@article {3995, title = {Exploiting Complex Media Photonics to Illuminate Brain{\textquoteright}s Hidden Depth}, journal = {NEUROPHOTONICS}, volume = {11}, year = {2024}, month = {SEP 1}, pages = {S11501}, keywords = {KF, MF}, issn = {2329-423X}, doi = {10.1117/1.NPh.11.S1.S11501}, author = {Uhlirova, Hana and Cizmar, Tomas and Pakan, Janelle M. P. and Gomes, Andre} } @article {4046, title = {Generating Airy beams through multimode fibres}, journal = {Optics Express}, volume = {32}, year = {2024}, note = {

Publisher: Optica Publishing Group

}, pages = {6838{\textendash}6847}, abstract = {

Focussing light through a multimode fibre (MMF) is the basis of holographic endoscopes, which currently enable detailed imaging of deep tissue. Achieving high fidelity and purity diffraction-limited foci has been shown to be possible, when fully controlling the amplitude, phase, and two orthogonal polarisation states of the input field. Yet, generating more complex field distributions with similar performance remains to be assessed. Here, we demonstrate the generation of Airy beams through an MMF containing in excess of 90 \% of the optical power delivered by the fibre. We discuss two distinct methods for generating optical landscapes: the direct field and the Fourier domain synthesis. Moreover, we showcase the flexibility of the Fourier domain synthesis to modify the generated beam.

}, keywords = {KF, MF}, issn = {1094-4087}, doi = {10.1364/OE.506926}, url = {https://opg.optica.org/oe/abstract.cfm?uri=oe-32-5-6838}, author = {Mich{\'a}lkov{\'a}, Ivana and Colombel, Simon and Gomes, Andr{\'e} D. and Cizmar, Tomas} } @article {3994, title = {{\textquoteleft}{\textquoteleft}There{\textquoteright}s plenty of room at the bottom{\textquoteright}{\textquoteright}: deep brain imaging with holographic endo-microscopy}, journal = {NEUROPHOTONICS}, volume = {11}, year = {2024}, month = {SEP 1}, keywords = {KF, MF}, issn = {2329-423X}, doi = {10.1117/1.NPh.11.S1.S11504}, author = {Uhlirova, Hana and Stib{\r u}rek, Miroslav and Pik{\'a}lek, Tom{\'a}{\v s} and Gomes, Andre and Turtaev, Sergey and Kolbabkova, Petra and Cizmar, Tomas} } @article {3727, title = {110 mu m thin endo-microscope for deep-brain in vivo observations of neuronal connectivity, activity and blood flow dynamics}, journal = {NATURE COMMUNICATIONS}, volume = {14}, year = {2023}, month = {APR 5}, pages = {1897}, keywords = {KF, MF}, doi = {10.1038/s41467-023-36889-z}, author = {Stib{\r u}rek, Miroslav and Ondr{\'a}{\v c}kov{\'a}, Petra and Tuckova, Tereza and Turtaev, Sergey and {\v S}iler, Martin and Pik{\'a}lek, Tom{\'a}{\v s} and J{\'a}kl, Petr and Gomes, Andre and Krejci, Jana and Kolbabkova, Petra and Uhlirova, Hana and Cizmar, Tomas} } @article {3810, title = {Downsizing the Channel Length of Vertical Organic Electrochemical Transistors}, journal = {ACS APPLIED MATERIALS \& INTERFACES}, volume = {15}, year = {2023}, month = {MAY 22}, pages = {27002-27009}, type = {Article}, abstract = {

Organic electrochemical transistors (OECTs) are promisingbuildingblocks for bioelectronic devices such as sensors and neural interfaces.While the majority of OECTs use simple planar geometry, there is interestin exploring how these devices operate with much shorter channelson the submicron scale. Here, we show a practical route toward theminimization of the channel length of the transistor using traditionalphotolithography, enabling large-scale utilization. We describe thefabrication of such transistors using two types of conducting polymers.First, commercial solution-processed poly-(dioxyethylenethiophene):poly-(styrenesulfonate), PEDOT:PSS. Next, we also exploit the short channel lengthto support easy in situ electropolymerization of poly-(dioxyethylenethiophene):tetrabutylammonium hexafluorophosphate, PEDOT:PF6. Both variantsshow different promising features, leading the way in terms of transconductance(g (m)), with the measured peak g (m) up to 68 mS for relatively thin (280 nm) channel layerson devices with the channel length of 350 nm and with widths of 50,100, and 200 mu m. This result suggests that the use of electropolymerizedsemiconductors, which can be easily customized, is viable with verticalgeometry, as uniform and thin layers can be created. Spin-coated PEDOT:PSSlags behind with the lower values of g (m); however, it excels in terms of the speed of the device and alsohas a comparably lower off current (300 nA), leading to unusuallyhigh on/off ratio, with values up to 8.6 x 10(4). Ourapproach to vertical gap devices is simple, scalable, and can be extendedto other applications where small electrochemical channels are desired.

