Darkfield

class deeptrack.optics.Darkfield(illumination_angle=1.5707963267948966, **kwargs)

Bases: Brightfield

Images coherently illuminated samples using Darkfield.

Images samples by creating a discretized volume, where each pixel represents the effective refractive index of that pixel. Light is propagated through the sample iteratively by first propagating the light in the fourier space, followed by a refractive index correction in the real space.

Parameters

illuminationFeature

Feature-set resolving the complex field entering the sample. Default is a field with all values 1.

NAfloat

The NA of the limiting aperature.

wavelengthfloat

The wavelength of the scattered light in meters.

magnificationfloat

The magnification of the optical system.

resolutionarray_like[float (, float, float)]

The distance between pixels in the camera. A third value can be included to define the resolution in the z-direction.

refractive_index_mediumfloat

The refractive index of the medium.

paddingarray_like[int, int, int, int]

Pads the sample volume with zeros to avoid edge effects.

output_regionarray_like[int, int, int, int]

The region of the image to output (x,y,width,height). Default None returns entire image.

pupilFeature

A feature-set resolving the pupil function at focus. The feature-set receive an unaberrated pupil as input.

illumination_anglefloat

The angle relative to the optical axis. Default is π/2 radians.

Methods Summary

get(illuminated_volume, limits, fields, **kwargs)

Retrieve the darkfield image of the illuminated volume.

Methods Documentation

get(illuminated_volume, limits, fields, **kwargs)

Retrieve the darkfield image of the illuminated volume.

Parameters

illuminated_volumearray_like

The volume of the sample being illuminated.

limitsarray_like

The spatial limits of the volume.

fieldsarray_like

The fields interacting with the sample.

**kwargsdict

Additional parameters passed to the super class’s get method.

Returns

numpy.ndarray

The darkfield image obtained by calculating the squared absolute difference from 1.