Rasmus_photoncount.zip (3.4 MB)
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Software related to "Impact of optical aberrations on axial position determination by photometry"

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posted on 26.08.2021, 07:40 by Rasmus ThorsenRasmus Thorsen, Christiaan HullemanChristiaan Hulleman, Mathias Hammer, David Grünwald, Sjoerd Stallinga, Bernd Rieger
Software distribution
This software is distributed as accompanying software for the article Impact of optical aberrations on axial position determination by photometry by Rasmus Ø. Thorsen, Christiaan N. Hulleman, Mathias Hammer, David Grünwald, Sjoerd Stallinga and Bernd Rieger.

This distribution contains Matlab software to run the algorithms described in the article.

Matlab
The provided scripts use Matlab (https://mathworks.com) and have been tested working in version R2017b. The scripts uses help functions from the DIPimage Toolbox and must be installed to make full use of the functions. DIPimage is a freely available image processing toolbox for Matlab (http://www.diplib.org).

In the directory matlabfun all relevant Matlab functions are included. There are three examples showcasing different computations: example1.m, shows the estimated photon count for a measured bead by a fully-fledged vectorial or simplified Gaussian PSF model compared to TRABI, example2.m, computes a vectorial through-focus PSF and the corresponding photometric ratio (Gaussian fit over TRABI value) as a function of the axial position, example3.m, computes the photometric ratio over six bead measurements. These examples depict part of the data shown in the figure from the article.

We hope that these examples are instructive enough to allow the interested user to apply our code. If you have any troubles please to not hesitate to contact us at the email address given below.

Data availability
Additional data is available for download at: https://doi.org/10.4121/uuid:557b6445-5d40-402a-b214-93d7c6415195.

Terms of use

Copyright (C) 2018

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details (https://www.gnu.org).

Quantitative Imaging Group
Faculty of Applied Sciences
Delft University of Technology
Lorentzweg 1, 2628 CJ Delft
The Netherlands
contact: Bernd Rieger, b.rieger@tudelft.nl

Funding

Optical nanoscopy at 1 nm resolution: far-field fluorescence control at cryogenic temperatures

European Research Council

Find out more...

Visualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging

National Institute of Biomedical Imaging and Bioengineering

Find out more...

History

Publisher

4TU.ResearchData

Format

zipped matlab code and description files

Organizations

TU Delft, Faculty of Applied Sciences, Department of Imaging Physics; University of Massachusetts, University of Massachusetts Medical School, RNA Therapeutics Institute