Processing Pipeline for Digitalizing the Lineage Tree of Early Zebrafish Embryogenesis from Multiharmonic Imaging

The reconstruction of the cell lineage tree of early zebrafish embryogenesis requires the use of in-vivo microscopy imaging and image processing strategies. Second (SHG) and third harmonic generation (THG) microscopy observations in unstained zebrafish embryos allows to detect cell divisions and cell membranes from 1-cell to 1K-cell stage. In this article, we present an ad-hoc image processing pipeline for cell tracking and cell membranes segmentation enabling the reconstruction of the early zebrafish cell lineage tree until the 1K-cell stage. This methodology has been used to obtain digital zebrafish embryos allowing to generate a quantitative description of early zebrafish embryogenesis with minute temporal accuracy and μm spatial resolution

The role of London forces in defining noncentrosymmetric order of high dipole moment–high hyperpolarizability chromophores in electrically poled polymeric thin films

Graphs of second harmonic generation coefficients and electro-optic coefficients (measured by ellipsometry, attenuated total reflection, and two-slit interference modulation) as a function of chromophore number density (chromophore loading) are experimentally observed to exhibit maxima for polymers containing chromophores characterized by large dipole moments and polarizabilities. Modified London theory is used to demonstrated that this behavior can be attributed to the competition of chromophore-applied electric field and chromophore–chromophore electrostatic interactions. The comparison of theoretical and experimental data explains why the promise of exceptional macroscopic second-order optical nonlinearity predicted for organic materials has not been realized and suggests routes for circumventing current limitations to large optical nonlinearity. The results also suggest extensions of measurement and theoretical methods to achieve an improved understanding of intermolecular interactions in condensed phase materials including materials prepared by sequential synthesis and block copolymer methods.

Crystalline lanthanum hydroxycarbonates with controlled phases and varied morphologies prepared on non-crystalline substrates

Lanthanum hydroxycarbonate crystals with controlled phases and varied morphologies were prepared on the surface of a non-crystalline substrate, glass. The phases and morphologies of the crystals were controlled conveniently by varying the reaction temperature and the quantity of starting materials. Orthorhombic crystals were obtained at 160 degreesC, distributed individually on the substrate and had a flaky rhombic shape. Hexagonal crystals were obtained at 180 degreesC. The crystals had a rhomboidal shape, were uniform and continuous enough to form a solid film on the substrate. The substrates were corroded under the hydrothermal conditions and offered a coarse surface for the crystal growth. The hexagonal lanthanum hydroxycarbonate was discovered to show significant second harmonic generation, which would be of interest for developing novel optical materials. (C) 2004 Elsevier Inc. All rights reserved.

Hydroxide carbonates and oxide carbonate hydrate of rare earths grown on glass via a hydrothermal route

Carbonates of rare-earths, specifically hydroxide carbonate or oxide carbonate hydrate, could be prepared on common glass by a hydrothermal process involving thiourea. Examples presented in this paper include LaOHCO3, CeOHCO3 and EU2O(CO3)(2) . H2O structures formed on glass from solutions of thiourea and the relevant rare-earth reactants. The crystal structure and habit on the substrates were dependent on the preparative conditions; the influence of the concentrations of reactants and temperature on the crystal morphologies is illustrated. Second harmonic generation was found to occur in the crystals. (C) 2004 Elsevier B.V. All rights reserved.

Experimental observations of watertable waves in an unconfined aquifer with a sloping boundary

Observations of horizontal and vertical variations in piezometric head in a homogeneous, laboratory aquifer are presented and discussed. The observed fluctuations are induced by a simple harmonic oscillation in the clear water reservoir acting across a sloping boundary. The data qualitatively supports existing theories in that higher harmonics are generated in the active forcing zone and that a significant increase in the inland, asymptotic watertable over height (relative to that found for the vertical boundary case) is observed. The observed overheight is shown to be accurately reproduced by existing small-amplitude perturbation theory. Detailed measurements in the vicinity of the sloping boundary reveal that the signal of generated higher harmonics is strongest near the sand surface and that vertical flows are significant in this region. The aquifer is of finite-depth and is influenced by capillary effects, the experimental data therefore exposes limitations of theories which are based on the assumption of a shallow aquifer free of capillary effects. The dispersive properties of the measured pressure wave in the aquifer are comparable to those found from field observations and likewise do not agree with those predicted by the capillary free, shallow aquifer theory. Although some improvement is obtained, discrepancies between the data and theory persist even when a finite-depth aquifer and capillary effects are considered in the theoretical model. Further sand column experiments eliminate a truncated capillary fringe as a possible contributor to these discrepancies. However, the neglect of horizontal flows in the fringe may have caused the discrepancies. (C) 2004 Elsevier Ltd. All rights reserved.

