Gaussian3D

public final class Gaussian3D implements PSF

Generates a digital representation of a three-dimensional Gaussian PSF. In this simple but unphysical model, the variance of the Gaussian PSF from an emitter at a distance z from the focal plane scales linearly with the amount of defocus.

Author:Kyle M. Douglass

Methods

generatePixelSignature

public double generatePixelSignature(int pixelX, int pixelY)

Computes the relative probability of receiving a photon at the pixel.

Parameters:
  • pixelX – The pixel’s x-position.
  • pixelY – The pixel’s y-position.
Throws:
  • org.apache.commons.math.MathException –
Returns:

The probability of a photon hitting this pixel.

generateSignature

public void generateSignature(ArrayList<Pixel> pixels)

Generates the digital signature of the emitter on its nearby pixels.

Parameters:
  • pixels – The list of pixels spanned by the emitter’s image.

getFWHM

public double getFWHM()

getNumericalAperture

public double getNumericalAperture()

getRadius

public double getRadius()

Computes the half-width of the PSF for determining which pixels contribute to the emitter signal. The effective width used here is five times the standard deviation when the emitter is exactly in focus. The larger factor of five accounts for the larger lateral PSF size when it is out of focus.

Returns:The width of the PSF.

setFWHM

public void setFWHM(double fwhm)

setNumericalAperture

public void setNumericalAperture(double numericalAperture)