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imodpasteur / ZOLA-3D

Zernike Optimized Localization Algorithm for 3D single molecule localizations
GNU General Public License v3.0
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Zernike Coefficients #5

Closed ajkurz closed 6 years ago

ajkurz commented 6 years ago

I am quite new to the this field of PSF engineering so I come across a lot of questions. One I am stuck with is the following:

when modeling a PSF with >fiji/Zola/additionaltools/BestPSF model optimization then >calibration:PSF modeling and checking the >CRLB you will end up with calibration file that also contains the zernike coefficients as well as the phase values. Having a closer look then at the control software for the deformable mirror of thorlabs (https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=5056&pn=DMP40/M-P01) and comparing the listed zernike coefficients there with a list in the article (https://en.wikipedia.org/wiki/Zernike_polynomials -- scroll down to the table of zernike polynoms) there is not really a match between the named coefficients! I am quite confused about the assignment. Did I miss any explanation in the paper or in the manual?

benoitbenoit commented 6 years ago

Hello, If I understand well, you use ZOLA to get the best PSF according to a given range, and try to apply it to your DM. In thorlabs (see "Physical Stroke" table in "Spec" tab), it seems that zernike polynomials follow the OSA/ANSI index after subtracting 1 to thorlabs Z value (because thorlabs index start at 1 instead of 0). ZOLA follows also OSA/ANSI index (starting at 0 as specified here: (https://en.wikipedia.org/wiki/Zernike_polynomials). So, columns #3 and #5 in Zola (astigmatism) correspond to Z4 and Z6 for thorlabs. Best

akurz-wue commented 6 years ago

ah perfect! I was looking for that information, thank you very much!