SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy

P Křížek, T Lukeš, M Ovesný, K Fliegel… - …, 2016 - academic.oup.com
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-…

Three-dimensional super-resolution structured illumination microscopy with maximum a posteriori probability image estimation

T Lukeš, P Křížek, Z Švindrych, J Benda, M Ovesný… - Optics express, 2014 - opg.optica.org
We introduce and demonstrate a new high performance image reconstruction method for
super-resolution structured illumination microscopy based on maximum a posteriori probability …

[HTML][HTML] Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging

T Lukeš, D Glatzová, Z Kvíčalová, F Levet… - Nature …, 2017 - nature.com
Quantitative approaches for characterizing molecular organization of cell membrane molecules
under physiological and pathological conditions profit from recently developed super-…

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

D Sage, TA Pham, H Babcock, T Lukes, T Pengo… - Nature …, 2019 - nature.com
With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule
localization microscopy (SMLM), a large set of different data analysis packages have …

[HTML][HTML] Correcting for photodestruction in super-resolution optical fluctuation imaging

…, W Vandenberg, S Duwé, A Bouwens, T Lukeš… - Scientific reports, 2017 - nature.com
Super-resolution optical fluctuation imaging overcomes the diffraction limit by analyzing
fluctuations in the fluorophore emission. A key assumption of the imaging is that the fluorophores …

[HTML][HTML] Open-source microscope add-on for structured illumination microscopy

MTM Hannebelle, E Raeth, SM Leitao, T Lukeš… - Nature …, 2024 - nature.com
Super-resolution techniques expand the abilities of researchers who have the knowledge
and resources to either build or purchase a system. This excludes the part of the research …

Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction

J Pospíšil, T Lukeš, J Bendesky, K Fliegel… - …, 2019 - academic.oup.com
Background Structured illumination microscopy (SIM) is a family of methods in optical fluorescence
microscopy that can achieve both optical sectioning and super-resolution effects. SIM …

[HTML][HTML] SOFI simulation tool: a software package for simulating and testing super-resolution optical fluctuation imaging

A Girsault, T Lukes, A Sharipov, S Geissbuehler… - PLoS …, 2016 - journals.plos.org
Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction
fluorescence microscopy of living cells. By analyzing the acquired image sequence with an …

[HTML][HTML] Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions

H Deschout, T Lukes, A Sharipov, D Szlag… - Nature …, 2016 - nature.com
Live-cell imaging of focal adhesions requires a sufficiently high temporal resolution, which
remains a challenge for super-resolution microscopy. Here we address this important issue by …

Self-blinking dyes unlock high-order and multiplane super-resolution optical fluctuation imaging

K Grußmayer, T Lukes, T Lasser, A Radenovic - ACS nano, 2020 - ACS Publications
Most diffraction-unlimited super-resolution imaging critically depends on the switching of
fluorophores between at least two states, often induced using intense laser light and …