Blue-to-red tunable SHG from a diode-pumped PPKTP waveguide

Summary form only given. Broadly tunable compact visible laser sources in the spectral region of 500-650 nm are valuable in biophotonics, photomedicine and for many applications including spectroscopy, laser projection and confocal microscopy. Unfortunately, commercially available lasers of this spectral range are in practice bulky and inconvenient in use. An attractive method for the realization of portable visible laser sources is the frequency-doubling of the infrared laser diodes in a nonlinear crystal containing a waveguide [1]. Nonlinear crystal waveguides that offer an order-of-magnitude increase in the IR-to-visible conversion efficiency also enable a very different approach to second-harmonic generation (SHG) tunability in periodically-poled crystals, promising order-of-magnitude increase of wavelength range for SHG conversion. This is possible by utilization of a significant difference in the effective refractive indices of the high-order and low-order modes in multimode waveguides [2]. The recent availability of low-cost, good quality semiconductor diode lasers, offering the coverage of a broad spectral range between 1 µ?? and 1.3 µp? [3,4], in combination with well-established techniques to fabricate good quality waveguides in nonlinear crystals, allows compact tunable CW laser sources in the visible spectral region to be realized [2].

Highly efficient SHG at 561 nm using a QD laser and a PPLN waveguide

Compact CW lasers in the visible spectral region are of great importance for vast number of applications including biophotonics, photomedicine, spectroscopy and confocal microscopy. Currently, commercially available lasers of this spectral region are bulky, expensive and inconvenient in use. Also, there is a lack of diode lasers emitting in the visible spectral range, particularly in the yellow region, where a range of important fluorescent probes are optimally excited. An attractive way to realize a compact yellow laser source is second harmonic generation (SHG) in a periodically poled nonlinear crystal containing a waveguide which allows high-efficient frequency conversion even at moderate power level. In this respect, periodically poled lithium niobate (PPLN) waveguided crystal is one of the best candidates for efficient SHG. In recent years, the progress made with the fabrication of good quality waveguides in PPLN crystals in combination with availability of low-cost, good quality semiconductor diode lasers, offering the coverage of a broad spectral range between 1 µm and 1.3 µm, allows compact CW laser sources in the visible spectral region to be realized.

SHG in a low-loss orientation patterned GaAs waveguide

We demonstrate second harmonic generation at 1621 nm in a low-loss orientation-patterned GaAs waveguide pumped by an optical parametric oscillator system. The losses were estimated to be 2.12 dB/cm.

Green-to-red tunable SHG of a quantum-dot laser in a PPKTP waveguide

Quasi-phase-matching is an important and widelyused technique in nonlinear optics enabling efficient frequency up-conversion. However, since its introduction almost half a century ago, this technique is well developed for near infrared (IR) but is intrinsically limited in spectral tunability in the visible range by the strict conditions set by the spatial modulation which compensates the momentum mismatch imposed by the dispersion. Here, we provide a fundamental generalization of quasi-phase-matching based on the utilization of a significant difference in the effective refractive indices of the high- and low-order modes in multimode waveguides. This concept enables to match the period of poling in a very broad wavelength range and opens up a new avenue for an order-ofmagnitude increase in wavelength range for frequency conversion from a single crystal. Using this approach, we demonstrate an all-room-temperature continuous-wave (CW) second harmonic generation (SHG) with over 60 nm tunability from green to red in a periodically-poled potassium titanyl phosphate (PPKTP) waveguide pumped by a single broadly-tunable quantumdot laser diode. © 2012 by Astro, Ltd.

Orange-to-red tunable picosecond pulses by frequency doubling in a diode-pumped PPKTP waveguide

A compact picosecond all-room-temperature orange-to-red tunable laser source in the spectral region between 600 and 627 nm is demonstrated. The tunable radiation is obtained by second-harmonic generation in a periodically poled potassium titanyl phosphate (PPKTP) multimode waveguide using a tunable quantum-dot external-cavity mode-locked laser. The maximum second-harmonic output peak power of 3.91 mW at 613 nm is achieved for 85.94 mW of launched pump peak power at 1226 nm, resulting in conversion efficiency of 4.55%. © 2013 Optical Society of America.

