DOI: 10.1093/bioinformatics/btv576. SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy

SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy

10.1093/bioinformatics/btv576

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract Summary: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). 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. Availability and implementation: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox. Contact: ghagen@uccs.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Bibliography

KÅÃÅ¾ek, P., LukeÅ¡, T., OvesnÃ½, M., Fliegel, K., & Hagen, G. M. (2015). SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. Bioinformatics, 32(2), 318â320.

Authors 5

Pavel Křížek (first)
Tomáš Lukeš (additional)
Martin Ovesný (additional)
Karel Fliegel (additional)
Guy M. Hagen (additional)

References 12 Referenced 64

10.1046/j.1365-2818.2001.00894.x / J. Microsc. / Time-domain whole-field fluorescence lifetime imaging with optical sectioning by Cole (2001)
10.1046/j.1365-2818.2000.00710.x / J. Microsc. / Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy by Gustafsson (2000)
10.1529/biophysj.107.120345 / Biophys. J. / Three-dimensional resolution doubling in widefield fluorescence microscopy by structured illumination by Gustafsson (2008)
10.1007/978-0-387-45524-2_13 / Handbook of Biological Confocal Microscopy / Structured illumination methods by Heintzmann (2006)
10.1117/12.336833 / Proc. SPIE / Laterally modulated excitation microscopy: improvement of resolution by using a diffraction grating by Heintzmann (1998)
10.1364/OE.20.024585 / Opt. Express / Flexible structured illumination microscope with a programmable illumination array by Křížek (2012)
{'key': '2023020110281461100_btv576-B7', 'first-page': '91293J', 'article-title': 'Comparison of image reconstruction methods for structured illumination microscopy', 'volume-title': 'SPIE Photonics Europe', 'author': 'Lukeš', 'year': '2014'} / SPIE Photonics Europe / Comparison of image reconstruction methods for structured illumination microscopy by Lukeš (2014)
10.1364/OE.22.029805 / Opt. Express / Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation by Lukeš (2014)
10.1364/OL.22.001905 / Opt. Lett. / Method of obtaining optical sectioning by using structured light in a conventional microscope by Neil (1997)
10.1093/bioinformatics/btu202 / Bioinformatics / ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging by Ovesný (2014)
10.1364/OE.21.024431 / Opt. Express / Image filtering in structured illumination microscopy using the Lukosz bound by Righolt (2013)
10.1111/j.1365-2818.2010.03457.x / J. Microsc. / Optical sectioning in fluorescence microscopy by Wilson (2011)

Dates

Type	When
Created	9 years, 10 months ago (Oct. 7, 2015, 9:29 p.m.)
Deposited	2 years, 6 months ago (Feb. 1, 2023, 4:35 p.m.)
Indexed	1 month, 1 week ago (July 20, 2025, 12:04 a.m.)
Issued	9 years, 10 months ago (Oct. 6, 2015)
Published	9 years, 10 months ago (Oct. 6, 2015)
Published Online	9 years, 10 months ago (Oct. 6, 2015)
Published Print	9 years, 7 months ago (Jan. 15, 2016)

Funders 0

None

BibTeX

@article{K_ek_2015, title={SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy}, volume={32}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btv576}, DOI={10.1093/bioinformatics/btv576}, number={2}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Křížek, Pavel and Lukeš, Tomáš and Ovesný, Martin and Fliegel, Karel and Hagen, Guy M.}, year={2015}, month=oct, pages={318–320} }

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