Brightfield

class deeptrack.optics.Brightfield(NA: float | Callable[[...], float] = 0.7, wavelength: float | Callable[[...], float] = 6.6e-07, magnification: float | Callable[[...], float] = 10, resolution: float | Callable[[...], float] = 1e-06, refractive_index_medium: float | Callable[[...], float] = 1.33, padding: Tuple[int, ...] | List[int] | ndarray | Callable[[...], Tuple[int, ...] | List[int] | ndarray] = (10, 10, 10, 10), output_region: Tuple[int, ...] | List[int] | ndarray | Callable[[...], Tuple[int, ...] | List[int] | ndarray] = (0, 0, 128, 128), pupil: Feature | None = None, illumination: Feature | None = None, upscale=1, **kwargs)

Bases: Optics

Images coherently illuminated samples.

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.

Methods Summary

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

Convolves the image with a pupil function

Methods Documentation

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

Convolves the image with a pupil function