SyMBac.PSF
- SyMBac.PSF.gaussian_2D(size, σ)[source]
Returns a 2D gaussian (numpy array) of size (pixels x pixels) and gaussian radius (σ)
- SyMBac.PSF.get_condensers()[source]
Returns a dictionary of common phase contrast condenser dimensions, where the numbers are W, R, diameter (in mm)
- SyMBac.PSF.get_fluorescence_kernel(Lambda, NA, n, radius, scale)[source]
Returns a 2D numpy array which is an airy-disk approximation of the fluorescence point spread function
- Parameters:
Lambda (float) – Wavelength of imaging light (micron)
NA (float) – Numerical aperture of the objective lens
n (float) – Refractive index of the imaging medium (~1 for air, ~1.4-1.5 for oil)
radius (int) – The radius of the PSF to be rendered in pixels
scale (float) – The pixel size of the image to be rendered (micron/pix)
- Return type:
2-D numpy array representing the fluorescence contrast PSF
- SyMBac.PSF.get_phase_contrast_kernel(R, W, radius, scale, NA, n, sigma, λ)[source]
Returns a 2D numpy array which is the phase contrast kernel based on microscope parameters
- Parameters:
R (float) – The radius of the phase contrast condenser (in mm)
W (float) – The width of the phase contrast condenser opening (in mm)
radius (int) – The radius of the PSF to be rendered in pixels
scale (float) – The pixel size of the image to be rendered (micron/pix)
NA (float) – Numerical aperture of the objective lens
n (float) – Refractive index of the imaging medium (~1 for air, ~1.4-1.5 for oil)
sigma (radius of a 2D gaussian of the same size as the PSF (in pixels) which is multiplied by the PSF to simulate apodisation of the PSF) –
λ (The mean wavelength of the imaging light (in micron)) –
- Return type:
2-D numpy array representing the phase contrast PSF