optics¶
Features for optically imaging of samples
Contains features which performs physical simulations of optical devices to create camera images of samples.
Classes¶
- Microscope
Image a sample using an optical system.
- Optics
Abstract base optics class.
- Fluorescence
Optical device for fluorescenct imaging.
- Brightfield
Images coherently illuminated samples.
Module classes¶
Brightfield¶
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class
deeptrack.optics.Brightfield(NA=0.7, wavelength=6.6e-07, magnification=1, resolution=(1e-06, 1e-06, 1e-06), refractive_index_medium=1.33, upscale=2, padding=(10, 10, 10, 10), output_region=(None, None, None, None), pupil: deeptrack.features.Feature = None, **kwargs)¶ 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
illumination (Feature) – Feature-set resolving the complex field entering the sample. Default is a field with all values 1.
NA (float) – The NA of the limiting aperature.
wavelength (float) – The wavelength of the scattered light in meters.
magnification (float) – The magnification of the optical system.
resolution (array_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_medium (float) – The refractive index of the medium.
upscale (int) – Upscales the pupil function for a more accurate result.
padding (array_like[int, int, int, int]) – Pads the sample volume with zeros to avoid edge effects.
output_region (array_like[int, int, int, int]) – The region of the image to output (x,y,width,height). Default None returns entire image.
pupil (Feature) – A feature-set resolving the pupil function at focus. The feature-set receive an unaberrated pupil as input.
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get(illuminated_volume, limits, **kwargs)¶ Convolves the image with a pupil function
Fluorescence¶
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class
deeptrack.optics.Fluorescence(NA=0.7, wavelength=6.6e-07, magnification=1, resolution=(1e-06, 1e-06, 1e-06), refractive_index_medium=1.33, upscale=2, padding=(10, 10, 10, 10), output_region=(None, None, None, None), pupil: deeptrack.features.Feature = None, **kwargs)¶ Optical 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
NA (float) – The NA of the limiting aperature.
wavelength (float) – The wavelength of the scattered light in meters.
magnification (float) – The magnification of the optical system.
resolution (array_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_medium (float) – The refractive index of the medium.
upscale (int) – Upscales the pupil function for a more accurate result.
padding (array_like[int, int, int, int]) – Pads the sample volume with zeros to avoid edge effects.
output_region (array_like[int, int, int, int]) – The region of the image to output (x,y,width,height). Default None returns entire image.
pupil (Feature) – A feature-set resolving the pupil function at focus. The feature-set receive an unaberrated pupil as input.
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get(illuminated_volume, limits, **kwargs)¶ Convolves the image with a pupil function
IlluminationGradient¶
-
class
deeptrack.optics.IlluminationGradient(gradient=(0, 0), constant=0, vmin=0, vmax=inf, **kwargs)¶ Adds a gradient in the illumination
- Parameters
gradient (array_like[float, float]) – Gradient of the plane to add to the amplitude of the field in pixels.
constant (float) – Constant value to add to the amplitude of the field.
vmin (float) – clips the amplitude of the field to be at least this value
vmax (float) – clips the amplitude of the field to be at most this value
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get(image, gradient, constant, vmin, vmax, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.
Microscope¶
-
class
deeptrack.optics.Microscope(sample: deeptrack.features.Feature, objective: deeptrack.features.Feature, **kwargs)¶ Image a sample using an optical system.
Wraps a feature-set defining a sample and a feature-set defining the optics.
- Parameters
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get(image, sample, objective, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.
Optics¶
-
class
deeptrack.optics.Optics(NA=0.7, wavelength=6.6e-07, magnification=1, resolution=(1e-06, 1e-06, 1e-06), refractive_index_medium=1.33, upscale=2, padding=(10, 10, 10, 10), output_region=(None, None, None, None), pupil: deeptrack.features.Feature = None, **kwargs)¶ Abstract base optics class.
Provides structure and methods common for most optical devices.
- Parameters
NA (float) – The NA of the limiting aperature.
wavelength (float) – The wavelength of the scattered light in meters.
magnification (float) – The magnification of the optical system.
resolution (array_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_medium (float) – The refractive index of the medium.
upscale (int) – Upscales the pupil function for a more accurate result.
padding (array_like[int, int, int, int]) – Pads the sample volume with zeros to avoid edge effects.
output_region (array_like[int, int, int, int]) – The region of the image to output (x,y,width,height). Default None returns entire image.
pupil (Feature) – A feature-set resolving the pupil function at focus. The feature-set receive an unaberrated pupil as input.