}, keywords = {KF, MF}, issn = {1944-8244}, doi = {10.1021/acsami.3c02049}, author = {Brodsk{\'y}, Jan and Gablech, Imrich and Migliaccio, Ludovico and Havli{\textquoteright}cek, Marek and Donahue, Mary J. J. and Glowacki, Eric D. D.} } @article {3503, title = {Endoscopic Imaging Using a Multimode Optical Fibre Calibrated with Multiple Internal References}, journal = {Photonics}, volume = {9}, year = {2022}, pages = {37}, keywords = {BF, KF, MF}, doi = {10.3390/photonics9010037}, url = {https://www.mdpi.com/2304-6732/9/1/37}, author = {J{\'a}kl, Petr and {\v S}iler, Martin and Je{\v z}ek, Jan and Cifuentes, Angel and Tr{\"a}g{\r a}rdh, Johanna and Zem{\'a}nek, Pavel and Cizmar, Tomas} } @article {3644, title = {How to Build the {\textquoteleft}{\textquoteleft}Optical Inverse{\textquoteright}{\textquoteright} of a Multimode Fibre}, journal = {Intelligent Computing}, volume = {2022}, year = {2022}, pages = {9816026}, keywords = {KF, MF}, isbn = {null}, doi = {10.34133/2022/9816026}, url = {https://doi.org/10.34133/2022/9816026}, author = {Butaite, Une G. and Kupianskyi, Hlib and Cizmar, Tomas and Phillips, David B.} } @article {3600, title = {Hybrid multimode - multicore fibre based holographic endoscope for deep-tissue neurophotonics}, journal = {Light: Advanced Manufacturing}, volume = {3}, year = {2022}, pages = {1}, keywords = {KF, MF}, issn = {2689-9620}, doi = {10.37188/lam.2022.029}, url = {https://www.light-am.com//article/id/5e7e4e57-462a-4c48-92ca-1aec395fed59}, author = {Yang Du and Sergey Turtaev and Ivo T Leite and Adrian Lorenz and Jens Kobelke and Katrin Wondraczek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3599, title = {A method for single particle tracking through a multimode fiber}, journal = {Opt. Express}, volume = {30}, year = {2022}, month = {Sep}, pages = {36055{\textendash}36064}, keywords = {KF, MF}, doi = {10.1364/OE.470111}, url = {http://opg.optica.org/oe/abstract.cfm?URI=oe-30-20-36055}, author = {Angel Cifuentes and Johanna Tr{\"a}g{\r a}rdh} } @article {3564, title = {Near perfect focusing through multimode fibres}, journal = {Opt. Express}, volume = {30}, year = {2022}, month = {Mar}, pages = {10645{\textendash}10663}, keywords = {KF, MF}, doi = {10.1364/OE.452145}, url = {http://opg.optica.org/oe/abstract.cfm?URI=oe-30-7-10645}, author = {Andr{\'e} D. Gomes and Sergey Turtaev and Yang Du and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3565, title = {Neurophotonic tools for microscopic measurements and manipulation: status report}, journal = {Neurophotonics}, volume = {9}, year = {2022}, keywords = {KF, MF}, doi = {10.1117/1.NPh.9.S1.013001}, url = {https://doi.org/10.1117/1.NPh.9.S1.013001}, author = {Ahmed Abdelfattah and Sapna Ahuja and Taner Akkin and Srinivasa Rao Allu and David A. Boas and Joshua Brake and Erin M. Buckley and Robert E. Campbell and Anderson I. Chen and Xiaojun Cheng and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Irene Costantini and Massimo De Vittorio and Anna Devor and Patrick R. Doran and Mirna El Khatib and Valentina Emiliani and Natalie Fomin-Thunemann and Yeshaiahu Fainman and Tom{\'a}s Fern{\'a}ndez Alfonso and Christopher G. L. Ferri and Ariel Gilad and Xue Han and Andrew Harris and Elizabeth M. C. Hillman and Ute Hochgeschwender and Matthew G. Holt and Na Ji and Kivilcim Kili{\c c} and Evelyn M. R. Lake and Lei Li and Tianqi Li and Philipp M{\"a}chler and Rickson C. Mesquita and Evan W. Miller and K.M. Naga Srinivas Nadella and U. Valentin N{\"a}gerl and Yusuke Nasu and Axel Nimmerjahn and Petra Ondr{\'a}{\v c}kov{\'a} and Francesco S. Pavone and Citlali Perez Campos and Darcy S. Peterka and Filippo Pisano and Ferruccio Pisanello and Francesca Puppo and Bernardo L. Sabatini and Sanaz Sadegh and Sava Sakad{\v z}ic and Shy Shoham and Sanaya N. Shroff and R. Angus Silver and Ruth R. Sims and Spencer L. Smith and Vivek J. Srinivasan and Martin Thunemann and Lei Tian and Lin Tian and Thomas Troxler and Antoine Valera and Alipasha Vaziri and Sergei A. Vinogradov and Flavia Vitale and Lihong V. Wang and Hana Uhl{\'\i}{\v r}ov{\'a} and Chris Xu and Changhuei Yang and Mu-Han Yang and Gary Yellen and Ofer Yizhar and Yongxin Zhao} } @article {3504, title = {Raman spectroscopy{\textemdash}a tool for rapid differentiation among microbes causing urinary tract infections}, journal = {Analytica Chimica Acta}, volume = {1191}, year = {2022}, pages = {339292}, keywords = {BF, KF, MF}, issn = {0003-2670}, doi = {https://doi.org/10.1016/j.aca.2021.339292}, url = {https://www.sciencedirect.com/science/article/pii/S0003267021011181}, author = {Katar{\'\i}na Rebro{\v s}ov{\'a} and Silvie Bernatov{\'a} and Martin {\v S}iler and Magdalena Uhlirova and Ota Samek and Jan Je{\v z}ek and Veronika Hol{\'a} and Filip R{\r u}{\v z}i{\v c}ka and Pavel Zem{\'a}nek} } @article {3627, title = {Roadmap on wavefront shaping and deep imaging in complex media}, journal = {Journal of Physics: Photonics}, volume = {4}, year = {2022}, month = {aug}, pages = {042501}, abstract = {

