Fluorescence#
- class deeptrack.optics.Fluorescence(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:
OpticsOptical device for fluorescenct imaging
Images samples by creating a discretized volume, where each pixel represents the intensity of the light emitted by fluorophores in the the voxel.
Parameters#
- 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, **kwargs)Convolves the image with a pupil function
Methods Documentation
- get(illuminated_volume, limits, **kwargs)#
Convolves the image with a pupil function