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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3

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    Enhancing resolution and contrast in fibre bundle-based fluorescence microscopy using generative adversarial network
    (Wiley, 2024) Morova, Berna; Aydin, Musa; Eren, Furkan; Pysz, Dariusz; Buczynski, Ryszard; Department of Physics; Ketabchi, Amir Mohammad; Uysallı, Yiğit; Bavili, Nima; Kiraz, Alper; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences
    Fibre bundle (FB)-based endoscopes are indispensable in biology and medical science due to their minimally invasive nature. However, resolution and contrast for fluorescence imaging are limited due to characteristic features of the FBs, such as low numerical aperture (NA) and individual fibre core sizes. In this study, we improved the resolution and contrast of sample fluorescence images acquired using in-house fabricated high-NA FBs by utilising generative adversarial networks (GANs). In order to train our deep learning model, we built an FB-based multifocal structured illumination microscope (MSIM) based on a digital micromirror device (DMD) which improves the resolution and the contrast substantially compared to basic FB-based fluorescence microscopes. After network training, the GAN model, employing image-to-image translation techniques, effectively transformed wide-field images into high-resolution MSIM images without the need for any additional optical hardware. The results demonstrated that GAN-generated outputs significantly enhanced both contrast and resolution compared to the original wide-field images. These findings highlight the potential of GAN-based models trained using MSIM data to enhance resolution and contrast in wide-field imaging for fibre bundle-based fluorescence microscopy. Lay Description: Fibre bundle (FB) endoscopes are essential in biology and medicine but suffer from limited resolution and contrast for fluorescence imaging. Here we improved these limitations using high-NA FBs and generative adversarial networks (GANs). We trained a GAN model with data from an FB-based multifocal structured illumination microscope (MSIM) to enhance resolution and contrast without additional optical hardware. Results showed significant enhancement in contrast and resolution, showcasing the potential of GAN-based models for fibre bundle-based fluorescence microscopy.
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    Resonant channel-dropping filter with integrated detector system based on optical fiber coupler and microsphere
    (IOP Publications, 2004) İşci, Şenol; Yılmaz, Yiğit; Department of Physics; Serpengüzel, Ali; Kurt, Adnan; Bilici, Temel; Faculty Member; Teaching Faculty; N/A; Department of Physics; College of Sciences; N/A; 27855; 194455; N/A
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    Exactly solvable pairing model using an extension of the Richardson-Gaudin approach
    (World Scientific Publ Co Pte Ltd, 2005) Balantekin, AB; Pehlivan, Y; Department of Physics; Dereli, Tekin; Faculty Member; Department of Physics; College of Sciences; 201358
    We introduce a new class of exactly solvable boson pairing models using the technique of Richardson and Gaudin. Analytical expressions for all energy eigenvalues and the first few energy eigenstates are given. In addition, another solution to Gaudin's equation is also mentioned. A relation with the Calogero-Sutherland model is suggested.
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    Enhancing capacity of coherent optical information storage and transfer in a Bose-Einstein condensate
    (2007) N/A; Department of Physics; Department of Physics; Müstecaplıoğlu, Özgür Esat; Tarhan, Devrim; Faculty Member; Other; Department of Physics; College of Sciences; College of Sciences; 1674; N/A
    The coherent optical information storage capacity of an atomic Bose-Einstein condensate is examined. The theory of slow light propagation in atomic clouds is generalized to the short-pulse regime by taking into account group velocity dispersion. It is shown that the number of stored pulses in the condensate can be optimized for a particular coupling laser power, temperature, and interatomic interaction strength. Analytical results are derived for a semi-ideal model of the condensate using the effective uniform density zone approximation. Detailed numerical simulations are also performed. It is found that the axial density profile of the condensate protects the pulse against group velocity dispersion. Furthermore, taking into account the finite radial size of the condensate, multimode light propagation in an atomic Bose-Einstein condensate is investigated. The number of modes that can be supported by a condensate is found. The single-mode condition is determined as a function of experimentally accessible parameters including trap size, temperature, condensate number density, and scattering length. Quantum coherent atom-light interaction schemes are proposed for enhancing multimode light propagation effects.
