@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 {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 {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 {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 {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 {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 {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} } @article { BrzobohatyNP13, title = {Experimental demonstration of optical transport, sorting and self-arrangement using a {\textquoteleft}tractor beam{\textquoteright}}, journal = {Nature Photon.}, volume = {7}, number = {2}, year = {2013}, pages = {123-127}, keywords = {MF}, doi = {10.1038/nphoton.2012.332}, author = {Oto Brzobohat{\'y} and V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and Luk{\'a}{\v s} Chv{\'a}tal and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { SilerAPL12, title = {Speed enhancement of multi-particle chain in a traveling standing wave}, journal = {Appl. Phys. Lett.}, volume = {100}, year = {2012}, pages = {051103}, keywords = {MF}, doi = {10.1063/1.3680234}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { BrzobohatyAPL11, title = {Dynamic size tuning of multidimensional optically bound matter}, journal = {Appl. Phys. Lett.}, volume = {99}, year = {2011}, pages = {101105}, keywords = {MF}, doi = {10.1063/1.3634007}, author = {Oto Brzobohat{\'y} and V{\'\i}t{\v e}zslav Kar{\'a}sek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { CizmarLPL11, title = {The holographic optical micro-manipulation system based on counter-propagating beams}, journal = {Laser Phys. Lett.}, volume = {8}, year = {2011}, pages = {50{\textendash}56}, keywords = {MF}, doi = {10.1002/lapl.201010100}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Oto Brzobohat{\'y} and Kishan Dholakia and P. Zem{\'a}nek} } @article { BrzobohatyOE10, title = {Experimental and theoretical determination of optical binding forces}, journal = {Opt. Express}, volume = {18}, number = {24}, year = {2010}, pages = {25389{\textendash}25402}, keywords = {MF}, issn = {1094-4087}, doi = {10.1364/OE.18.025389}, author = {Oto Brzobohat{\'y} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V{\'\i}t{\v e}zslav Kar{\'a}sek and M {\v S}iler and Kishan Dholakia and P. Zem{\'a}nek} } @article { BrzobohatyOE08, title = {High quality quasi-Bessel beam generated by round-tip axicon}, journal = {Opt. Express}, volume = {16}, year = {2008}, pages = {12688{\textendash}12700}, keywords = {MF}, doi = {10.1364/OE.16.012688}, author = {Oto Brzobohat{\'y} and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article { KarasekPRL08, title = {Long-range one-dimensional longitudinal optical binding}, journal = {Phys. Rev. Lett.}, volume = {101}, number = {14}, year = {2008}, pages = {143601}, keywords = {MF}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.101.143601}, author = {V{\'\i}t{\v e}zslav Kar{\'a}sek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and Oto Brzobohat{\'y} and P. Zem{\'a}nek and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia} } @article { JaklAPL08, title = {Static optical sorting in a laser interference field}, journal = {Appl. Phys. Lett.}, volume = {92}, number = {16}, year = {2008}, pages = {161110:1{\textendash}3}, keywords = {MF}, issn = {0003-6951}, doi = {10.1063/1.2913759}, author = {P J{\'a}kl and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M. {\v S}er{\'y} and P. Zem{\'a}nek} } @article { SilerNJP08, title = {Surface delivery of a single nanoparticle under moving evanescent standing-wave illumination}, journal = {New. J. Phys.}, volume = {10}, year = {2008}, pages = {113010}, keywords = {MF}, issn = {1367-2630}, doi = {10.1088/1367-2630/10/11/113010}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and A. Jon{\'a}{\v s} and P. Zem{\'a}nek} } @article { DholakiaMCB07, title = {Cellular and colloidal separation using optical forces}, journal = {Methods in Cell Biology}, volume = {82}, year = {2007}, pages = {467{\textendash}495}, keywords = {MF}, doi = {10.1016/S0091-679X(06)82017-0}, author = {Kishan Dholakia and MacDonald, M. P. and P. Zem{\'a}nek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r} } @article { CizmarOE07, title = {Optical tracking of spherical micro-objects in spatially periodic interference fields}, journal = {Opt. Express}, volume = {15}, year = {2007}, pages = {2262{\textendash}2272}, keywords = {MF}, doi = {10.1364/OE.15.002262}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and P. Zem{\'a}nek} } @article {JezekOE06, title = {Formation of long and thin polymer fiber using nondiffracting beam}, journal = {Opt. Express}, volume = {14}, year = {2006}, pages = {8506-8515}, keywords = {MF}, doi = {10.1364/OE.14.008506}, author = {J Je{\v z}ek and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Ned{\v e}la and P. Zem{\'a}nek} } @article {SilerAPB06, title = {Optical forces generated by evanescent standing waves and their usage for sub-micron particle delivery}, journal = {Appl. Phys. B}, volume = {84}, year = {2006}, pages = {157{\textendash}165}, keywords = {MF}, doi = {10.1007/s00340-006-2235-9}, author = {M {\v S}iler and Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M. {\v S}er{\'y} and P. Zem{\'a}nek} } @article {CizmarAPB06, title = {An optical nanotrap array movable over a milimetre range}, journal = {Appl. Phys. B}, volume = {84}, year = {2006}, pages = {197{\textendash}203}, keywords = {MF}, doi = {10.1007/s00340-006-2221-2}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M {\v S}iler and P. Zem{\'a}nek} } @article {CizmarPRB06, title = {Optical sorting and detection of sub-micron objects in a motional standing wave}, journal = {Phys. Rev. B}, volume = {74}, year = {2006}, pages = {035105:1-6}, keywords = {MF}, doi = {10.1103/PhysRevB.74.035105}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and M {\v S}iler and M. {\v S}er{\'y} and P. Zem{\'a}nek and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia} } @article {CizmarNJP06, title = {Sub-micron particle organization by self-imaging of non-diffracting beams}, journal = {New. J. Phys.}, volume = {8}, year = {2006}, pages = {43}, keywords = {MF}, doi = {10.1088/1367-2630/8/3/043}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Koll{\'a}rov{\'a} and Zden{\v e}k Bouchal and P. Zem{\'a}nek} } @article {CizmarAPL05, title = {Optical conveyor belt for delivery of submicron objects}, journal = {Appl. Phys. Lett.}, volume = {86}, year = {2005}, pages = {174101-1{\textendash}174101-3}, keywords = {MF}, doi = {10.1063/1.1915543}, author = {Tom{\'a}{\v s} {\v C}i{\v z}m{\'a}r and V. Garc{\'e}s-Ch{\'a}vez and Kishan Dholakia and P. Zem{\'a}nek} }