73 nm wavelength tuning from a frequency-doubled quantum-dot laser in PPKTP waveguides

A compact all-room-temperature CW 73-nm tunable laser source in the visible spectral region (574nm-647nm) has been demonstrated by frequency-doubling of a broadly-tunable InAs/GaAs quantum dot external-cavity diode laser in periodically-poled potassium titanyl phosphate waveguides with a maximum output power in excess of 12mW and a maximum conversion efficiency exceeding 10%. Three waveguides with different cross-sectional areas (4×4μm2, 3×5μm2 and 2x6μm2) were investigated. Introduction - Development of compact broadly tunable laser sources in the visible spectral region is currently very attractive area of research with applications ranging from photomedicine and biophotonics to confocal fluorescence microscopy and laser projection displays. In this respect, semiconductor lasers with their small size, high efficiency, reliability and low cost are very promising for realization of such sources by frequency­doubling of the infrared light in nonlinear crystal waveguides. Furthermore, the wide tunability offered by quantum-dot (QD) external-cavity diode lasers (ECDL), due to the temperature insensibility and broad gain bandwidth [1,2], is very promising for the development of tunable visible laser sources [3,4]. In this work we show a compact green-to-red tunable all­room-temperature CW laser source using a frequency-doubled InAs/GaAs QD-ECDL in periodically-poled potassium titanyl phosphate (PPKTP) crystal waveguides. This laser source generates frequency-doubled light over the 574nm-647nm wavelength range utilizing the significant difference in the effective refractive indices of high-order and low-order modes in multimode waveguides [3]. Experimental results - Experimental setup used in this work was similar to that described in [3] and consisted of a QD gain chip in the quasi­Littrow configuration and a PPKTP waveguide. Coarse wavelength tuning of the QD-ECDL between 1140 nm and 1300 nm at 20°C was possible for pump current of 1.5 A. The laser output was coupled into the PPKTP waveguide using an AR-coated 40x aspheric lens (NA ~ 0.55). The PPKTP frequency-doubling crystal (not AR coated) used in our work was 18 mm in length and was periodically poled for SHG (with the poling period of ~ 11.574 11m). The crystal contained 3 different waveguides with cross-sectional areas of ~ 4x4 11m2, 3x5 11m2 and 2x6 11m2. Both the pump laser and the PPKTP crystal were operating at room temperature. The waveguides with cross-sectional areas of 4x411m2, 3x511m2 and 2x611m2 demonstrated the tunability in the wavelength ranges of 577nm - 647nm, 576nm -643nm and 574nm - 641nm, respectively, with a maximum output power of 12.04mW at 606 nm Conclusion - We demonstrated a compact all-room-temperature broadly­tunable laser source operating in the visible spectral region between 574nm and 647nm. This laser source is based on second harmonic generation in PPKTP waveguides with different cross-sectional areas using an InAs/GaAs QD-ECDL References [I] E.U. Rafailov, M.A. Cataluna, and W. Sibbett, Nat. Phot. 1,395 (2007). [2] K.A. Fedorova, M.A. Cataluna, I. Krestnikov, D. Livshits, and E.U. Rafailov, Opt. Express 18(18), 19438-19443 (2010). [3] K.A. Fedorova, G.S. Sokolovskii, P.R. Battle, D.A. Livshits, and E.U. Rafailov, Laser Phys. Lett. 9, 790-795 (2012). [4] K.A. Fedorova,G.S. Sokolovskii, D.T. Nikitichev, P.R. Battle, I.L. Krestnikov, D.A. Livshits, and E.U. Rafailov, Opt. Lett. 38(15), 2835-2837 (2013) © 2014 IEEE.

Optical properties of chiral thin films and microparticles

In this work I study the optical properties of helical particles and chiral sculptured thin films, using computational modeling (discrete dipole approximation, Berreman calculus), and experimental techniques (glancing angle deposition, ellipsometry, scatterometry, and non-linear optical measurements). The first part of this work focuses on linear optics, namely light scattering from helical microparticles. I study the influence of structural parameters and orientation on the optical properties of particles: circular dichroism (CD) and optical rotation (OR), and show that as a consequence of random orientation, CD and OR can have the opposite sign, compared to that of the oriented particle, potentially resulting in ambiguity of measurement interpretation. Additionally, particles in random orientation scatter light with circular and elliptical polarization states, which implies that in order to study multiple scattering from randomly oriented chiral particles, the polarization state of light cannot be disregarded. To perform experiments and attempt to produce particles, a newly constructed multi stage thin film coating chamber is calibrated. It enables the simultaneous fabrication of multiple sculptured thin film coatings, each with different structure. With it I successfully produce helical thin film coatings with Ti and TiO_{2}. The second part of this work focuses on non-linear optics, with special emphasis on second-harmonic generation. The scientific literature shows extensive experimental and theoretical work on second harmonic generation from chiral thin films. Such films are expected to always show this non-linear effect, due to their lack of inversion symmetry. However no experimental studies report non-linear response of chiral sculptured thin films. In this work I grow films suitable for a second harmonic generation experiment, and report the first measurements of non-linear response.