The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working in this field, which has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead.

}, keywords = {KF, MF}, doi = {10.1088/2515-7647/ac76f9}, url = {https://dx.doi.org/10.1088/2515-7647/ac76f9}, author = {Sylvain Gigan and Ori Katz and Hilton B de Aguiar and Esben Ravn Andresen and Alexandre Aubry and Jacopo Bertolotti and Emmanuel Bossy and Dorian Bouchet and Joshua Brake and Sophie Brasselet and Yaron Bromberg and Hui Cao and Thomas Chaigne and Zhongtao Cheng and Wonshik Choi and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Meng Cui and Vincent R Curtis and Hugo Defienne and Matthias Hofer and Ryoichi Horisaki and Roarke Horstmeyer and Na Ji and Aaron K LaViolette and Jerome Mertz and Christophe Moser and Allard P Mosk and Nicolas C P{\'e}gard and Rafael Piestun and Sebastien Popoff and David B Phillips and Demetri Psaltis and Babak Rahmani and Herv{\'e} Rigneault and Stefan Rotter and Lei Tian and Ivo M Vellekoop and Laura Waller and Lihong Wang and Timothy Weber and Sheng Xiao and Chris Xu and Alexey Yamilov and Changhuei Yang and Hasan Y{\i}lmaz} } @article {3509, title = {Suppression of the Non-Linear Background in a Multimode Fibre CARS Endoscope}, journal = {Biomedical Optics Express}, volume = {13}, year = {2022}, pages = {862{\textendash}864}, keywords = {KF, MF}, issn = {2156-7085}, doi = {10.1364/BOE.450375}, author = {Pik{\'a}lek, Tom{\'a}{\v s} and Stib{\r u}rek, Miroslav and Simpson, Stephen and Cizmar, Tomas and Tr{\"a}g{\r a}rdh, Johanna} } @article {3435, title = {All-optical manipulation of photonic membranes}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {May}, pages = {14260{\textendash}14268}, abstract = {

We demonstrate the all-optical manipulation of polymeric membranes in microfluidic environments. The membranes are decorated with handles for their use in holographic optical tweezers systems. Our results show that due to their form factor the membranes present a substantial increase in their mechanical stability, respect to micrometric dielectric particles. This intrinsic superior stability is expected to improve profoundly a wide range of bio-photonic applications that rely on the optical manipulation of micrometric objects.

