Complex Photonics

Understanding life has huge implications on our development and wellbeing. The outstanding complexity of living organisms brings questions we can’t answer, because there are strong limitations of available technologies giving sufficiently detailed insight through scattering tissues.
Amongst other activities we develop a new class of endoscopes that can break through this barrier. This technology can potentially go as far as reaching super-resolution with instruments having a footprint comparable to the dimensions of a single cell.

WP1Technological boost is essential for all aspect of our research agenda. Our activities focus on imaging with new types of multimode optical fibers. We focus mainly on gradient-index fibers, which offer low dispersion as well as high resilience to bending.
We develop new the fiber terminations and end-face coatings to improve applicability in challenging conditions.
For fast and reliable image recovery we develop advanced data processing algorithms using parallel processing.
Further we focus on development of modular imaging systems and user-friendly interface that may by readily deployed in laboratories of our partners.
Lastly we develop the applications of MEMS technology for ultra-fast wavefront shaping required for methods of holographic endoscopy.

Tomáš Pikálek
+420 541 514 259

Miroslav Stibůrek
+420 541 514 134

WP2Better understanding of light-transport processes will enable faster and more precise light control especially in highly dynamic regimes of imaging. Multimode fibres deliver light signals in the form of apparently random speckled patterns, in a very similar fashion to other random media. Although multimode fibres feature remarkably faithful cylindrical symmetry they are frequently classified as unpredictable optical systems. Our research challenges this commonly held notion. We develop holographic geometries for complete and accurate analysis of light signals traveling throughout the fibre and verify the observations by advanced numerical modelling. Harnessing the predictability of multimode waveguides in endoscopy will allow for numerous enhancements of deep tissue imaging.

Tomáš Čižmár
+420 541 514 131

Tomáš Tyc
+420 541 514 133

WP4In-vivo applications represents the culmination of our efforts to introduce new imaging platform for observations inside living organisms. The methodology of holographic endoscopy utilises light transport through standard multimode optical fibres to perform lensless minimally invasive micro-endoscopy. These possibilities represent a great promise for in-vivo bio-medical imaging, allowing advanced methods such microscopy to be introduced into deep regions of unrestraint and awake animal models. Our current research efforts focus on allowing these methods in flexible geometries, increasing the speed of acquisition and first in-vivo experiments in animal models.


Hana uhlířová
+420 541 514 340


Latest publications:

Stibůrek M, Ondráčková P, Tuckova T, Turtaev S, Šiler M, Pikálek T, Jákl P, Gomes A, Krejci J, Kolbabkova P, Uhlirova H, Cizmar T. “110 mu m thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics” NATURE COMMUNICATIONS, 14, 1897 (2023) (ABSTRACT)

Cifuentes A., Trägårdh J. , "A method for single particle tracking through a multimode fiber", Opt. Express 30, 36055-36064 (2022) (ABSTRACT)

A Abdelfattah et al. , "Neurophotonic tools for microscopic measurements and manipulation: status report", Neurophoton. 9(S1) 013001(2022) (ABSTRACT)

Jákl P, Šiler M, Ježek  J, and Cifuentes  A, Trägårdh J, Zemánek P and Čižmár T, "Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References.", Photonics, 9, 37 (2022) (ABSTRACT)

Stellinga D, Phillips DB, Mekhail SP, Selyem A, Turtaev S, Čižmár T, Padgett MP, "Time-of-flight 3D imaging through multimode optical fibers.", Science, 374, 1395-1399 (2021) (ABSTRACT)

Tučková T., Šiler M., Boonzajer Flaes DE, Jákl P., Turtaev S., Krátký S., Heintzmann R., Uhlířová H., Čižmár T., "Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes.", Opt. Express, 29, 38206–38220 (2021) (ABSTRACT)

Silveira BM, Pikálek T., Stibůrek M., Ondráčková P., Jákl P., Leite IT, Čižmár T., "Side-view holographic endomicroscopy via a custom-terminated multimode fibre.", Opt. Express, 29, 23083–23095 (2021) (ABSTRACT)

Cifuentes A., Pikálek T., Ondráčková P., Amezcua-Correa R., Antonio-Lopez J. E., Čižmár T., Trägårdh J., "Polarization-resolved second-harmonic generation imaging through a multimode fiber.", Optica 8, 1065-1074 (2021) (ABSTRACT)

Boonzajer Flaes DE , Štolzová H., Čižmár T., "Time-averaged image projection through a multimode fiber.", Opt. Express, 29, 28005–28020 (2021) (ABSTRACT)

Trägårdh J., Pikálek T., Šerý M., Meyer T., Popp J., Čižmár T., "Label-free CARS microscopy through a multimode fiber endoscope", Opt. Express 27, 30055–30066 (2019) (ABSTRACT)

Sergey Turtaev, Ivo T. Leite, Kevin J. Mitchell, Miles J. Padgett, David B. Phillips, Tomáš Čižmár, "Comparison of nematic liquid-crystal and DMD based spatial light modulation in complex photonics", Opt. Express 25, 29874-29884 (2017)

Pikálek T., Trägårdh J., Simpson S., Čižmár T., "Wavelength dependent characterization of a multimode fibre endoscop”, Opt. Express, 27 28239–28253 (2019) ( ABSTRACT)

Sergey Turtaev, Ivo T. Leite, Tristan Altwegg-Boussac, Janelle M. P. Pakan, Nathalie L. Rochefort, Tomáš Čižmár, "High-fidelity multimode fibre-based endoscopy for deep brain in vivo imaging", Light: Science & Applications, volume 7, Article number: 92 (2018) (ABSTRACT)

Ivo T. Leite, Sergey Turtaev, Xin Jiang, Martin Šiler, Alfred Cuschieri, Philip St.J. Russell, Tomáš Čižmár, "3-D holographic optical manipulation through high-NA soft-glass multimode fibre”, Nature Photonics (advanced online publication) (2017) ( ABSTRACT)




Team leader: Tomáš Čižmár

+420 541 514 131