Software for Simultaneous orientation and 3D localization microscopy with a Vortex point spread function

This code is distributed as accompanying software for the article Simultaneous orientation and 3D localization microscopy with a Vortex point spread function by Christiaan N. Hulleman, Rasmus Ø. Thorsen, Sjoerd Stallinga, and Bernd Rieger.

Any reuse of this code should cite the original associated publication.

General concept

The code uses a vectorial point-spread-function model to perform a maximum likelihood estimate on single-molecule emitters. The parameters of interest are the emitter position, photon counts, and orientation together with rotational constraint. The found values are used to calculate the Cramer-Rao Lower Bound (CRLB) for each parameter, and the CRLBs are returned along with the estimated parameters.

Using vecfitcpu

Several examples of how to use the code on simulated and experimental data are shown in the following MATLAB scripts

• vecfitcpu_vortex_simfits.m
• vecfitcpu_vortex_lambdaDNA.m
• vecfitcpu_zstack_bead.m
• generate_zernike_surfaces.m

Additional experimental data can be found via https://doi.org/10.4121/c.5136125.

MATLAB

The code is written in MATLAB, and tested to work in MATLAB R2018-R2020. The DIPImage toolbox for MATLAB is required, please see http://www.diplib.org for installation instructions.

Further questions

For further questions feel free to create an issue on GitHub. You can also contact the authors:

Christiaan N. Hulleman (c.n.hulleman@tudelft.nl)

Rasmus Ø. Thorsen (r.o.thorsen@tudelft.nl)

Sjoerd Stallinga (s.stallinga@tudelft.nl)

Bernd Rieger (b.rieger@tudelft.nl)

Reference

If you find this code useful for your research, please cite

@article {Hulleman2020.10.01.322834,
	author = {Hulleman, Christiaan N. and Thorsen, Rasmus {\O}. and Stallinga, Sjoerd and Rieger, Bernd},
	title = {Simultaneous orientation and 3D localization microscopy with a Vortex point spread function},
	year = {2020},
	doi = {10.1101/2020.10.01.322834},
	journal = {bioRxiv}
}