}, keywords = {KF, MF}, doi = {10.1364/OE.420364}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-29-10-14260}, author = {Meisam Askari and Blair C. Kirkpatrick and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Andrea Di Falco} } @article {3436, title = {Compressively sampling the optical transmission matrix of a multimode fibre}, journal = {LIGHT-SCIENCE \& APPLICATIONS}, volume = {10}, year = {2021}, month = {APR 21}, pages = {88}, keywords = {KF, MF}, issn = {2047-7538}, doi = {10.1038/s41377-021-00514-9}, author = {Li, Shuhui and Saunders, Charles and Lum, Daniel J. and Murray-Bruce, John and Goyal, Vivek K. and Cizmar, Tomas and Phillips, David B.} } @article {3479, title = {Computational image enhancement of multimode fibre-based holographic endo-microscopy: harnessing the muddy modes}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {Nov}, pages = {38206{\textendash}38220}, keywords = {KF, MF}, doi = {10.1364/OE.434848}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-23-38206}, author = {Tereza Tu{\v c}kov{\'a} and Martin {\v S}iler and DE Boonzajer Flaes and Petr J{\'a}kl and Sergey Turtaev and Stanislav Kr{\'a}tk{\'y} and Rainer Heintzmann and Hana Uhl{\'\i}{\v r}ov{\'a} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3470, title = {Memory effect assisted imaging through multimode optical fibres}, journal = {Nature Communications}, volume = {12}, year = {2021}, pages = {3751}, abstract = {

When light propagates through opaque material, the spatial information it holds becomes scrambled, but not necessarily lost. Two classes of techniques have emerged to recover this information: methods relying on optical memory effects, and transmission matrix (TM) approaches. Here we develop a general framework describing the nature of memory effects in structures of arbitrary geometry. We show how this framework, when combined with wavefront shaping driven by feedback from a guide-star, enables estimation of the TM of any such system. This highlights that guide-star assisted imaging is possible regardless of the type of memory effect a scatterer exhibits. We apply this concept to multimode fibres (MMFs) and identify a {\textquoteleft}quasi-radial{\textquoteright} memory effect. This allows the TM of an MMF to be approximated from only one end - an important step for micro-endoscopy. Our work broadens the applications of memory effects to a range of novel imaging and optical communication scenarios.

}, keywords = {KF, MF}, issn = {2041-1723}, doi = {10.1038/s41467-021-23729-1}, url = {https://doi.org/10.1038/s41467-021-23729-1}, author = {Li, Shuhui and Horsley, Simon A. R. and Tyc, Tom{\'a}{\v s} and Cizmar, Tomas and Phillips, David B.} } @article {3437, title = {Observing distant objects with a multimode fiber-based holographic endoscope}, journal = {APL Photonics}, volume = {6}, year = {2021}, pages = {036112}, keywords = {KF, MF}, doi = {10.1063/5.0038367}, url = {https://doi.org/10.1063/5.0038367}, author = {Leite,Ivo T. and Turtaev,Sergey and Boonzajer Flaes,Dirk E. and {\v C}i{\v z}m{\'a}r,Tom{\'a}{\v s}} } @article {3450, title = {Polarization-resolved second-harmonic generation imaging through a multimode fiber}, journal = {Optica}, volume = {8}, year = {2021}, pages = {1065{\textendash}1074}, keywords = {KF, MF}, author = {Cifuentes, Angel and Pik{\'a}lek, Tom{\'a}{\v s} and Ondr{\'a}{\v c}kov{\'a}, Petra and Amezcua-Correa, Rodrigo and Antonio-Lopez, Jos{\'e} Enrique and Cizmar, Tomas and Tr{\"a}g{\r a}rdh, Johanna} } @article {3410, title = {Rapid detection of antibiotic sensitivity of Staphylococcus aureus by Raman tweezers}, journal = {Eur. Phys. J. Plus}, volume = {136}, year = {2021}, pages = {233}, keywords = {BF, KF, MF}, doi = {10.1140/epjp/s13360-021-01152-1}, url = {https://doi.org/10.1140/epjp/s13360-021-01152-1}, author = {Bernatov{\'a}, S. and K. Rebro{\v s}ov{\'a} and Pil{\'a}t, Z. and M. {\v S}er{\'y} and Gjevik, A. and Samek, O. and Je{\v z}ek, J. and {\v S}iler, M. and Kizovsk{\'y}, M. and Klementov{\'a}, T. and Hol{\'a}, V. and F. R{\r u}{\v z}i{\v c}ka and Zem{\'a}nek, P.} } @article {3471, title = {Side-view holographic endomicroscopy via a custom-terminated multimode fibre}, journal = {Opt. Express}, volume = {29}, year = {2021}, pages = {23083{\textendash}23095}, abstract = {

