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

Version 1.1
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
Learn about Data Citation Standards.
Contact Owner Share
Dataset Metrics
157 Downloads
Description
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. (2022-01-04)
Subject Physics
Keyword vectorial diffraction, dipole, simulation, image formation, microscopy, lithography
Related Publication 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. doi: 10.1002/jemt.24060
License/Data Use Agreement

Custom Dataset Terms

Table
Tree
Filter by
1 to 9 of 9 Files
00_README.txt
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/Plain Text - 884 B
Published Jan 5, 2022
18 Downloads
MD5: aab6013bcd3b5b191f7937ffd3b9e057
Main Readme file for the whole simulation package.
Preview "Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/00_README.txt"
dipole_simulator.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/MATLAB Source Code - 5.2 KB
Published Jan 5, 2022
17 Downloads
MD5: 1bc4a49c2ffe32e795dd1279418a75f7
Main program file. Only this file needs to be modified for parameter setting or alternative simulations.
01_README.txt
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.debye/Plain Text - 186 B
Published Jan 5, 2022
20 Downloads
MD5: 657bc27a7980345e996a4b259667af0e
Readme file for Debye backbone by James Manton.
Preview "Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.debye/01_README.txt"
fft_propagate.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.debye/MATLAB Source Code - 1.0 KB
Published Jan 5, 2022
16 Downloads
MD5: 5eb92f346c9ba1a88edf30a72c8e2a19
paddedfft2.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.debye/MATLAB Source Code - 630 B
Published Jan 5, 2022
17 Downloads
MD5: 08e7113640223e5615ce4fdabe0643c3
propagate.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.debye/MATLAB Source Code - 874 B
Published Jan 5, 2022
15 Downloads
MD5: 8e39e1880d1a1ea352d8f7343438ec7b
02_README.txt
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.dipole/Plain Text - 190 B
Published Jan 5, 2022
26 Downloads
MD5: fb6c69f9a369e3a12a5e27b699426ddb
Readme file for dipole propagator with Jones matrices by Florian Ströhl.
Preview "Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.dipole/02_README.txt"
polarisation_in_back_aperture.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.dipole/MATLAB Source Code - 1.7 KB
Published Jan 5, 2022
14 Downloads
MD5: cc7f14e07f255253323054b24912cac6
propagate_principle_plane_polarisation.m
Software for Quantification of the NA dependent change of shape in the image formation of a z-polarised fluorescent molecule using vectorial diffraction simulations/.dipole/MATLAB Source Code - 1.3 KB
Published Jan 5, 2022
14 Downloads
MD5: 233be5802ad0903e22abf305fcdbd85b
Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Enable access request
You must enable request access or add terms of access to restrict file access.
Save Changes
Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.
Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.
Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue
Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.
Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

You may request access to any restricted file(s) by clicking the Request Access button.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

You may request access to any restricted file(s) by clicking the Request Access button.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 4.7 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Private URL

Private URL can only be used with unpublished versions of datasets.

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details
 
Version:
Last Updated:
Version:
Last Updated:
Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

  You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

The following files and folders in this dataset may be reused as described in the CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ :

  • 00_README.txt
  • dipole_simulator.m
  • .dipole folder, including:
    • 02_README.txt
    • polarisator_in_back_aperature.m
    • propagate_principles_plane_polarisation.m

The following files and folders may be reused according to the LGPL Version 3+ license as described here: http://www.gnu.org/licenses/lgpl.html

  • .debey folder, including:
    • 01_README.txt
    • fft_propagate.m
    • paddedfft2.m
    • propagate.m

The files in the folder ".debye" may be reused according to the LGPL Version 3+ license as described here: http://www.gnu.org/licenses/lgpl.html . 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.


All other files in this dataset may be reused as described in the CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ : Our Community Norms (https://dataverse.org/best-practices/dataverse-community-norms) as well as good scientific practices expect that proper credit is given via citation.

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

https://dataverse.no/api/access/datafile/

Compute Batch
Clear Batch
Dataset Persistent Identifier Change Compute Batch
Compute Batch
Submit for Review

You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Publish Dataset

This dataset cannot be published until UiT The Arctic University of Norway is published by its administrator.

Publish Dataset

This dataset cannot be published until UiT The Arctic University of Norway and DataverseNO are published.

Return to Author

Return this dataset to contributor for modification.