simtoolbox/simtoolbox

All released versions of SIMToolbox MATLAB codes

SIMToolbox: a MATLAB toolbox for structured illumination microscopy

SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy. Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination.

Authors: Pavel Křížek, Tomáš Lukeš, Martin Ovesný, Jakub Pospíšil, Vojtěch Terš, Karel Fliegel, and Guy M. Hagen

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Associated publications:

T. Lukeš, P. Křížek, Z. Švindrych, J. Benda, M. Ovesný, K. Fliegel, M. Klíma, G. M. Hagen, Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation, Optics Express, 22(24), 29805-29817, (2014). doi:10.1364/OE.22.029805

P. Křížek, T. Lukeš, M. Ovesný, K. Fliegel, G. M. Hagen, SIMToolbox: A MATLAB toolbox for structured illumination fluorescence microscopy, Bioinformatics, 32(2), 318–320, (2016). doi:10.1093/bioinformatics/btv576

J. Pospíšil, T. Lukeš, J. Bendesky, K. Fliegel, K. Spendier, G.M. Hagen, Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction, GigaScience, 8(1), 1-12, (2019). doi:10.1093/gigascience/giy126

M. T. M. Hannebelle, E. Raeth, S. M. Leitao, T. Lukeš, J. Pospíšil, C. Toniolo, O. F. Venzin, A. Chrisnandy, P. P. Swain, N. Ronceray, M. P. Lütolf, A. C. Oates, G.M. Hagen, T. Lasser, A. Radenovic, J. D. McKinney, G. E. Fantner, Open-source microscope add-on for structured illumination microscopy, Nature Communications, 15(1550), 1-8, (2024). doi:10.1038/s41467-024-45567-7

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All standalone application installers can be found on the project's Google Drive.

simtoolbox's Issues

Question: OTF of SR-SIM reconstruction

The OTF in SR-SIM function seems generated automatically. But sometimes we want to input our own OTF or PSF.
So, do you have given a shot on this request yet or is it too difficult to modify the source code?
Even if it is not possible to input custom OTF or PSF, is it possible to give several parameters to modify OTF so it can get much closer to the real OTF?