Microendoscopes based on optical fibres have recently come to the fore as promising candidates allowing in-vivo observations of otherwise inaccessible biological structures in animal models. Despite being still in its infancy, imaging can now be performed at the tip of a single multimode fibre, by relying on powerful holographic methods for light control. Fibre based endoscopy is commonly performed en face, resulting in possible damage of the specimen owing to the direct contact between the distal end of the probe and target. On this ground, we designed an all-fibre probe with an engineered termination that reduces compression and damage to the tissue under investigation upon probe insertion. The geometry of the termination brings the field of view to a plane parallel to the fibre\&\#x2019;s longitudinal direction, conveying the probe with off-axis imaging capabilities. We show that its focusing ability also benefits from a higher numerical aperture, resulting in imaging with increased spatial resolution. The effect of probe insertion was investigated inside a tissue phantom comprising fluorescent particles suspended in agarose gel, and a comparison was established between the novel side-view probe and the standard en face fibre probe. This new concept paves the way to significantly less invasive deep-tissue imaging.

}, keywords = {KF, MF}, doi = {10.1364/OE.426235}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-15-23083}, author = {Beatriz M. Silveira and Tom{\'a}{\v s} Pik{\'a}lek and Miroslav Stib{\r u}rek and Petra Ondr{\'a}{\v c}kov{\'a} and Petr J{\'a}kl and Ivo T. Leite and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3497, title = {Thermal stability of wavefront shaping using a DMD as a spatial light modulator}, journal = {Opt. Express}, volume = {29}, year = {2021}, month = {Dec}, pages = {41808{\textendash}41818}, keywords = {KF, MF}, doi = {10.1364/OE.442284}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-25-41808}, author = {Benjamin Rudolf and Yang Du and Sergey Turtaev and Ivo T. Leite and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3469, title = {Time-averaged image projection through a multimode fiber}, journal = {Opt. Express}, volume = {29}, year = {2021}, pages = {28005{\textendash}28020}, abstract = {

Many disciplines, ranging from lithography to opto-genetics, require high-fidelity image projection. However, not all optical systems can display all types of images with equal ease. Therefore, the image projection quality is dependent on the type of image. In some circumstances, this can lead to a catastrophic loss of intensity or image quality. For complex optical systems, it may not be known in advance which types of images pose a problem. Here we show a new method called Time-Averaged image Projection (TAP), allowing us to mitigate these limitations by taking the entire image projection system into account despite its complexity and building the desired intensity distribution up from multiple illumination patterns. Using a complex optical setup, consisting of a wavefront shaper and a multimode optical fiber illuminated by coherent light, we succeeded to suppress any speckle-related background. Further, we can display independent images at multiple distances simultaneously, and alter the effective sharpness depth through the algorithm. Our results demonstrate that TAP can significantly enhance the image projection quality in multiple ways. We anticipate that our results will greatly complement any application in which the response to light irradiation is relatively slow (one microsecond with current technology) and where high-fidelity spatial distribution of optical power is required.