Laser IInduced Liinear and Nonlliinear Optiicall Studiies on Certaiin Metall Halliides and Tartrate Crystalls ffor Photoniic Applliicatiions

Nonlinear optics is a broad field of research and technology that encompasses subject matter in the field of Physics, Chemistry, and Engineering. It is the branch of Optics that describes the behavior of light in nonlinear media, that is, media in which the dielectric polarization P responds nonlinearly to the electric field E of the light. This nonlinearity is typically only observed at very high light intensities. This area has applications in all optical and electro optical devices used for communication, optical storage and optical computing. Many nonlinear optical effects have proved to be versatile probes for understanding basic and applied problems. Nonlinear optical devices use nonlinear dependence of refractive index or absorption coefficient on the applied field. These nonlinear optical devices are passive devices and are referred to as intelligent or smart materials owing to the fact that the sensing, processing and activating functions required for optical processes are inherent to them which are otherwise separate in dynamic devices.The large interest in nonlinear optical crystalline materials has been motivated by their potential use in the fabrication of all-optical photonic devices. Transparent crystalline materials can exhibit different kinds of optical nonlinearities which are associated with a nonlinear polarization. The choice of the most suitable crystal material for a given application is often far from trivial; it should involve the consideration of many aspects. A high nonlinearity for frequency conversion of ultra-short pulses does not help if the interaction length is strongly limited by a large group velocity mismatch and the low damage threshold limits the applicable optical intensities. Also, it can be highly desirable to use a crystal material which can be critically phasematched at room temperature. Among the different types of nonlinear crystals, metal halides and tartrates have attracted due to their importance in photonics. Metal halides like lead halides have drawn attention because they exhibit interesting features from the stand point of the electron-lattice interaction .These materials are important for their luminescent properties. Tartrate single crystals show many interesting physical properties such as ferroelectric, piezoelectric, dielectric and optical characteristics. They are used for nonlinear optical devices based on their optical transmission characteristics. Among the several tartrate compounds, Strontium tartrate, Calcium tartrate and Cadmium tartrate have received greater attention on account of their ferroelectric, nonlinear optical and spectral characteristics. The present thesis reports the linear and nonlinear aspects of these crystals and their potential applications in the field of photonics.

NONLINEAR EFFECTS IN MAGNETIC GARNET FILMS AND NONRECIPROCAL OPTICAL BLOCH OSCILLATIONS IN WAVEGUIDE ARRAYS

This dissertation presents detailed experimental and theoretical investigations of nonlinear and nonreciprocal effects in magnetic garnet films. The dissertation thus comprises two major sections. The first section concentrates on the study of a new class of nonlinear magneto-optic thin film materials possessing strong higher order magnetic susceptibility for nonlinear optical applications. The focus was on enlarging the nonlinear performance of ferrite garnet films by strain generation and compositional gradients in the sputter-deposition growth of these films. Under this project several bismuth-substituted yttrium iron garnet (Bi,Y) 3 (Fe,Ga)5 O12(acronym as Bi:YIG) films have been sputter-deposited over gadolinium gallium garnet (Gd 3 Ga5 O12 ) substrates and characterized for their nonlinear optical response. One of the important findings of this work is that lattice mismatch strain drives the second harmonic (SH) signal in the Bi:YIG films, in agreement with theoretical predictions; whereas micro-strain was found not to correlate significantly with SH signal at the micro-strain levels present in these films. This study also elaborates on the role of the film's constitutive elements and their concentration gradients in nonlinear response of the films. Ultrahigh sensitivity delivered by second harmonic generation provides a new exciting tool for studying magnetized surfaces and buried interfaces, making this work important from both a fundamental and application point of view. The second part of the dissertation addresses an important technological need; namely the development of an on-chip optical isolator for use in photonic integrated circuits. It is based on two related novel effects, nonreciprocal and unidirectional optical Bloch oscillations (BOs), recently proposed and developed by Professor Miguel Levy and myself. This dissertation work has established a comprehensive theoretical background for the implementation of these effects in magneto-optic waveguide arrays. The model systems we developed consist of photonic lattices in the form of one-dimensional waveguide arrays where an optical force is introduced into the array through geometrical design turning the beam sideways. Laterally displaced photons are periodically returned to a central guide by photonic crystal action. The effect leads to a novel oscillatory optical phenomenon that can be magnetically controlled and rendered unidirectional. An on-chip optical isolator was designed based on the unidirectionality of the magneto-opticBloch oscillatory motion. The proposed device delivers an isolation ratio as high as 36 dB that remains above 30 dB in a 0.7 nm wavelength bandwidth, at the telecommunication wavelength 1.55 μm. Slight modifications in isolator design allow one to achieve an even more impressive isolation ratio ~ 55 dB, but at the expense of smaller bandwidth. Moreover, the device allows multifunctionality, such as optical switching with a simultaneous isolation function, well suited for photonic integrated circuits.