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    Vortex lattice of a Bose-Einstein condensate as a photonic band gap material
    (Institute of Physics (IOP) Publishing, 2009) Tasgin, M. E.; Oktel, M. O.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674
    Photonic crystal behavior of a rotating Bose-Einstein condensate with a triangular vortex lattice is reviewed and a scheme for getting much wider band gaps is proposed. It is shown that photonic band gaps can be widened an order of magnitude more by using a Raman scheme of index enhancement, in comparison to previously considered upper level microwave scheme.
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    FRET optofluidic microlasers enhance biological sensing
    (Pennwell Publ. Co., 2016) Karadağ, Yasin; Jonas, Alexandr; Department of Physics; Kiraz, Alper; Faculty Member; Department of Physics; College of Sciences; 22542
    The marriage of liquid-based optical microcavities with engineered biological gain media using fluorescence resonance energy transfer (FRET) creates unique miniature lasers capable of ultra-sensitive biochemical detection.
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    Dispersive propagation of ultras low pulses in an atomic Bose-Einstein condensate
    (Polish Acad Sciences Inst Physics, 2011) Tarhan, Devrim; Sefi, Seçkin; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674
    One-dimensional propagation of ultraslow optical pulses in an atomic Bose-Einstein condensate taking into account the dispersion and the spatial inhomogeneity is investigated. Analytical and semi-analytical solutions of the dispersive inhomogeneous wave equation modeling the ultraslow pulse propagation are developed and compared against the standard wave equation solvers based upon Cranck-Nicholson and pseudo-spectral methods. The role of curvature of the trapping potential of the condensate on the amount of dispersion of the ultraslow pulse is pointed out.
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    Quantum entanglement of spin-1 bosons with coupled ground states in optical lattices
    (Iop Publishing Ltd, 2009) Öztop, B.; Öktel, M. O.; You, L.; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674
    We examine particle entanglement, characterized by pseudo-spin squeezing, of spin-1 bosonic atoms with coupled ground states in a one-dimensional optical lattice. Both the superfluid and Mott-insulator phases are investigated separately for ferromagnetic and antiferromagnetic interactions. Mode entanglement is also discussed in the Mott-insulating phase. The role of a small but nonzero angle between the polarization vectors of counter-propagating lasers forming the optical lattice on quantum correlations is investigated as well.
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    Some anisotropic universes in the presence of imperfect fluid coupling with spatial curvature
    (Springer, 2011) Kılınç, Can Battal; Department of Physics; Akarsu, Özgür; Researcher; Department of Physics; College of Sciences; N/A
    We consider Bianchi VI spacetime, which also can be reduced to Bianchi types VI0-V-III-I. We initially consider the most general form of the energy-momentum tensor which yields anisotropic stress and heat flow. We then derive an energy-momentum tensor that couples with the spatial curvature in a way so as to cancel out the terms that arise due to the spatial curvature in the evolution equations of the Einstein field equations. We obtain exact solutions for the universes indefinitely expanding with constant mean deceleration parameter. The solutions are beriefly discussed for each Bianchi type. The dynamics of the models and fluid are examined briefly, and the models that can approach to isotropy are determined. We conclude that even if the observed universe is almost isotropic, this does not necessarily imply the isotropy of the fluid (e.g., dark energy) affecting the evolution of the universe within the context of general relativity.
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    Quantum entanglement via superradiance of a bose-einstein condensate
    (2010) Öktel, M. O.; You, L.; Müstecaplıoğlu, Özgür E.; Department of Physics; Taşgın, Mehmet Emre; Researcher; Department of Physics; College of Sciences; 177874
    We adopt the coherence and built-in swap mechanism in sequential superradiance as a tool for obtaining continuous-variable (electric/magnetic fields) quantum entanglement of two counter-propagating pulses emitted from the two end-fire modes. In the first-sequence, end-fire modes are entangled with the side modes. In the second sequence, this entanglement is swapped to in between the two opposite end-fire modes. Additionally, we also examine the photon number correlations. No quantum correlations is observed in this variable.