}, keywords = {KF, MF}, doi = {10.1364/OE.431842}, url = {http://www.osapublishing.org/oe/abstract.cfm?URI=oe-29-18-28005}, author = {Dirk Boonzajer Flaes and Hana {\v S}tolzov{\'a} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3498, title = {Time-of-flight 3D imaging through multimode optical fibers}, journal = {Science}, volume = {374}, year = {2021}, pages = {1395-1399}, keywords = {KF, MF}, doi = {10.1126/science.abl3771 URL = https://www.science.org/doi/abs/10.1126/science.abl3771}, author = {Daan Stellinga and David B. Phillips and Simon Peter Mekhail and Adam Selyem and Sergey Turtaev and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Miles J. Padgett} } @article {3337, title = {Analysis of bacteriophage-host interaction by Raman tweezers}, journal = {Analytical Chemistry}, volume = {92}, year = {2020}, pages = {12304{\textendash}12311}, keywords = {BF, KF, MF}, author = {Pil{\'a}t, Z and Jon{\'a}{\v s}, A and Pil{\'a}tov{\'a}, J and Klementov{\'a}, T and Bernatov{\'a}, S and {\v S}iler, M and Ma{\v n}ka, T and Kizovsk{\'y}, M and R{\r u}{\v z}i{\v c}ka, F and Pan{\r u}{\v c}ek, R and Neugebauer, U and Samek, O and Zem{\'a}nek, P} } @article {3327, title = {Cellular locomotion using environmental topography}, journal = {Nature}, volume = {582}, year = {2020}, pages = {582{\textendash}585}, keywords = {KF, MF}, author = {Anne Reversat and Florian Gaertner and Jack Merrin and Julian Stopp and Saren Tasciyan and Juan Aguilera and Ingrid de Vries and Robert Hauschild and Miroslav Hons and Matthieu Piel and Andrew Callan-Jones and Raphael Voituriez and Michael Sixt} } @article {3368, title = {Entropy Production in an Elementary, Light Driven Micro-Machine}, journal = {Frontiers in Physics}, volume = {8}, year = {2020}, pages = {538}, abstract = {

We consider the basic, thermodynamic properties of an elementary micro-machine operating at colloidal length scales. In particular, we track and analyze the driven stochastic motion of a carefully designed micro-propeller rotating unevenly in an optical tweezers, in water. In this intermediate regime, the second law of macroscopic thermodynamics is satisfied only as an ensemble average, and individual trajectories can be temporarily associated with decreases in entropy. We show that our light driven micro-propeller satisfies an appropriate fluctuation theorem that constrains the probability with which these apparent violations of the second law occur. Implications for the development of more complex micro-machines are discussed.

}, keywords = {KF, LF, MF}, issn = {2296-424X}, doi = {10.3389/fphy.2020.593122}, url = {https://www.frontiersin.org/article/10.3389/fphy.2020.593122}, author = {Box, Stuart J. and Allen, Michael P. and Phillips, David B. and Simpson, Stephen H.} } @article {3189, title = {Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy}, journal = {Future Microbiology}, volume = {14}, year = {2019}, pages = {509-517}, abstract = {

Aim: Finding rapid, reliable diagnostic methods is a big challenge in clinical microbiology. Raman spectroscopy is an optical method used for multiple applications in scientific fields including microbiology. This work reports its potential in identifying biofilm positive strains of Candida parapsilosis and Staphylococcus epidermidis. Materials \& methods: We tested 54 S. epidermidis strains (23 biofilm positive, 31 negative) and 51 C. parapsilosis strains (27 biofilm positive, 24 negative) from colonies on Mueller-Hinton agar plates, using Raman spectroscopy. Results: The accuracy was 98.9\% for C. parapsilosis and 96.1\% for S. epidermidis. Conclusion: The method showed great potential for identifying biofilm positive bacterial and yeast strains. We suggest that Raman spectroscopy might become a useful aid in clinical diagnostics.

}, keywords = {BF, KF, MF}, doi = {10.2217/fmb-2018-0297}, url = {https://doi.org/10.2217/fmb-2018-0297}, author = {Rebro{\v s}ov{\'a}, Katar{\'\i}na and {\v S}iler, Martin and Samek, Ota and R{\r u}{\v z}i{\v c}ka, Filip and Bernatov{\'a}, Silvie and Je{\v z}ek, Jan and Zem{\'a}nek, Pavel and Hol{\'a}, Veronika} } @article {3191, title = {Label-free CARS microscopy through a multimode fiber endoscope}, journal = {Opt. Express}, volume = {27}, year = {2019}, pages = {30055{\textendash}30066}, abstract = {

