pynwb.retinotopy module

class pynwb.retinotopy.RetinotopyImage(name, data, bits_per_pixel, dimension, format, field_of_view)

Bases: 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.

class pynwb.retinotopy.FocalDepthImage(name, data, bits_per_pixel, dimension, format, field_of_view, focal_depth)

Bases: 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.

class pynwb.retinotopy.RetinotopyMap(name, data, field_of_view, dimension)

Bases: NWBData

Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude)

Parameters:

• name (str) – the name of this axis map

• data (Iterable) – data field.

• field_of_view (Iterable) – Size of viewing area, in meters.

• dimension (Iterable) – Number of rows and columns in the image

class pynwb.retinotopy.AxisMap(name, data, field_of_view, unit, dimension)

Bases: RetinotopyMap

Abstract two-dimensional map of responses to stimuli along a single response axis (e.g., altitude) with unit

Parameters:

• name (str) – the name of this axis map

• data (Iterable) – data field.

• field_of_view (Iterable) – Size of viewing area, in meters.

• unit (str) – Unit that axis data is stored in (e.g., degrees)

• dimension (Iterable) – Number of rows and columns in the image

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')

Bases: 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

property axis_1_phase_map

Phase response to stimulus on the first measured axis.

property 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.

property axis_2_phase_map

Phase response to stimulus on the second measured axis.

property 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.

property axis_descriptions

Two-element array describing the contents of the two response axis fields. Description should be something like [“altitude”, “azimuth”] or [“radius”, “theta”].

property focal_depth_image

Gray-scale image taken with same settings/parameters (e.g., focal depth, wavelength) as data collection. Array format - [rows][columns].

property sign_map

Sine of the angle between the direction of the gradient in axis_1 and axis_2.

property vasculature_image

Gray-scale anatomical image of cortical surface. Array structure - [rows][columns].

namespace = 'core'

neurodata_type = 'ImagingRetinotopy'