Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations (doi:10.18710/Z37SBD)

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Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations

doi:10.18710/Z37SBD

DataverseNO

2022-01-05

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Ströhl, Florian, 2022, "Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations", https://doi.org/10.18710/Z37SBD, DataverseNO, V1

Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations

doi:10.18710/Z37SBD

Ströhl, Florian (UiT The Arctic University of Norway)

Ströhl, Florian

Manton, James

UiT The Arctic University of Norway

2022-05-01

Matlab

836355

314546

DataverseNO

UiT The Arctic University of Norway

Ströhl, Florian

Ströhl, Florian

2022-01-04

https://doi.org/10.18710/Z37SBD

Physics, vectorial diffraction, dipole, simulation, image formation, microscopy, lithography

The point spread function of a fixed fluorophore with its dipole axis colinear to the optical axis appears donut-shaped when seen through a microscope, but can change to a spot when increasing the tube lens numerical aperture. This phenomenon can be simulated and studied using this Matlab software package, which implements vectorial Jones matrix formalism for the optical setup and the Debye diffraction integral for synthesis of the electric field and intensity distribution in the focal region.

software

<p>The files in the folder ".debye" may be reused according to the LGPL Version 3+ license as described here: <a>http://www.gnu.org/licenses/lgpl.html </a> . When reusing the files in the ".debye" folder, reference must be given to the author of the file, James Manton and in line with the LGPL Version 3+ license. </p> <br> <p>All other files in this dataset may be reused as described in the CC0 public domain dedication: <a >https://creativecommons.org/publicdomain/zero/1.0/ : </a> Our Community Norms <a>(https://dataverse.org/best-practices/dataverse-community-norms)</a> as well as good scientific practices expect that proper credit is given via citation.</p>

Ströhl, F., Bruggeman, E., Rowlands, C. J., Wolfson, D. L., & Ahluwalia, B. S. (2022). Quantification of the NA dependent change of shape in the image formation of a z-polarized fluorescent molecule using vectorial diffraction simulations. Microscopy Research and Technique, 85( 5), 2016– 2022.

10.1002/jemt.24060

Ströhl, F., Bruggeman, E., Rowlands, C. J., Wolfson, D. L., & Ahluwalia, B. S. (2022). Quantification of the NA dependent change of shape in the image formation of a z-polarized fluorescent molecule using vectorial diffraction simulations. Microscopy Research and Technique, 85( 5), 2016– 2022.

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00_README.txt

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Main Readme file for the whole simulation package.

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dipole_simulator.m

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Main program file. Only this file needs to be modified for parameter setting or alternative simulations.

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01_README.txt

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Readme file for Debye backbone by James Manton.

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fft_propagate.m

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paddedfft2.m

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propagate.m

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02_README.txt

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Readme file for dipole propagator with Jones matrices by Florian Ströhl.

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polarisation_in_back_aperture.m

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propagate_principle_plane_polarisation.m

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