Multimode fibres have recently been employed as high-resolution ultra-thin endoscopes, capable of imaging biological structures deep inside tissue in vivo. Here, we extend this technique to label-free non-linear microscopy with chemical contrast using coherent anti-Stokes Raman scattering (CARS) through a multimode fibre endoscope, which opens up new avenues for instant and in-situ diagnosis of potentially malignant tissue. We use a commercial 125 \&\#x00B5;m diameter, 0.29 NA GRIN fibre, and wavefront shaping on an SLM is used to create foci that are scanned behind the fibre facet across the sample. The chemical selectivity is demonstrated by imaging 2 \&\#x00B5;m polystyrene and 2.5 \&\#x00B5;m PMMA beads with per pixel integration time as low as 1 ms for epi-detection.

}, keywords = {KF, MF}, doi = {10.1364/OE.27.030055}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-21-30055}, author = {Johanna Tr{\"a}g{\r a}rdh and Tom{\'a}{\v s} Pik{\'a}lek and Mojm{\'\i}r {\v S}er{\'y} and Tobias Meyer and J{\"u}rgen Popp and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {3232, title = {Nanobore fiber focus trap with enhanced tuning capabilities}, journal = {Opt. Express}, volume = {27}, year = {2019}, month = {Dec}, pages = {36221{\textendash}36230}, keywords = {KF, MF}, doi = {10.1364/OE.27.036221}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-25-36221}, author = {Malte Plidschun and Stefan Weidlich and Martin {\v S}iler and Karina Weber and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Markus A. Schmidt} } @article {3190, title = {Wavelength dependent characterization of a multimode fibre endoscope}, journal = {Opt. Express}, volume = {27}, year = {2019}, pages = {28239{\textendash}28253}, abstract = {

Multimode fibres have recently shown promise as miniature endoscopic probes. When used for non-linear microscopy, the bandwidth of the imaging system limits the ability to focus light from broadband pulsed lasers as well as the possibility of wavelength tuning during the imaging. We demonstrate that the bandwidth is limited by the dispersion of the off-axis hologram displayed on the SLM, which can be corrected for, and by the limited bandwidth of the fibre itself. The selection of the fibre is therefore crucial for these experiments. In addition, we show that a standard prism pulse compressor is sufficient for material dispersion compensation for multi-photon imaging with a fibre endoscope.

}, keywords = {KF, MF}, doi = {10.1364/OE.27.028239}, url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-27-20-28239}, author = {Tom{\'a}{\v s} Pik{\'a}lek and Johanna Tr{\"a}g{\r a}rdh and Stephen Simpson and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {TurtaevLSA18, title = {High-fidelity multimode fibre-based endoscopy for deep brain in vivo imaging}, journal = {Light: Sci. Appl.}, volume = {7}, year = {2018}, pages = {92}, keywords = {KF, MF}, doi = {10.1038/s41377-018-0094-x}, author = {S. Turtaev and I.T. Leite and Altwegg-Boussac, T. and Pakan, J.M.P. and Rochefort, N.L. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {FlaesPRL18, title = {Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides}, journal = {Phys. Rev. Lett.}, volume = {120}, year = {2018}, pages = {233901:1-5}, keywords = {KF, MF}, doi = {10.1103/PhysRevLett.120.233901}, author = {Flaes, D.E.B. and Stopka, Jan and S. Turtaev and de Boer, J.F. and Tyc, T. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article {Vasquez-LopezLSA18, title = {Subcellular spatial resolution achieved for deep-brain imaging in vivo using a minimally invasive multimode fiber}, journal = {Light: Sci. Appl.}, volume = {7}, year = {2018}, pages = {110}, keywords = {KF, MF}, doi = {10.1038/s41377-018-0111-0}, author = {Vasquez-Lopez, S.A. and Turcotte, R. and Koren, V. and Ploschner, M. and Padamsey, Z. and Booth, M. and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Emptage, N.J.} } @article { LeiteNP18, title = {Three-dimensional holographic optical manipulation through a high-numerical-aperture soft-glass multimode fibre}, journal = {Nature Photon.}, volume = {12}, year = {2018}, pages = {33{\textendash}39}, keywords = {KF, MF}, doi = {10.1038/s41566-017-0053-8}, author = {I.T. Leite and S. Turtaev and Xin Jiang and M {\v S}iler and Alfred Cuschieri and Philip St. J. Russell and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} }