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View Code? Open in Web Editor NEWImageJ plugin for the fast generation of microscopy PSF
Home Page: http://www.ee.cuhk.edu.hk/~jzli/MicroscPSF
License: MIT License
ImageJ plugin for the fast generation of microscopy PSF
Home Page: http://www.ee.cuhk.edu.hk/~jzli/MicroscPSF
License: MIT License
Hi, it is a useful, and fast ij plugin! It seems that, even this plugin is based on Gibson-Lanni theory, I can use it to generate the Born&Wolf type PSF. But I have some trouble to do so, can you give me some advice about how to do this?
Many thanks!
I discovered that the OPD calculation is inconsistent with the MATLAB version of this library. The problem, I think, is that some of the fields of GibsonLanni.java
like ng0 and ni0 are not used in the calculation.
Below is a portion of the code that I ported to another Java library and which produces an output that agrees with the MATLAB and Python versions. You might be able to use this to check or correct this library's output.
Please note that you may need to change some of the variable names because I use a slightly different notation.
// Oil thickness. I use only a single number for z (not an array),
// so you will need to change the line below.
ti = (this.ti0 + z);
double sqNA = this.NA * this.NA;
double rhoNA2;
for (int rhoi = 0; rhoi < this.numSamples; rhoi++) {
rho = rhoi * deltaRho;
rhoNA2 = rho * rho * sqNA;
// OPD in the sample
OPD = this.eZ * Math.sqrt(this.ns * this.ns - rhoNA2);
// OPD in the immersion medium
OPD += ti * Math.sqrt(this. ni * this.ni - rhoNA2) -
this.ti0 * Math.sqrt(this.ni0 * this.ni0 - rhoNA2);
// OPD in the coverslip
OPD += this.tg * Math.sqrt(this.ng * this.ng - rhoNA2) -
this.tg0 * Math.sqrt(this.ng0 * this.ng0 - rhoNA2);
W = k0 * OPD;
// You will need to change the second index back to that used in your notation
Ffun[rhoi][0] = Math.cos(W);
Ffun[rhoi][1] = Math.sin(W);
}
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