus on the first measured axis. - axis_1_power_map (
AxisMap
) – 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. - axis_2_phase_map (
AxisMap
) – Phase response to stimulus on the second measured axis. - axis_2_power_map (
AxisMap
) – 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. - axis_descriptions (
Iterable
) – Two-element array describing the contents of the two response axis fields. Description should be something like [“altitude”, “azimuth”] or [“radius”, “theta”]. - focal_depth_image (
FocalDepthImage
) – Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format: [rows][columns]. - vasculature_image (
RetinotopyImage
) – Gray-scale anatomical image of cortical surface. Array structure: [rows][columns]. - name (
str
) – the name of this container
-
axis_1_phase_map
¶ Phase response to stimulus on the first measured axis.
-
axis_1_power_map
¶ 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.
-
axis_2_phase_map
¶ Phase response to stimulus on the second measured axis.
-
axis_2_power_map
¶ 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.
-
axis_descriptions
¶ Two-element array describing the contents of the two response axis fields. Description should be something like [“altitude”, “azimuth”] or [“radius”, “theta”].
-
focal_depth_image
¶ [rows][columns].
Type: Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format
-
sign_map
¶ Sine of the angle between the direction of the gradient in axis_1 and axis_2.
-
vasculature_image
¶ [rows][columns].
Type: Gray-scale anatomical image of cortical surface. Array structure
-
namespace
= 'core'¶
-
neurodata_type
= 'ImagingRetinotopy'¶
- sign_map (